BIOL 103 - Final Exam Guide - Comprehensive Notes For The Exam (258 Pages Long!) - 2

Queen's
BIOL 103
FINAL EXAM
STUDY GUIDE
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January 4, 2016
BIOL103 Week 13.1 Lecture Notes
WALKER’S RESEARCH
- freeze and freeze-thaw resistance in plants, invertebrates and microbes:
o freeze resistance in organisms from brine lakes in B.C.
o how do microbes form brine lakes survive? etc.
- use of nanoparticles and their applications: impact of manufactured nanoparticles on microorganisms and animals
o carbon nanotubes  fetal abnormalities in pregnant mouse mums
NUTRITION AND DIGESTION CHAPTER 41
- black bear foraging on berries
1. autotrophs (Greek: self nutrition): harvest light or chemical energy and store it in carbon compounds
a. can exist in inorganic environment and manufacture organic compounds
b. primary producers
c. e.g. take CO2 + water  glucose
2. heterotrophs (Greek: other nutrition): get complex nutrients from environment
a. receive nutrition by eating other organisms
b. found in higher trophic levels
c. evolved multiple strategies for obtaining food
d. e.g. python, humans
- if you are a heterotroph, how do you get large organic compounds past the cell membranes?
- are all heterotrophs animals?  no
- are all non-animal life autotrophic  no
EXTRACELLULAR DIGESTION
- e.g. fungi: bread mold fungus:
o mold digests polysaccharide  extracellular digestion
o produces enzymes, secretes enzymes onto bread, bread gets digested extracellularly, fungus can take in the
material
- e.g. fungi: parasites:
o athlete’s foot fu gus: e te ds fu gal a hes h phae i to ells of foot to a so ut ie ts
o fungus is producing digestive enzymes that go into the feet  then absorbs nutrients
- e.g. Dactylella dreschsleri: predator fungus:
o fungus has sticky knobs along hyphae that can hold nematode worms
o h phae the pe et ate the o ’s od , digesti e e z es a e eleased a d e t a ellula digestio takes
place
- e.g. Arthrobotrys dactyloides (cowboy fungus): fungus that makes traps that are used to capture nematode worms
o traps made by three cells, cells swell and constrict essentially lassoing the worm
o hyphae penetrate the worm  extracellular digestion takes place
o signal transduction complex to initiate the trapes from fungi
- fu gi a e parasiti or predatory e.g. pla t parasiti fu gi, Athlete’s foot, ow oy fu gi
o even if hyphae penetrates cells  extracellular digestion
INTRACELLULAR DIGESTION
- protozoa: simple, single cell
o produces invagination  surrounds food with membrane  food vacuole  phagocytosis
- phagocytosis: food vacuole fuses with lysosome  digestive enzymes digest food  exocytosis can release undigested
food
o membrane is negatively charged (phospholipid)
- e.g. Okada and colleagues showed that there were 85 different proteins involved in process in genus that infects up
to 10% of people

o do not need to look this up

- e.g. white cells using a type of phagocytosis:
o cancer cells, foreign cells have blocking signals that prevent white cell phagocytosis
▪ inhibits signal
- various proteins (including SNARES) and Ca ++ are involved
o Ca ++: positively charged ions  neutralizes negative charges of phospholipids
- some microbes have evolved mechanisms to escape phagocytosis (preventing our protection from microbes):
o e.g. streptococcus: bacterium covered with coat of glycoprotein
▪ white blood cells try to capture bacterium but is unable to use phagocytosis
▪ after a few weeks  body recognizes glycoprotein as foreign  produces antibodies  covers
bacterium with antibodies  helps phagocytosis to take place
• white blood cells can engulf the bacterium  recovery
January 6, 2016
Week 13.2 lecture notes
FOOD VACUOLES IN PARAMECIUM (SLIPPER-FOOTED)
-
- intracellular digestion: food  oral groove  membrane surrounds it  lysosomes fuse with vacuoles  digestion
- not phagocytosis
EXTRACELLULAR DIGESTION: HYDRA
- tentacles capture prey (prey is too big for intracellular digestion)
- rest of digestion takes place as intracellular digestion
- indigestible products are returned and goes out the mouth  one opening only
HUMANS AND ALIMENTARY CANAL  OPENINGS AT BOTH ENDS
- not perfect: cannot digest cellulose/ plant material
- cellulose:
o difficult to hydrolyze, 1,4 linkages
▪ only microorganisms, bacteria, protozoa can produce enzymes that can digest cellulose
EQUINE DIGESTIVE TRACT

- microorganisms are found in the cecum (pouch between large and small intestine)
- cellulases are made up there and mixed up with food  enzymes hydrolyze cellulose
- horses have an enormous cecum (15%, 30L of fluid with microorganisms)
o horse feces: very fibrous  not as perfect in digesting cellulose
o
RABBITS
- changed their behaviour instead of anatomy
- at night feces  morning they eat feces  day time feces (not edible, nothing nutritious)
- much better change of digesting all cellulose
- cecum is between small and large intestine  much of digestion takes place in small intestine
RUMINANTS IN COWS
- dairy cows have enormous breasts/ otters
o grass is low in amino acids (methionine, lysine, leucine)  cows need supplements for proteins
▪ mad cow disease  grind up dead cows and given to live cows (for proteins)
▪ farmers have to supplement dairy cows with protein supplements
- artificial rumen: bacteria producing cellulases  enhance bacteria found in cows and supplement proteins
o insert gene in plasmid that encodes proteins high in methionine, leucine, lysine inside the bacteria in rumen
o microbes not only produce cellulase but also high proteins
o would save money and supplements
- Dr. Steven Chu: termites are more efficient at converting cellulose into ethanol  cheaper way of producing green
energy
o termite DNA produces enzymes that enhance production of cellulases  symbiotic relationship
DIGESTION
- complex organic molecules  convert them to simpler molecules
- salivary amylase produced by salivary glands:
o selective pressure: what you eat  how much saliva produced by gene determination
o oral cavity: teeth, salivary glands
- saliva: lubrication + enzyme (optimum pH of 7)
o amylase is inactivated when food is swallowed  only works in mouth (hydrolysis with water)
o
o starch: 1,4 linkages and easy to hydrolyze by amylase into maltose (2 glucose units)

o not all organisms produce salivary amylase (e.g. wolf) but can have saliva (lubrication)
- e.g. tsetse fly: adult sucks blood from various vertebrates
o li uid diet: should ’t eed sali a, a lase
o presence of salivary glands: saliva contains anticoagulant  prevents blood from clotting
▪ take away salivary glands  soon died
- stomach: pH of stomach drops to 2  amylase does not work
o gastric juice (2L/ day): HCl + pepsin
▪ carnivores can dissolve bones (and omnivores like us)
- pepsin (usually in vertebrates): hydrolyzes proteins (protease)
o results in polypeptides by hydrolyzing peptide bonds (with water)
- e.g. ala-his-gly-/tyr-thr-lys-leu-ser-arg-gly-asp-his-thr-gly-gly-/phe-
o convention: N-terminus (amino terminal)  C-terminus (carboxyl terminal)
o pepsin only hydrolyzes peptide bonds associated with ringed amino acids
▪ tyr, phe
▪ on amino terminal sides
- h do ’t e digest ou o sto a h:
1. pepsin is first inactive
a. gastric glands in chief cells produce inactive pepsinogen (zymogens, pepsin zymogen)
b.
c. activates with HCl  pepsin
d. pepsin  activates other pepsinogens  more pepsin
2. goblet cells that line stomach produce viscous mucous layer with pH ~6
3. parietal cells release ions  HCl
a.
o
4. cells lining stomach have particular resistant membranes
- ulcers: caused by excess stomach acid (from helicobacteria)
o hormone stimulates growth of bacteria in stomach
o mucus layer erodes
o bacteria feed on cells  bleeding
o can treat the with antibiotics
January 8, 2016

Week 13.3 Lecture Notes

- e.g. Oetzi the Iceman: suffered from stomach bug
o H. pylori in stomach  stomach mucosa has not survived but clear possibility of stomach issues (ulcers)
SMALL INTESTINE
- acid chyme passes onto small intestine where there is large # of digestive enzymes
- digestive enzymes produced by:
1. intestinal glands: cells lining the intestine
a. acid pH  induction signals for digestive enzymes
b. produce proteases
c. maltase: hydrolyzes maltose into glucose (absorption possible)
2. pancreas:
a. duct that goes into small intestine
i. increases the pH  bicarbonate ions
b. produce proteases (e.g. trypsin) + other enzymes
c. pancreas produces trypsin: particular hydrolysis  lys, arg (carboxyl side)
i. e.g. ala-his-gly-/tyr-thr-lys/-leu-ser-arg/-gly-asp-his-thr-gly-gly-/phe-
1. convention: N-terminus (amino terminal)  C-terminus (carboxyl terminal)
2. pepsin only hydrolyzes peptide bonds associated with ringed amino acids
a. tyr, phe
b. on amino terminal sides
d. produces chymotrypsin: hydrolyzes try, phe, trp, leu, met  carboxyl side
e. produces elastase: hydrolyzes ala, lys, val  carboxyl side
o how does pancreas not get digested: zymoge lo ge fo o e z e that’s i a ti e  hydrolyzes 
exposes active site  acts as protease
▪ trypsinogen  trypsin: activating protease = enterokinase (enteropeptidase) made by intestinal
glands
• needs to get into small intestine  clever mechanism
▪ chymotrypsinogen  chymotrypsin: activating protease = trypsin
▪ proelastase  elastase: activating protease = trypsin
- endoproteases: hydrolyzes peptide bonds within polypeptide
- exoproteases: hydrolysis of terminal peptide bonds: only 3 to remember
o aminopeptidase: hydrolyzes peptide bond so to release amino terminal amino acid
o dipeptidase: hydrolyzes dipeptides
▪ very efficient
o carboxylpeptidase: hydrolyzes peptide bond so to release carboxyl terminal amino acid
3. liver:
a. digestion of fats
- e.g. celiac disease: intolerant of gluten
o gluten: storage protein by wheat and barley
▪ lots of proline amino acid  kinks polypeptide  extremely difficult for proteases to digest
▪ generally, remains undigested (fibre)  feces
▪ celiac disease: undigested gluten can activate white blood cells  lead to inflammation  erode lining
of small intestine  malabsorption  diarrhea etc.
o some bacteria can produce enzyme that digests gluten
▪ prolyl endopeptidase  does ’t o k  susceptible to digestion by other proteases
o must change genetics of people with celiac disease

-
o pepsin – stomach, trypsin – pancreas
-
DIGESTION OVERVIEW
-
o bicarbonate ions  pH increases for enzymes to work
o bile: emulsifying agent  smaller fat droplets  worked on by lipase
- bacteria (microbiome): abundance of bacteria determined by DNA sequencing
o with Ag nanoparticles: good bacteria go down, E. coli increase

ABSORPTION
- small intestine: vitamins, minerals, water, digested products
o huge surface area by villi (lacteals + capillaries) and microvilli
-


-
Textbook Notes
Concept 41.2 the main stages of food processing are ingestion, digestion, absorption, and elimination
- food processing in 4 stages: ingestion  digestion  absorption  elimination
o ingestion: act of eating or feeding
o digestion: food is broken down into molecules small enough for body to absorb
▪ mechanical: breaks food into smaller pieces  increases surface area available for chemical processes
▪ chemical: animals cannot directly use proteins, carbohydrates, nucleic acids, fats, and phospholipids
in food (too large, not all identical to those the animal needs for particular tissues and functions)
• hydrolysis, enzymatic hydrolysis
o a so ptio : a i al’s ells take up s all ole ules su h as a i o a ids a d si ple suga s
o elimination: undigested material passes out of digestive system
DIGESTIVE COMPARTMENTS
- processing of food within specialized compartments  intracellular or extracellular
INTRACELLULAR DIGESTION
- food vacuoles: cellular organelles in which hydrolytic enzymes break down food  simplest digestive compartments
- intracellular digestion: hydrolysis of food inside vacuoles
o begins after cell engulfs solid food by phagocytosis or liquid food by pinocytosis
o food vacuoles fuse with lysosomes (containing hydrolytic enzymes)  digestion occurs safely within
compartment enclosed by a protective membrane
- e.g. few animals like sponges digest their food entirely by intracellular mechanisms
EXTRACELLULAR DIGESTION
- most animals: hydrolysis begins with extracellular digestion
- extracellular digestion: reakdow of food i o part e ts that are o ti uous with outside of a i al’s ody
- having one or more extracellular compartments for digestion  able to devour much larger pieces of food than
phagocytosis
o simple body plan animals  digestive compartment with single opening:
▪ gastrovascular cavity: pouch that functions in digestion as well as in distribution of nutrients
throughout body (vascular)
- e.g. carnivorous cnidarians (hydras): uses its tentacles to stuff captured pretty through its mouth into gastrovascular
cavity  specialized gland cells of gastrodermis (tissue layer lining cavity) secrete digestive enzymes  break soft
tissues of prey into tiny pieces  other cells of gastrodermis engulf these food particles  most of hydrolysis of
macromolecules occurs intracellularly (like sponges)
o undigested materials remaining (e.g. exoskeletons) in gastrovascular cavity eliminated through same opening
by which food entered
o many flatworms also have a gastrovascular cavity with single opening

o
- complete digestive track/ alimentary canal: most animals have a digestive tube extending between mouth and anus
o moves along in single direction  tube organized into specialized compartments  carry out digestion and
nutrient absorption in stepwise fashion
o animal can ingest food while earlier meals are still being digested (difficult with just gastrovascular cavities)
o
Concept 41.3 organs specialized for sequential stages of food processing form the mammalian digestive system
- in mammals, digestive system: alimentary canal + various accessory glands (secrete digestive juices through ducts into
canal)
o accessory glands: 3 pairs of salivary glands + pancreas + liver + gallbladder
- peristalsis: alternating waves of contraction and relaxation in smooth muscles lining canal
o food pushed along alimentary canal
- sphincters: muscular layer forms ring-like valves
o at some of junctions between specialized compartments
o sphincters regulate passage of material between compartments
THE ORAL CAVITY, PHARYNX, AND ESOPHAGUS
- oral cavity: ingestion and initial steps of digestion occur in mouth/ oral cavity
- mechanical digestion: teeth  increases surface area of food
- salivary glands: delivers saliva through ducts to the oral cavity
o presence of food stimulates nervous reflex  causes salivary glands to produce saliva
o saliva initiates chemical digestion while also protecting oral cavity
▪ salivary amylase hydrolyzes starch and glycogen into smaller polysaccharides and disaccharide
maltose
▪ mucus: viscous mixture of water, salts, cells, and slippery glycoproteins (mucins)
• protects lining of mouth from abrasion and lubricates food for easier swallowing

• also includes buffers (prevents tooth decay by neutralizing acids) and antimicrobial agents
(e.g. lysozyme) that protect against bacteria that enter mouth with food
- tongue: aids digestive processes by evaluating ingested material and then enabling its further passage
o distinguishes which foods should be processed further
- bolus: chewing commences, tongue movements manipulate food into ball
- pharynx: throat region opens two passageways  esophagus and trachea (windpipe)
- esophagus: connects to stomach
o epiglottis: flap of cartilage that covers glottis (vocal cords and opening between them)
▪ larynx (upper part of respiratory tract) directs each bolus into entrance of esophagus by swallowing
reflex  failure: chocking, blockage of trachea
o contains both striated and smooth muscle
▪ striated muscle: at the top of esophagus and active during swallowing
▪ smooth muscle: functions in peristalsis
• rhythmic cycles of contraction move each bolus to stomach
- trachea: leads to lungs
-
DIGESTION IN THE STOMACH
- stomach: located below diaphragm, stores food, begins digestion of proteins
o folds and very elastic wall: can stretch to accommodate about 2L of food and fluid
o secretes digestive fluid, gastric juice  mixes secretion with food through churning action  produces chyme
(mixture of ingested food and digestive juice)
CHEMICAL DIGESTION IN THE STOMACH
- gastric juice: HCl + pepsin
o HCl: disrupts extracellular matrix binding cells together in meat and plant material
▪ concentration is high  pH 2  can dissolve iron nails and kills most bacteria  acid denatures
proteins in food  increases exposure of their peptide bonds
o pepsin: protease (protein-digesting enzyme), works best in acidic environment
▪ breaks peptide bonds, cleaves proteins into smaller polypeptides  further digestion in intestine
o gastric juice is kept inactive until they are released into lumen (cavity) of stomach

o components of gastric juice are produced by cells in gastric glands of stomach

▪ parietal cells secrete H+ and Cl-  expels H+ into lumen with ATP pump  draws Cl- out of cell
through specific membrane channels  form HCl
▪ chief cells: release pepsin into lumen as pepsinogen (chief cells)  converted by HCl to active pepsin
by clipping off small portion and exposing active site
o HCl and pepsin form in lumen of stomach, not within cells of gastric glands
o pepsin itself activates remaining pepsinogen  exposes active site  generates more pepsin  more active
enzymes  positive feedback: amplifies effect of an initially small input
- stomach lining protects against self-digestion by secreting mucus
o cell division adds new epithelial layer every 3 days  replaces cells eroded by digestive juices
o damaged areas of stomach lining  gastric ulcers (e.g. infection by acid-tolerant bacterium Helicobacter pylori)
STOMACH DYNAMICS
- chemical digestion by gastric juice assisted by churning action of stomach
o mixes stomach contents every 20 seconds
o stomach contents  acidic, nutrient-rich broth  chyme
- sphincter between esophagus and stomach normally opens when bolus arrives
o acid reflux: backflow of chyme from stomach into lower end of esophagus  heartburn
- contents of stomach pass into small intestine within 2 – 6 hours after meal
o sphincter helps regulate passage into small intestine allowing only one squirt of chyme at a time
-
DIGESTION IN THE SMALL INTESTINE
- most enzymatic hydrolysis of macromolecules occurs in the small intestine
- small intestine: ali e ta a al’s lo gest compartment (small diameter compared to large intestine)
o duodenum: first 25 cm  chyme mixes with digestive juices from pancreas, liver, gallbladder, gland cells of
intestinal wall
o hormones released by stomach and duodenum control digestive secretions into alimentary canal
PANCREATIC SECRETIONS
- pancreas: produces alkaline solution rich in bicarbonate (along with other enzymes)

o bicarbonate neutralizes acidity of chyme

o trypsin, chymotrypsin enzymes (proteases): secreted into duodenum in inactive forms
▪ activated when safely located in lumen within duodenum
BILE PRODUCTION BY THE LIVER
- digestion of fats and other lipids begins in small intestine and relies on bile
- bile: mixture of substances made in liver
o contains bile salts  emulsifiers (detergents)  aid in digestion and absorption of lipids
o bile stored and concentrated in gallbladder
o destruction of non-functional red blood cells
▪ liver incorporates pigments that are by-products of red blood cell disassembly when producing bile
• bile pigments eliminated from body with feces
▪ in some liver/ blood disorders: bile pigments accumulate in skin  yellowing of skin called jaundice
SECRETIONS OF THE SMALL INTESTINE
- epithelial lining of duodenum: source of several digestive enzymes
o some secrete into lumen of duodenum, others bound to surface of epithelial cells
- peristalsis moves mixture of chyme and digestive juices along small intestine during enzymatic hydrolysis
- jejunum and ileum: remaining parts of intestine  functions in absorption of nutrients and water
-
ABSORPTION IN THE SMALL INTESTINE
- nutrients first cross lining of alimentary canal
o occurs across highly folded surface of small intestine
o large folds in lining encircle intestine and studded with villi
- villi: finger-like projections

o microvilli: each epithelial cell of villus has microscopic projections of microvilli on its apical surface
o exposed to intestinal lumen
o brush border appearance, 300 m2 of surface area (tennis court), increases nutrient absorption
- transport across epithelial cells can be passive or active
o fructose sugar: facilitated diffusion from intestine to epithelial cells  absorbed into blood vessels, capillaries
o amino acids, small peptides, vitamins, most glucose molecules: pumped against concentration gradients by
epithelial cells of villus  allows much more absorption of nutrients than passive diffusion alone
- capillaries and veins carry nutrient-rich blood away from villi  converge into hepatic portal vein
o hepatic portal vein: blood vessel leading directly to liver
o from liver, blood travels to heart and then to other tissues and organs
1. allows liver to regulate distribution of nutrients to rest of the body  liver can interconvert many organic
molecules
a. blood that leaves liver may have very different nutrient balance than blood that entered via
hepatic portal vein
2. allows liver to remove toxic substances before blood circulates broadly
a. liver = primary site for detoxification of many organic molecules that are foreign (e.g. drugs)
- some products of fat (triglyceride) digestion take different path:
o hydrolysis of fats by lipase in small intestine  generates fatty acids and monoglycerides  absorbed by
epithelial cells and recombined into triglycerides  coated with phospholipids, cholesterol, proteins  water
soluble globules of chylomicrons
▪ chylomicrons first transported into lacteal
▪ lacteal: vessel at core of each villus, part of vertebrate lymphatic system
• lymphatic system: network of vessels filled with clear fluid of lymph
▪ chylomicrons pass into larger vessels of lymphatic system  into large veins that return blood to heart
-
ABSORPTION IN LARGE INTESTINE
- alimentary canal ends with large intestine
- large intestine = colon + cecum + rectum
o T shaped junction: small intestine connects to large intestine at junction
▪ one arm is 1.5 m long = colon
▪ next leads to rectum and anus
▪ other arm is a pouch = cecum
o cecum: fermenting ingested material (especially for animals that eat lots of plants, humans have small cecum)

▪ appendix: small extension of human cecum: minor and dispensable role in immunity
o colon: recovers water that has entered alimentary canal as the solvent of digestive juices
▪ 90% of fluid is reabsorbed in small intestine and colon
▪ water is reabsorbed by osmosis when Na+ and other ions are pumped out of lumen of the colon
- feces: wastes of digestive system  becomes increasingly solid as they are moved along colon by peristalsis
o 12-24 hours for material to travel the length of colon
o irritation of lining by viral or bacterial infection: less water than normal may be reabsorbed  diarrhea
o constipation: feces move along the colon too slowly  excess of water is reabsorbed
- bacteria in colon: often harmless and dry weight of feces
o e.g. E. coli
o many colon bacteria generate gases (e.g. methane, hydrogen sulfide) as by-products of their metabolism 
offensive odour  expelled through anus with air
o some bacteria produce vitamins (e.g. vitamin K), biotin, folic acid  supplement dietary intake
- feces can contain undigested material: e.g. cellulose fibre
o fibre helps move food along alimentary canal (no caloric value to humans)
- rectum: terminal portion of large intestine  stores feces until it can be eliminated
o 2 sphincters between anus and rectum:
▪ inner: involuntary
▪ outer: voluntary
▪ strong contractions of colon  urge to defecate
▪ filling of stomach  triggers reflex that increases rate of contractions in colon  urge to defecate
after meal
Concept 41.4 Evolutionary adaptations of vertebrate digestive systems correlate with diet
DENTATION
- nonmammalian vertebrates: have less specialized dentition
o exceptions: poisonous snakes (rattlesnakes) have fangs  inject venom into prey
▪ fangs can be hollow (syringes), or can drip poison along grooves of surface
STOMACH AND INTESTINAL ADAPTATIONS
- carnivorous vertebrates: large, expandable stomachs  long time between meals  must eat as much as they can
when catching prey
- herbivores, omnivores: longer alimentary canals relative to body size than carnivores
o vegetation is more difficult to digest than meat because of cell walls
o e.g. koala’s i testi es (cecum, colon) are much longer  processing of fibrous, protein poor eucalyptus leaves
MUTUALISTIC ADAPTATIONS
- mutualistic symbiosis: mutually beneficial interaction between two species
o microbes benefit from accessing nutrients in protected environment  animal gains improved nutrition
▪ microbes help herbivores digest plants: many vertebrates have mutualistic bacteria and protists in
fermentation chambers in alimentary canals  they have enzymes that digest cellulose  can
produce variety of essential nutrients to animals
- location of mutualistic microbes depending on type of herbivore:
1. hoatzin: herbivorous bird that has a large muscular crop (esophageal pouch) that houses mutualistic
microorganisms
a. hard ridges in wall of crop grinds plant leaves  microorganisms break down cellulose
2. horses: mutualistic microorganisms in large cecum
a. koala: enlarged cecum  mutualistic bacteria ferment finely shredded eucalyptus leaves
3. rabbits and some rodents: bacteria live in large intestine as well as in cecum
a. most nutrients absorbed in small intestine  nourishing by-products of fermentation by bacteria in
large intestine lost with feces
b. they recover lost nutrients by feeding on their feces and passing food through alimentary canal a
second time

c. rabbit pellets are feces eliminated after food has passed through digestive tract twice
4. ruminants: deer, sheep, cattle
a. rumen: boluses enter the rumen  prokaryotes and protists (mainly ciliates) work on cellulose rich
meal  by-product is fatty acids
b. reticulum: some boluses enter reticulum  prokaryotes and protists (mainly ciliates) work on
cellulose rich meal  by-product is fatty acids
c. cow periodically regurgitates and rechews cud  further breaks down fibres  more accessible to
microorganisms
d. omasum: cow reswallows cud  moves to omasum  water is removed
e. abomasum: cud with microorganisms passes to abomasum  digestio o ’s o e z es
-
- tubeworms: no mouth nor digestive system  rely entirely on mutualistic bacteria to generate energy and nutrients
from CO2, O2, H2S, and nitrate available in vents

Week 14.1 Excretion Lecture Notes
DIGESTION IN INSECTS
- no pepsin in insects: neutral ph/ alkaline ph  do not have pepsin
- adaptations: salivary glands, active proteases eliminated with feces
o tsetse fly: produces anticoagulant  coagulation of the blood
- marino sheep: produce fine wool
o sheep bull fly eats dead animals  folds of wool keep sheep warm  flies lay their eggs on living flesh
▪ starts eating live sheep  active proteases in their feces  orks outside of the sheep’s ody
EXCRETION AND ION TRANSPORT
-
AMINO ACIDS
- amino acids within blood circulation  humans cannot store great quantities of amino acids  deamination of
amino acid in liver
-
o deaminated amino acid  can be stored (alpha ketoglutaric acid)  can enter citric acid cycle etc.
▪ can be used for energy
o ammonia: enters urea cycle because it is toxic
- urea
o liver converts ammonia by using ATP into a safer form (urea)
o 4-5 steps
- e.g. sharks/ rays: carry out urea cycle even though they live in the sea
o enables them to osmoregulate, they are isotonic to seawater
o urea in tissues  makes them isotonic to seawater  shark does not need to regulate water/ solute
concentrations
o shark steaks: soak steaks in milk for about an hour  neutralizes strong taste of urea  needs to be
dialyzed (because shark osmoregulates with urea)
o warming  disturbs shark homeostasis

SALTWATER FISH (BONY FISH)

- hypotonic with respect to the surrounding: in danger of dehydrating with water lost across the gills
- they have to drink lots of water
- excreted ammonia diluted with minimum amount of water  concentrated urine
- excess salt transported out of body by specialized cells in gills
FRESHWATER FISH
- hypertonic with respect to the freshwater: water naturally runs into them
- produces large amounts of dilute urine
- specialized gill epithelial cells transport Na+ and Cl- fro ater i to fish’s apillaries  concentrate salts
-
o sharks drink some water (a little bit hypertonic)
o marine fish: hypotonic with seawater
o osmoconformers: isotonic with seawater, surrounding etc.
o osmoregulators: octopus, shrimps, corals, etc. isotonic
HUMAN DISEASES
- liver cirrhosis caused by alcoholism
o
- infectious disease (hepatitis)
- fatty liver disease: scar tissues in liver cannot efficiently process the urea cycle  ammonia circulates through blood
o urea cycle: deamination in liver  ammonia converted to urea
o symptoms: show manifest signs of toxicity to nervous systems: irritable, confused, slurred words
o cures: dialysis, liver transplant
IN BIRDS, REPTILES, INSECTS
- no urea cycle
- makes uric acid from NH3 and CO2  uric acid: not toxic, insoluble

-
- saves a lot of water
URIC ACID AS THE NITROGENOUS WASTE OF BIRDS
- uric acid stored in allantois and left behind at hatching
- ammonia, urea are toxic, slightly toxic  cannot be in shell for 3 weeks  needs absolutely nontoxic wastes 
nitrogenous wastes are deposited in inside of shells
GUANO: birds excrete uric acid as droppings with digestive waste
- uric acid high in nitrogen  used as fertilizer
-
LUNG FISH (Protopterus)
- precursors of land vertebrates
- produces ammonia  puddles dry up  produces stress  stress changes enzymes  produces urea  rain
comes again and produces ammonia
- no liver damage in high levels of ammonia
- nitrogenous waste ammonia  urea when water is not available

Week 14.2 Excretion Lecture Notes

SALMON
-
o salmon life: fresh water  salt water  fresh water
o change in behaviour + change physiology
o sea: drink water, produces concentrated urea of ammonia
o fresh ater: do ’t dri k ater, dilute uri e
▪ specialized gill epithelial cells concentrate salts
- gill epithelial cells are able to transport both Na and Cl against the concentration gradient using ATP
- needs 1 week to change their physiology  e.g. stays in fish farm for a week
EELS
- American eel: found in fresh + sea waters along coasts and into Lake Ontario
- migrate from fresh water to Sargasso Sea
- in one day: fresh water  sea water
o drinks a huge amount of water (experiment: decrease in volume of urine, dehydrated because of balloon in
esophagus)
EXCRETORY ORGANS
FUNCTIONS
1. filtration: filter to remove water and small solutes form body fluids/ blood while leaving behind blood cells, proteins
and other large solutes  filtrate
2. reabsorption: useful material in filtrate recaptured and returned to blood
3. secretion: additional solutes into filtrate (elimination of toxins)
IN VERTEBRATES
- kidney: 10 cm bean shaped organ x 2  gets rid of nitrogenous wastes

NEPHRON
- functional unit of kidney in higher vertebrates (several million nephrons in each kidney)
o number depends on ethnic background
1. apillary et ork i re al orpus le Bo a ’s apsule + glo erulus  forms filtrate
2. long tubule performing secretion/ reabsorption
3. collecting duct empties into central activity of kidney  urine
4. enters bladder as urine
URINE
- water + urea + NaCl + KCl + organic + inorganic (e.g. uric acid) molecules
- figure 44.16  why we have kidneys and what they do
- energy spend to pump out Na and Cl ions against gradient
- discovery of water pores  aquapores  water can diffuse through kidneys
-
- 13 members of the aquaporin family  cloned in humans
o some of them expressed in different parts of kidney
o humans  increased gene copy number
o water pore is just the right size for water molecules
- nephrogenic diabetes insipidus: mutation in aquaporin 2: lots of urine, dehydration headache etc., constipation 
drugs, kidney transplant (not related to diabetes mellitus/ honey)
- there are protei s + lood ells i plas a ut ot kid ey’s glo erular filtrate
ACTIVE TRANSPORT IN THE KIDNEYS
- passive diffusion: water, ethanol, gases, oxygen, CO2 etc.
- facilitated diffusion:
1. permeases
-
o concentration of K+ ions inside cell is high  permeases  allows K+ to excrete to the outside
▪ facilitated diffusion

- after digestion of carbohydrates, fructose enters cells lining small intestine using facilitated diffusion (permeases)
2. secondary active transport/ co transport
▪ sodium goes downhill  drags glucose uphill

(inside the cell)
3. transporters  utilize energy
o
o sodium/ potassium ATPase
o
o phosphorylated pump  change in conformation  sodium exposed to outside  exposes 2 potassium
attachment site  dephosphorylated  original conformation  potassium exposed to inside of cell
- consequences:

o 3 Na+ out for every 2 K+ in  outside becomes more positive compared to inside  electrical gradient
o Na+ gradient  co transport or secondary transport
o low Na+ concentration inside cell  lowers osmotic potential inside the cell  cell is a less hypertonic cell
o expensive process to run these pumps
-
EXAMPLES OF OTHER PUMPS
1. P-gly oprotei pu p: per ease  drug efflux transporters
a. takes hydrophobic molecules and pump them out/ against concentration gradient  uses ATP
b.
c. anticancer drugs: prevent cell division  cells cannot divide
i. rapidly dividing tumor cells are hit first
ii. resistance: in cancer cell  mutation  increase gene copy number of P-glycoprotein
iii. gene copy number increases  pumps out the anticancer drug right away
1. too much anticancer drug  may kill the patient before killing the tumor
2. bile salt export pump (BSEP):
a.
o bile in liver pumped out  bile as emulsifying agent (+ and - charges)  can be used as soap

o ATP dependent bile salt transporter in liver: produces bile

o mutations: poor fat metabolism, blockage in liver cells  damage  scar tissue etc.  liver failure
o mutations: cholestasis, poor fat metabolism, dark urine, severe itching, jaundice, liver failure, death
3. cystic fibrosis transmembrane conductance regulator protein (CFTR permease)
a. protein in membrane, has binding site for ATP ( ADP)
b. pumps out chloride ions
c. layer of mucus inside lung: pumps chloride ions into mucus  osmotic potential of mucus goes up  water
comes out into mucus too  makes it less viscous  easier for oxygen/ carbon dioxide to diffuse across
mucus
d. mutant CFTR permeases: do not pump out chloride ions  no water following  thick mucus  oxygen
and CO2 cannot be easily transported across  bacterial habitat  must pump out mucus
i. 4% of Canadians have mutant gene  high frequency of cystic fibrosis
ii. heterozygote: medium effect  may have originated from cholera  legacy of high frequency of
mutant allele in population-
SUMMARY OF EXCRETION
- gout: have to cut down of meat intake
MOVEMENT AND MUSCLE CONTROL
- plants can move by stimulus: plants move using turgor pressure  uses aquaporins
o water can move very fast  movement for plants
- protists: can move using cilia or flagella (microtubules)
ANIMAL CELLS MOVE USING CONTRACTILE PROTEINS IN MICROFILAMENTS
- stained for actin (rat smooth muscle cell stained for actin)
MOVEMENT OF AMOEBA

- adds actin to the pseudopodia of the amoeba
PHAGOCYTOSIS AND MOVEMENT
- cell moves because of filaments
VERTEBRATES MOVE USING SKELETAL MUSCLES THAT ACT ON SKELETON
- two major proteins: actin and myosin

o alpha actin filament: made by actin monomers polymerized
▪
▪ alpha actin: found in skeletal muscles
o myosin: dimer  myosin filament or thick filament
▪ can convert ATP  ADP/ ATPase
▪
▪ myosin filament/ thick filament

- minor proteins:
o alpha actinin: structural protein that anchors actin filament to the cell
▪
o appi g protei : i either e d of a ti fila e ts so us le fi res do ’t lose the
o tropomyosin: long thin dimer that sits on actin filament
▪
o troponin complex: 3 polypeptides that bind to something different
▪ calcium ion
▪ actin
▪ tropomyosin
o other proteins: dystrophin
▪ dystrophin: no role in contraction of muscle; rather structural integrity of muscle cell; lack of
dystrophin  muscle cells breaks down/ muscular dystrophin
SKELETAL MUSCLES
-
MUSCLE CONTRACTION MECHANISM
1. o tra tio sig al: Ca2+ i side us le fi re’s e doplas i reti ulu sarcoplasmic reticulum)  Ca2+ secreted
2. Ca2+ binds to troponin complex  change in conformation in troponin complex  pulls tropomyosin  exposes
active binding site  myosin binds to that actin
3. myosin loses ADP, phosphate (dephosphorylated)  change in conformation  myosin head moves forward 
pulls actin filament
4. ATP binds to myosin  ATP converted to ADP, P  myosin drops actin
5. ratchet system (incrementally)
6. about 75nm pull (10x diameter), 10times/ sec  lots of ATP used

- first step: ATP is already converted into ADP and P (unlike the diagram suggests)
- death: they ha e to get rid of the stiff
o rigor mortis: stiff ess i death
o after death  body becomes rigid  things start to break down
o calcium leaks out of sarcoplasmic reticulum  contraction
o ATP is not produced  myosin head does not come off actin
- e.g. how to make a tender steak
o meat must be hung to be tender: allow rigor mortis to release calcium and contract muscle  proteases
eventually digest myosin and actin  breaks myosin actin cross bridges
▪ amino peptitase and calpain (Ca2+ activated protease)
SKELETAL MUSCLE STRUCTURE
-
- unit of contraction: sarcomere

-
-

Week 14 Osmoregulation and Excretion Textbook Notes

- osmoregulation: regulation of solute concentrations and water balance by cell or organism
- breakdown of nitrogenous molecules  ammonia (toxic)  excretion rids body of nitrogenous metabolites and
other metabolic waste
- excretion: rids body of nitrogenous metabolites and other metabolic waste products
Concept 441 osmoregulation balances the uptake and loss of water and solutes
- depends on balancing uptake and loss of water and solutes  controlled movement of solutes between internal
fluids and external environment
- solute movement  movement of water by osmosis  net effect: regulate both solutes and water
OSMOSIS AND OSMOLARITY
- osmolarity: difference in osmotic pressure  expressed in molarity milliOsmoles per litre (mOsm/ L)
o isosmotic: same osmolarity of two solutions separated by selectively permeable membrane
▪ water crosses at equal rates in both directions  no net movement of water by osmosis
o hyperosmotic: two solutions differ in osmolarity, greater concentration of solutes  hyperosmotic
o hyposmotic: more dilute solution
o osmosis: hyposmotic solution  hyperosmotic solution
-
OSMOTIC CHALLENGES
- maintaining water balance: move ions into or out of tissues  integrated processes of ion/ water regulation
o osmoconformer: isosmotic with its surroundings
▪ all marine animals  no tendency to gain/ lose water
▪ in parts of ocean where external osmolarity is nearly constant  nearly constant internal osmolarity
o osmoregulator: control internal osmolarity independent of that of its environment
▪ terrestrial/ aquatic environments, both freshwater and marine
▪ can survive changes in external osmolarity
▪ osmoregulators in salt water: must resist loss of water from tissues
- stenohaline: cannot tolerate substantial changes in external osmolarity (most animals)
- euryhaline: survive large fluctuations in external osmolarity (barnacles, mussels)
MARINE ANIMALS
- most marine invertebrates  osmoconformers  same as sweater  no substantial challenges
o differ considerably from seawater in concentrations of specific solutes  must actively transport solutes for
homeostasis
- many marine vertebrates and some marine invertebrates  osmoregulators
o ocean is strongly dehydrating environment:
▪ marine fishes (cod) constantly lose water by osmosis  balance water loss by drinking large
amounts of seawater  use gills and kidneys to remove salts
▪ gills: chloride cells actively transport chloride ions out and allow sodium ions to follow passively

▪ kidney: excess calcium, magnesium, sulphate ions excreted with loss of only small amounts of water
-
- e.g. marine sharks and most chondrichthyans: have internal salt concentration much lower than seawater  salts
diffuse into bodies from water (gills)
o shark tissue contains high concentrations of urea  body fluids contain trimethylamine oxide (TMAO) 
not hypoosmotic to seawater  osmolarity close to that of sweater  sharks considered as
osmoconformers
▪ still, ater slo ly e ters shark’s ody and in food  disposed in urine produced by kidneys  rest is
lost in feces or secreted in specialized glands
o TMAO protects proteins from damage by urea
FRESHWATER ANIMALS
- body fluids of freshwater animals are hyperosmotic  gain water by osmosis and loses salts by diffusion
- bony fishes + freshwater animals  drinks almost no water + excrete large amounts of dilute urine  salts lost by
diffusion and urine replenished by eating
- e.g. perch freshwater fish  replenish salts by uptake across grills  chloride cells in gills actively transport Cl- into
body and Na+ follows
-
ANIMALS THAT MOVE BETWEEN FRESHWATER AND SEAWATER
- diadromous fishes (e.g. salmon, eels): life in fresh water and part in sea water
o smoltification: physiological and anatomical remodelling  prepares fish to enter sweater  in seawater
undergoes final steps of acclimatization  fish can maintain homeostasis in seawater
o euryhaline: able to resist disruption of internal ion and water homeostasis  e.g. many sweater fishes
ANIMALS THAT LIVE IN TEMPORARY WATERS
- anyhdrobiosis (e.g. tardigrades, aquatic invertebrates): dormant state when their habitats dry up or in extreme
dehydration/ desiccation  requires adaptations that require cell membranes intact  can contain large amounts
of sugar (trehalose) that protect cells by replacing water normally associated with proteins/ membrane lipids

LAND ANIMALS
- body covering prevents dehydration: waxy layers of insect exoskeletons, shells of land snails, layers of keratinized
skin cells, nocturnal (lower T and higher humidity of night air)
- many desert animals can minimize water loss that they can survive for long periods of time without drinking
-
-
ENERGETICS OF OSMOREGULATION
- osmoregulators must expend energy to maintain osmotic gradients that cause water to move in/ out  activate
transport to manipulate solute concentrations in their body fluids
- minimizing osmotic difference between body fluids and surrounding environment decreases E the animal expends
TRANSPORT EPITHELIA IN OSMOREGULATION
- hemolymph fluid in insects and other animals with open circulatory system
- vertebrates and other animals with closed circulatory system  fluid contains mixture of solutes controlled
indirectly by blood  composition depends on structures of cells to complex organs (kidneys)
- transport epithelia: one or more layers of epithelial cells specialized for moving particular solutes in controlled
amounts in specific directions
o in seabirds: salt solution was produced by pair of structures/ nasal glands  salt glands eliminate excess salt
from bodies of sea turtles and marine iguanas
-
- nasal gland: removes excess NaCl from blood by countercurrent exchange

- countercurrent exchange: occurs between two fluids separated by one or more membranes and flowing in opposite
directions (humans must use greater volume of water to excrete salt load if drinking seawater  dehydration)
- transport epithelia also often function in disposal of metabolic wastes
Co ept 44.2 A a i al’s itroge ous wastes refle t its phyloge y a d ha itat
- ammonia: nitrogenous waste, toxic due to ammonium which interferes with diverse biochemical processes (pH,
electrochemical gradient, exocytosis, enzyme function)  many animals expend E to convert it to less toxic
compounds prior to excretion (urea/ uric acid)
FORMS OF NITROGENOUS WASTE
- 3 forms of nitrogenous waste: ammonia, urea, uric acid  differ in toxicity and E costs of production
o ammoniotelism (ammonia), ureotelism (urea), uricotelism (uric acid)
AMMONIA
- excreting nitrogenous wastes as ammonia  need access to lots of water  common in aquatic species
- highly soluble  easily pass through membranes  readily lost by diffusion to surrounding water
- invertebrates: ammonia released across whole body surface
- fishes: most ammonia lost as NH4+ across epithelium of gills, kidneys excrete only minor amounts of nitrogenous
waste (fishes can still switch their main nitrogenous waste product)
UREA
- most terrestrial animals + many marine species  do not have access to sufficient water to routinely excrete
ammonia  excretes urea
- amphibians, sharks, some marine bony fishes, turtles
- produced in vertebrate liver  product as urea of metabolic cycle that combines ammonia with CO2
- urea: low toxicity  can transport in circulatory system and store safely at high concentrations  much less water
lost than dilute solution of ammonia
- disadvantage: energy cost to produce urea from ammonia
o amphibians: excrete mainly ammonia when aquatic tadpoles  urea excretion when they become land
dwelling adults
URIC ACID
- insects, land snails, reptiles, birds (guano = uric acid + brown feces)
- non toxic, does not readily dissolve in water  excreted as semisolid paste with very little water loss  great
advantage for animals with little access to water
o cost: uric acid is more energetically expensive to produce than urea
- humans and other animals: small amount of uric acid due to purine breakdown
o genetic defect in purine metabolism  uric acid stones in bladder
o gout: joint inflammation caused by deposits of uric acid crystals

THE INFLUENCE OF EVOLUTION AND ENVIRONMENT OF NITROGENOUS WASTES

- waste depends on habitat  terrestrial turtles: excrete mainly uric acid, aquatic turtles: excrete urea and ammonia
- depends on immediate environment of animal egg:
o soluble wastes can diffuse out of shell-less amphibian egg or be carried away from mammalian embryo by
other’s lood
o shelled eggs produced by birds and other reptiles permeable to gases but not liquids  soluble nitrogenous
wastes released by embryo would be trapped within egg and accumulate to dangerous levels
o uric acid as waste product  precipitates out of solution and stored within egg as a harmless solid left
behind animal hatches
- endotherms: use energy at high rates  eat more food  produce more nitrogenous waste than ectotherms
- predators: derive much energy from protein  excrete more nitrogen than animals that rely mainly on lipids/
carbohydrates as energy sources
Concept 44.3 Diverse excretory systems are variations on a tubular theme
- water balance: regulation of solute movement between internal fluids and external environment
EXCRETORY PROCESSES
-
1. body fluid brought in contact with selectively permeable barrier/ biological filter  hydrostatic pressure drives
filtration
2. filtration: cells, proteins, large molecules encounter filter but cannot penetrate it and remain in body fluid
3. water and small solutes, salts, sugars, amino acids, nitrogenous wastes cross filter  filtrate solution
4. filtrate converted to waste fluid by specific transport of materials into/ out of filtrate
5. selective reabsorption: recovers useful molecules + water from filtrate  returns them to body fluids
6. valuable solutes: glucose, certain salts, vitamins, hormones, amino acids reabsorbed by active transport
7. selective secretion: nonessential solutes and wastes left in filtrate/ added to it  by active transport
8. pumping solutes  adjusts osmotic movement of water
9. excretion: processed filtrate containing nitrogenous wastes released from body as urine

SURVEY OF EXCRETORY SYSTEMS

- protonephridia: network of dead-end tubules connected to external openings  branch throughout body
o flatworms, rotifers, some annelids, mollusc larvae, lancelets
-
- metanephridia: excretory organs that collect fluid directly from coelom  excretory and osmoregulatory functions
o most annelids such as earthworms
- Malpighian tubules: remove nitrogenous wastes and also function in osmoregulation
o insects and other terrestrial arthropods
- kidneys: specialized organ consisting of tubules functioning in both osmoregulation and excretion
o in vertebrates and some other chordates
o tubules compacted in highly organized manner  associated with network of capillaries  also includes
ducts, other structures that carry urine from tubules out of kidney and body
o vertebrate usually nonsegmented but some invertebrate kidneys are segmented
Concept 44.4 The nephron is organized for stepwise processing of blood filtrate
FROM BLOOD FILTRATE TO URINE: A CLOSER LOOK
1. proximal tubule: reabsorption in the proximal tubule critical for recapture of ions, water, valuable nutrients from
initial filtrate
a. NaCl (salt) in filtrate diffuses into cells of transport epithelium where Na+ is actively transported into
interstitial fluid  transfer of positive charge out of tubule  drives passive transport of Cl- + movement of
more Na+ from lumen into cells of tubule wall by facilitated diffusion and cotransport mechanisms
b. salt moves from filtrate to interstitial fluid  water follows by osmosis  salt and water diffuse from
interstitial fluid into peritubular capillaries
c. glucose, amino acids, K+, other essential substances actively/ passively transported from filtrate to
interstitial fluid then into peritubular capillaries
d. processing of filtrate maintains relatively constant ph in body fluids: cells of transport epithelium secrete H+
into lumen of tubule + synthesize and secrete ammonia  buffer to trap H+ as NH4+
e. more acidic filtrate  more ammonia cells produce and secrete (most nitrogenous waste excreted as urea)
f. proximal tubules reabsorb 90% of buffer bicarbonate (HCO3-) from filtrate  further ph balance in fluids
g. materials to be excreted become concentrated throughout proximal tubule  wastes leave body fluids
during nonselective filtration and remain in filtrate while water + salts reabsorbed
h. toxic materials actively secreted into filtrate from surrounding tissues/ transport epithelium into lumen
2. descending limb of loop of Henle: reabsorption of water continues as filtrate moves into descending limb
a. aquaporin proteins make transport epithelium freely permeable to water
b. no channels for salt and other small solutes  low permeability for these substances
c. interstitial fluid bathing tubule must be hyperosmotic to filtrate  water moves out of tubule by osmosis

i. descending limb: osmolarity of interstitial fluid increases progressively from outer cortex to inner
medullar of kidney  filtrate loses water  solute concentration increase down descending limb
3. ascending limb of loop of Henle: has transport epithelium studded with ion channels but not water channels
a. impermeable to water
b. thin segment near loop tip: NaCl (concentrated in descending limb) diffuses out of permeable tubule into
interstitial fluid  maintain osmolarity of interstitial fluid in medulla
c. thick segment adjacent to distal tube: movement of NaCl out of filtrate continues  epithelium actively
transports NaCl into interstitial fluid  filtrate becomes progressively more dilute as it moves up to cortex in
ascending limb
4. distal tubule: regulation of K+ and NaCl concentration of body fluids
a. amount of K+ secreted into filtrate + amount of NaCl reabsorbed from filtrate
b. contributes to ph regulation by controlled secretion of H+ and reabsorption of HCO3-
5. collecting duct: carries filtrate through medulla to renal pelvis
a. processes filtrate  forms urine
b. epithelium: reabsorption of solutes and water: 1600L of blood flows through kidneys  nephrons and
collecting ducts process about 180L of initial filtrate (99% of which is reabsorbed into blood  1.5L of urine
to bladder)
c. hormonal control of permeability and transport determines extent to which urine becomes concentrated
d. conserving water: aquaporin channels in collecting duct allow water molecules to cross epithelium 
remains impermeable to salt and urea (in renal cortex)
e. traverses gradient of osmolarity in kidney  filtrate becomes increasingly concentrated  loses more water
by osmosis to hyperosmotic interstitial fluid
f. inner medulla: duct becomes permeable to urea  high urea concentration in filtrate  some urea diffuses
out of duct into interstitial fluid  contributes to high osmolarity of interstitial fluid in medulla  net result:
hyperosmotic urine to general body fluids
g. producing dilute urine: kidney actively reabsorbs salts without allowing water to follow by osmosis 
epithelium lacks water channels  NaCl actively transported out of filtrate
h. state of collecting duct epithelium controlled by hormones  maintain homeostasis for osmolarity


-
Concept 50.5 The physical interaction of protein filaments is required for muscle function
- muscle cell function relies on active filaments (like microfilaments of cytoskeleton)
o microfilaments lengthen/ shorten, polymerize/ depolymerize
o thin filaments in muscles arranged in fixed array within cell and do not change in length  they are pulled
toward each other  cell changes shape
▪ drive by motor protein myosin and requires ATP
VERTEBRATE SKELETAL MUSCLE
- moves bones and body, characterized by hierarchy of smaller and smaller units
- muscle fibre/ cell: contains multiple nuclei  formation by fusion of embryonic cells
o bundle of myofibrils arranged in parallel  composed of thin filaments/ thick filaments
- thin filaments: two strands of actin + two strands of regulatory protein coiled around one another
- thick filaments: staggered arrays of myosin molecules

- skeletal muscle = striated muscle: regular arrangement of filaments creates pattern of light/ dark bands
o sarcomere: repeating unit/ basic contractile unit of muscle
o sarcomeres lined up in adjacent myofibrils and contribute to striations visible with light microscope
o thin filaments attached to Z lines; project toward centre of sarcomere
o thick filaments attached to M lines centered in sarcomere
- muscle fibre at rest: thick and thin filaments only partially overlap
o edge of sarcomere: only thin filaments; zone in centre: only thick filaments  sarcomere can contract
THE SLIDING-FILAMENT MODEL OF MUSCLE CONTRACTION
- sliding filament model: neither thick nor thin filaments change in length when sarcomere shortens  thin and thick
filaments slide past each other  increases overlap
-
- interaction of actin and myosin:
1. myosin molecule has a long tail region and globular head region
2. tail adheres to tails of other myosin molecules that form the thick filament
3. head (extends to side) can bind to ATP and hydrolyze it to ADP  high energy form
4. high energy form of myosin binds to actin  forms cross bridge
5. pulls thin filament towards centre of sarcomere
6. cross bridge broken when new molecule of ATP binds to myosin head
- each cycle, myosin head free from cross bridge cleaves newly bound ATP and binds again to actin
o thin filament moved toward centre of sarcomere in previous cycle  myosin head now attaches to new
binding site farther along thin filament
o 350 heads of thick filament forms and reforms about 5 cross bridges/ sec  drives filaments past

MUSCLE ENERGY PRODUCTION

- alternate form of energy equivalent needed  creatine phosphate
- ATP levels decline  enzyme transfers phosphate group from creatine phosphate to ADP  ATP
o resting supply of creatine phosphate can sustain contractions for about 15 seconds
- ATP stores replenished when carbon fuels are broken down (mitochondria, oxidative phosphorylation)
o lipids, carbohydrates, amino acids  water, CO2  supply of ATP
o glycolysis: fermentation of carbohydrates  faster but less efficient
- glycolysis and fermentation:
o carbohydrate partially broken down  lactate  1 minute of repetitive contractions
THE ROLE OF CALCIUM AND REGULATORY PROTEINS
1. tropomyosin: regulatory protein bound to actin strands of thin filaments
a. at muscle fibre rest: tropomyosin covers myosin binding sites along thin filament  prevents actin and
myosin from interacting
b. accumulation of Ca2+ in cytosol  binds to troponin complex  tropomyosin bound along actin strands
shift position  exposes myosin binding sites on thin filament
- rise in Ca2+ concentration in cytosol  thin/ thick filaments slide past each other  muscle fibre contracts
- low Ca2+ concentration  binding sites covered  contraction stops
c. troponin complex: set of additional regulatory proteins bound to actin strands of thin filaments
-
- motor neurons  trigger release of Ca2+ into cytosol of muscle cells  form synapses
o multistep process involving membranes, compartments within muscle cell
Concept 50.6 Skeletal systems transform muscle contraction into locomotion
TYPES OF SKELETAL SYSTEMS
- hardened support structures can be external (exoskeletons), internal (endoskeletons) or absent (hydrostatic)
HYDROSTATIC SKELETONS
- consists of fluid held under pressure in closed by compartment
- most cnidarians, flatworms, nematodes, annelids
- uses muscles to change shape of fluid filled compartments
o e.g. hydra elongates by closing its mouth and using contractile cells in its body wall to constrict its central
gastrovascular cavity  decreasing diameter of cavity  cavity becomes longer
o e.g. worms: muscles in body wall exert localized forces against interstitial fluid

▪ peristalsis: movement produced by rhythmic waves of muscle contractions passing from front to
back  used in earthworms and other annelids
- well suited for life in aquatic environments

o land: provide support for crawling + burrowing and may cushion internal organs from shocks
o hydrostatic skeleton cannot support walking/ running  a i al’s ody is held off grou d
EXOSKELETONS
- exoskeleton: hard e ase e t deposited o a i al’s surface
o e.g. shells of clams and most other molluscs made of calcium carbonate secreted by mantle (extension of
body wall)
o clams and other bivalves close their hinged shell using muscles attached to inside of exoskeleton 
enlarges shell with age to outer edge
- insects + other arthropods: jointed exoskeleton cuticle  nonliving coat secreted by epidermis
o chitin: fibrils of chitin embedded in protein matrix  composite material of strength + flexibility
o cuticle hardened with organic compounds that crosslink proteins of matrix and salts may be added (in
crustaceans like lobsters)
o flexible body parts (e.g. leg joints): cuticle remains unhardened
o muscles attached to knobs and plates of cuticle that extend into interior of body
o growth spurt  arthropod sheds its exoskeleton (moult)  produces larger one
ENDOSKELETONS
- endoskeleton: hardened internal skeleton buried within soft tissues
o sponges: endoskeleton: hard needle-like structures of inorganic material or fibres made of protein
- echinoderms: bodies reinforced by ossicles (hard plates of magnesium carbonate and calcium carbonate crystals)
o sea urchins: ossicles tightly bound
o sea stars: loosely linked ossicles  sea star can change shape of arm
- chordates: endoskeleton of cartilage, bone, or some combination
- mammalian skeleton: more than 200 bones, some fused together, others connected at joints by ligaments 
freedom of movement

Bio Week 15.1 Lecture Notes

- shut down Na+ K+ pump: accumulate sodium ions in the inside  osmotic potential increases  cell bursts
MUSCLE CONTRACTION
- Ca2+ binding on troponin complex  pulls tropomyosin
- sarcomere: two thin filaments pulled along as muscle contracts
- strength training: contracting muscles against resistance  increases number of myofilaments in each muscle fibre
o more proteins in to their cells
o short burst of activity
- endurance training: increases number of blood vessels in muscle and increases in number of mitochondria in muscle
o brings oxygen to mitochondria for oxidative respiration
- fibres  increases ability to sustain muscle contraction over long period
- disuse atrophy: decrease in number of myofilaments in each muscle fibre
o not losing cells, muscle fibres
o losing amount of myosin and actin molecules in each of the cells
DISUSE ATROPHY IN SPACE
- daily exercises using full range of motion in space  minimize contractile protein loss
- i spa e, ou do ’t ha e to ork agai st gra it
TYPES OF MUSCLE FIBRES (3)
1. slow oxidative fibres: contain type of myosin with relatively low ATPase activity
a. numerous mitochondria  prolonged, regular activity (red muscles, leg meat of chicken)
b. leg muscles, oxidative proteins that transport oxygen to tissues
2. fast oxidative fibres:
a. higher ATPase activity
b. lots of mitochondria
c. rapid actions
d. e.g. rattle snake tails, wings of Canada goose
3. fast glycolytic fibres:
a. myosin with high ATPase activity
b. fewer mitochondria, little available myoglobin
c. pale colour  white muscles/ meat (breast meat of chicken)
d. rapid, intense actions but muscle fatigues quickly
e. glycolysis occurs for a long time  energy
f. e.g. wings of chicken (not for flying)
MUSCLE ANATOMY (skeletal muscle fibres)

o sarcolemma (plasma membrane), sarcoplasmic reticulum (endoplasmic reticulum), sarcoplasm (cytoplasm),

mitochondria, nuclei, etc.
o multi nuclei cell for skeletal muscle
- multi nuclei cell of skeletal muscle:
1. repeated nuclei division (mitosis) with no cytokinesis  wrong
2. fusion of cells  correct
- myoblasts: immature muscle cells experiment
o
o single nucleus  rich medium  mitosis
▪ produces beta actin (from myoblasts)
o add stress: starve myoblasts through poor medium (no serum)  cells start to fuse  multinucleic
▪ produces alpha actin
- humans are incapable of regenerating muscle
o frogs and shit can do it
o scientists: generating mature, functional skeletal muscles in mice
- e.g. lab grown sausages:
o biopsy from muscle of the pig  extracts myoblasts  puts it in non growth serum (poor medium)  cells
fuse  forms myofibres  exercise the meat so more proteins can be stuffed in each one of the fibres
▪ exercise: polysaccharides derived from fungi/ invertebrate exoskeletons  template  contracts/
expands depending on temperature  exercises meat fibres
o myofibres bundle together
NEURAL TRANSMISSION AND NERVOUS CONTROL
- nervous system: CNS, PNS
o CNS: brain + spinal cord
o PNS: anything else
NEURONS
- cells in nervous system that send/ receive electrical/ chemical signals throughout body
o all animals except sponges have neurons

- dendrites: receive information

- cell body: nucleus, neuropeptides encoded in the nucleus
- axon: sends signals (only one)
o glial cells: holds nervous cells together and makes myelin sheath
▪ myelin sheath: helps insulate neurons when they are together
• glycoproteins etc.  good insulators
• formed by non neuronal cells (Schwann cell: type of gial cell)
o can be very long
DEFINITIONS
- nerve: hundreds of neurons with associated with glial cells
- glial cells: produce connective tissue and organize zones around neurons
o produces myelin for certain nerves
- nerve tract: bundle of axons
- ganglion: collection of neuron cell bodies
o all the cell bodies together  expanded area of the nerve
- myelin sheath: by glial cells and acts an insulating material
TYPES OF NEURONS
- sensory neuron: information from outside
o dendrites are very long  highly branched
- motor neuron: interacts with skeletal muscles etc.
o sends signals away from sensory neurons
o axons are long in motor neurons
- interneurons: can make connections with other neurons
o highly branched dendrites
o often in the brain
NEURAL CIRCUIT OR PATHWAY
-
o section 50.1 (1162 – 1164)  brief overview of reception types
VOLTAGE SENSITIVE/ VOLTAGE ACTIVATED/ GATED ION CHANNELS

o high concentration of sodium outside of cell

▪ lower concentration of sodium inside of cell
o negative charge inside cell and positive charge outside cell
o high concentration of potassium inside of cell
▪ lower concentration of potassium outside of cell
o resting membrane potential -70 mV
- signal:
1. activates/ change conformation of sodium channels
2. opens  sodium rushes into cell (passive diffusion) down gradient
a. changes conformation of sodium channel beside
b. build up of localized positive charge in the vicinity inside cell
c. this opens voltage gated potassium channels
3. inside becomes a bit more positive
4. potassium channels open  potassium moves out of cell (passive diffusion) down gradient
a. voltage gated sodium channels shut down with inactivation gate  no more sodium out
b. positive charges of sodium inside membrane boots out potassium ions OUT THEY GO
ACTION POTENTIAL
- action potential generated when neuron stimulated over a threshold
1. -70 mV
2. +50/ +40 mV
3. -80 mV
4. -70 mV
NEURAL CIRCUIT OR PATHWAY
- read chapter 50
- neurons have millions of ion channels (sodium potassium ATPase)

1. resting state: both channels are closed

2. depolarization: sodium channels open  sodium rush inside into cell  more positive
3. rising phase of action potential: electric current changes conformation of next sodium channel down the line
4. falling phase of action potential: few amino acids close the sodium channel  sodium cannot leave cell
5. potassium channel opens  potassium goes out (down concentration gradient and electrical gradient)
6. undershoot: too many potassium leaves (K+ channels are little bit slow in closing/ changing conformation)
7. sodium potassium ATPase restores resting potential
-
o always go from dendrites  cell body  down the axon
▪ voltage sensitive sodium channels fold over the few amino acids and prevent sodium to leave cell
▪ when sodium channels open, nerve impulse is long gone
-
SPEED OF SIGNAL
1. diameter of axon:
a. broader axons provide less resistance and action potential moves faster
b. e.g. squid: broad axon  goes quickly
2. myelination:
a. faster than unmyelinated
b. myelin sheath is not continuous: gaps at nodes of Ranvier  action potential jumps or flows through cytosol
to next node
c.

- no loss of signal in neuro transmission  opening/ closing of voltage channels  renewal of signal as it goes
down
o not fastest but signal strength continuous throughout
SYNAPSES
- junction where neuron meets another neuron or muscle cell etc.
o presynaptic cell/ neuron: sends signal
o postsynaptic cell/ neuron: receives signal
- 2 types of synapse:
1. electrical: really really close together
a. charge flows through gap junctions from cell to cell
2. chemical: neurotransmitter acts as signal from presynaptic to postsynaptic cell
a. ost euro s a d shit, gaps are ’t lose e ough
b.
CHEMICAL NEURAL TRANSMISSION ACROSS SYNAPSES
- synaptic terminal: end of neuron of presynaptic cell
- neurotransmitters diffuse across gap (synaptic cleft) between neuron and target cell (postsynaptic cell)
- neurotransmitters bind receptors in the postsynaptic cell membrane  open ion channels
1. excitatory neurotransmitter: presynaptic cell depolarized  depolarize postsynaptic cell
2. inhibitory neurotransmitter: presynaptic cell  decrease probability of action potential
ACETYLCHOLINE
- released at neuromuscular junctions
- most widespread neurotransmitters
- excitatory in brain and skeletal muscles  allows action potential
- inhibitory in cardiac muscles  inhibits action potential
BIOGENIC AMINES
- derived from amino acids, lost carboxyl end
- abnormally high or low levels associated with variety of disorders
o schizophrenia, Parkinson disease, depression
- dopamine: derived from tyrosine tyr (take off carboxyl group)  useful in the brain
o effects moods
- histamine: histamine his, important for signalling cells for production of HCl, gastric juice
AMINO ACIDS
- glutamate: widespread excitatory neurotransmitter
- GABA (gamma aminobutyric acid): most common inhibitory neurotransmitter in brain
- glycine: important in spinal cord
NEUROPEPTIDES
- may have hormone action
- neuromodulators: can alter response of postsynaptic neuron to other neurotransmitters
- work in concert with other neurotransmitters  important in brain, lactation, child birth etc.

- helping neurotransmitters
- e.g. opiate peptides, oxytocin
GASEOUS NEUROTRANSMITTERS
- produced locally as needed and are short acting  influences cells after diffusion across membranes
- several drugs for male sexual dysfunction (Viagra)  enhance/ mimic action of NO by relaxing smooth muscles in
penis and allowing increased blood flow
o nitric oxide (NO)
- CO carbon monoxide: poison, important in smooth muscle contraction  uncertain function
- CO2: acting as neurotransmitter  concern regarding increased levels due to pollution  effects on fish
PROCESS OF SYNAPSE
- synaptic vesicles release neurotransmitter at terminal of axon (except for gaseous ones)
o signal can cross synaptic cleft
- receptors on postsynaptic neuron
-
1. end of axon: more positive outside than inside
2. depolarization of membrane: voltage gated sodium channels open  sodium comes inside
3. voltage gated Ca2+ channel: calcium rushes inside cell
4. calcium mediates fusion of synaptic vesicle with membrane
5. neurotransmitters are released into synaptic cleft
6. postsynaptic membrane (effector) receptors bind neurotransmitters
a. e.g. acetylcholine: two neurotransmitters have to bind to receptor
7. voltage gated sodium channels open  depolarizes postsynaptic membrane
a. for skeletal muscle: only closest nucleus encodes mRNA for building receptors
b. sarcoplasmic reticulum: releases calcium into cell  contraction of muscle cell
- figure 48.14
o 2 for acetylcholine

- HOMEWORK: FIGURE 50.30
-
RECYCLING
1. Na+ K+ ATPase restores ion balance
2. after repolarization, Ca2+ goes out of cells, using Na+ gradient
3.
a. destroys acetylcholine by an enzyme released into synaptic cleft into acetate + choline
b. small products are taken up by pre synaptic membrane  later stuffed into new synaptic vesicles for
next contraction
PRACTICAL AND MEDICAL APPLICATIONS
1. insecticides: organophosphates (Ops) inhibit acetylcholinesterase (ACE)
a. binds to esterase and inactivates it
b. muscle cells continue to depolarize  prevented esterase from inactivating/ destroying neurotransmitter
c. neurotransmitter in cleft  depolarization in muscle cells
d. resistance: increase gene copy number of esterase
e. DDT & pyrethroids: act on voltage gated Na+ channels  jams it open  cannot close  cannot repolarize
2. myasthenia gravis (autoimmune disease): reduces number of functional acetylcholine receptors
a. autoimmune disease: recognizes receptors as foreign
b. antibodies bind to receptors  non functional receptors  block of neuromuscular transmission  muscle
weaknesses and fatigue
c. sustained activity of muscles increases weakness/ fatigue: takes time for ACh recycling  reduces number
of ACh coming out/ fewer  inactivated by antibodies

3. multiple sclerosis (autoimmune disease): myelin is destroyed

a. myelin is recognized as foreign  antibodies attach to them
b. difficulty in speaking, walking
4. other poisons:
a. bungarotoxin: poison from banded krait: inhibits acetylcholine receptor
i. shuts receptor complete  paralysis
b. tetrodotoxin: binds to voltage sensitive Na+ channel
i. made from puffer fish (fugu)
ii. they want the prey to be paralyzed  shuts down Na+ channel
c. local anaesthetics: briefly paralyzes in local region  dissipates in time
5. hot pepper receptor: heat receptor  opens at about 50 centrigrade
a. peppers sit beside the heat receptor due to similar structure of capsaicin (in hot peppers)
b. peppers do ’t a t us to eat the  seeds are not viable (only wants birds)  discourages mammals to
eat them and does all the hot shit on the tongue
c. with capsaicin: heat receptor opens at 37 centigrade  sodium and calcium rushes in  after a while,
cannot depolarize anymore
i. hydrophobic  water has no effect  use milk (lipids)
REPRESENTATIVE NERVOUS SYSTEMS
-
o except for sponges, all animals have a nervous system
o nerve net is a simple nervous system found in cnidarians (jellyfish, hydras, anemones)
▪ neurons connect to each other in a network
- echinoderms: nerve ring around mouth connected to larger radial nerves extending to arms
- planaria: nerve cords extend length of animal connected by transverse nerves and a collection of neurons in head 
form ganglia that performs integration function
- annelids: more neurons and ventral nerve cords that have ganglia in each segment
- simple mollusks: pair of anterior ganglia and paired nerve cords
- trend toward cephalization: increasingly complex brain in head
o flies: centralized brain with subdivisions with separate functions (some of ganglia does integration)
o advanced mollusks have brains with well developed subdivisions
▪ some of the ganglia does integration
▪ predators: need good vision  sophisticated brain

-
HUMANS
- everything is centralized/ coordinated in brain (at least for sophisticated behaviour)
- vertebrates and simple chordates have CNS and a PNS
- organization shows similarities to segmentation of invertebrates
- e.g. researcher counted the cells in a brain by counting cell bodies (only nerve cells have cell bodies)
o 84 billion neurons
o experimental brains were all men
SUMMARY OF EARLY STEPS IN ORIGINS OF NERVOUS SYSTEM
1. more neurons
2. concentration of neurons in specialized structures
3. specialization of function:
a. afferent neurons: carry signals toward brain
b. efferent neurons: carry away form brain
4. complex synaptic contacts:
a. many synapses from a single neuron
b. many interneurons (neurons connecting neurons)
-
THE FUTURE
- SPAUN (sematic pointer architecture unified network): aritificial brain with 2.5 million neurons that do several tasks
including number puzzles  unlike Watson (information retrieval)
o takes a long time to think but actually works out information itself

CARDIOVASCULAR SYSTEM
- major functions:
1. transport of gases between environment and tissues (O2 to tissues, CO2 from tissues)
2. transport of nutrients and metabolic waste products between tissues
3. defence: immune system
BLOOD COMPONENTS
-
Concept 48.1 Neuron organization and structure reflect function in information transfer
INTRODUCTION TO INFORMATION PROCESSING
- information processing: sensory input  integration  motor output
- central nervous system (CNS): neurons carrying out integration  brain + longitudinal nerve cord
- peripheral nervous system (PNS): neurons carrying information into and out of CNS
- nerves: neurons bundled together
1. sensory neutrons: transmit information from sensors detecting external stimuli or internal conditions
a. information sent to grain or ganglia (clusters of nerve cell bodies in CNS)
b. sensory input integrated
2. interneurons: local circuits connecting neurons in brain (where sensory input is integrated)
3. motor neurons: transmit signals to muscle cells/ triggers muscle or gland activity

NEURON STRUCTURE AND FUNCTION

- cell body: includes ost of euro ’s orga elles a d u leus
- dendrites: highly branched extensions and part of typical neuron; they receive signals from other neurons
- axon: neuron has single axon; transmits signals to other cells
o larger than detritus and very long (those that reach from spinal cord of giraffe to muscle cells in feet)
o axon hillock: cone shaped base where signals travel down are generated
o near its other end --. axon usually divides into many branches
- synapse: space between axon terminal and target cell
o chemical messengers or neurotransmitters pass information from transmitting neuron to receiving cell
o transmitting neuron: presynaptic cell
o neuron, muscle, gland cell receiving signal: postsynaptic cell
o highly branched axon: can transmit info to many targets
o highly branched dendrites: can receive input through large # of synapses
-
- glial cells/ glia: supporting cells of nerve in vertebrates and most invertebrates
o nourish neurons, insulate axons, regulate extracellular fluid surrounding neurons
o outnumber neurons in mammalian brain
-
Concept 48.2 Ion gradients and ion channels establish the resting membrane potential of a neuron
- animal cells have high concentration of K+ inside cell
o high concentration of Na+ outside cell
o ion gradients and ion channels  minor differences in charge
- membrane potential: charge difference/ voltage due to interactions across membrane  source of PE
- resting membrane potential: membrane potential of inactive neuron that is not sending a signal
o between – 60 and – 80 mV

- input from other neurons/ stimuli  change in neuron membrane potential  acts as signal  transmits/ processes
information
o rapid changes in membrane potential  sight etc.
THE RESTING MEMBRANE POTENTIAL
- cell is more negative inside in general
- electroneutral: equal number of cations and anions in any solution
o separated by membrane  minor differences in ions
- convention: membrane potential expressed relative to outside of cell
o e.g. -70 mV: inside of cell is more negative than outside
o 0 mV: polarized
o membrane potential changes when ions move across membrane through ion channels
- hyperpolarization: increase membrane potential
- depolarization: decrease membrane potential
- depends on both gradients of ions across membrane + permeability of membrane to ions
1. cell cytoplasm has high concentration of proteins + other macromolecules that possess net negative charge and
cannot move across membrane  retaining/ attracting cations that are able to move
a. K+ ions that are most permeable to move  accumulates in cells  drawn by large impermeable anions
2. if ion cannot cross membrane  it cannot contribute to membrane potential even if ion has steep concentration
gradient
a. ion suddenly made permeable  ion goes down concentration gradient of ion and membrane potential
b. at rest, low permeability to Na+  Na+ channels open  Na+ flows into cell (chemical gradient + electrical
gradient)  reduces membrane potential  less negative  depolarization
- equilibrium: chemical and electrical forces exactly counterbalance each other  no net movement of Na+
-
DETERMINING THE RESTING MEMBRANE POTENTIAL
- equilibrium potential: membrane potential at which equilibrium occurs (Eion)
o can predict direction of ion movement under certain concentration gradient

o Nernst equation: = Nernst potential

o depends on ion gradients and permeability of ions
-
o higher KCl inside  membrane permeably only to K+  K+ moves out  inside more negative
o movement of K+ stops when Nernst potential reached for K+ (Ek) of -90 mV
o higher NaCl outside  opening of Na+ channels  some Na+ moves inward  inside less negative
o movement of Na+ stops when Nernst potential reached for Na+ (ENa) of + 62 mV
- neuron K+: multiple concentration gradients and ion channels
o membrane potential: -60 to -80 mV
o when K+ channels open: K+ moves out of cell (because resting potential for K+ is -90 mV)
o membrane is hyperpolarized relative to resting state
o outward force from chemical gradient (more K+ inside cell) > inward electrical force (more negative
inside)  movement of K+ until membrane potential hyperpolarized to -90 mV (Ek)
o
- neuron Na+: typical concentration: 150 mM outside and 15 mM inside

o Ena = + 62 mV  Na channels open  Na+ enters cell depolarizing membrane  net movement of Na+
stops when 62 mV reached
- resting membrane potential of neuron is close to Ek because K+ is most permeable of ions
o minor Na+ leak tends to depolarize cell; any Cl- permeability has little effect on resting potential
- cells are able to pump ions across membrane by active transport (e.g. Na/ K ATPase pump)
o Na+ gradient  vital for neuronal function
o unequal transport of Na and K contributes to increasing membrane potential
▪ main function: maintain Na+ gradient across membrane  source of energy to drive other
processes such as transport
▪ neurons can induce changes in Na+ permeability to rapidly depolarize cell  action potential
▪ if Na+ moves toward Ena it moves away from Ek
- nerve impulse: change in chemical concentration than generating resting potential
Concept 48.3 Action potentials are the signals conducted by axons
- gated ion channels: ion channels that open/ close in response to stimuli  changes in membrane potential
o voltage gated ion channels: open with changes in membrane potential
o ligand gated channels: open in response to changes in concentration of specific signalling molecules
o stretch activated ion channels: open in response to changes in cell shape
HYPERPOLARIZATION AND DEPOLARIZATION
1. hyperpolarization: makes inside of membrane more negative
a. opening K+ channels  K+ diffuses out toward Ek (-90 mV)
b. results from any stimulus that increases outflow of positive ions or inflow of negative ions
2. depolarization: reduction in magnitude of membrane potential and makes inside of membrane more positive
a. Na+ channels: stimulus  voltage gated sodium channels open  permeable to Na+  Na+ diffuses into
cell  depolarization towards Ena (62 mV)
GRADED POTENTIALS AND ACTION POTENTIALS
- graded potential: shift in membrane potential; has a magnitude that varies with strength of stimulus
o induce small electrical current that leaks out of neuron as it flows along membrane
o graded potentials decay with distance from their source
o not nerve signals that travel along axis  but has major effect on generation of nerve signals
- active potential: massive change in membrane voltage
o depolarization shifts membrane potential sufficiently
o constant magnitude and can regenerate in adjacent regions of the membrane
o can spread along axons  transmitting signal over long distances
- voltage gated ion channels: opens or closes when membrane potential passes particular level
o depolarization opens voltage gated sodium channels  flow of Na+ into neuron  further depolarization
▪ increased depolarization causes more sodium channels to open  greater flow of current 
positive feedback  rapid opening of all voltage gated sodium channels
- action potential occurs whenever depolarization increase membrane voltage to particular value/ threshold
o initiated  action potential has a magnitude that is independent of strength of triggering stimulus
o occur fully or not at all (all or none response)
o positive feedback loop of depolarization and channel opening triggers action potential whenever membrane
potential reaches threshold
GENERATION OF ACTION POTENTIALS: A CLOSER LOOK

-
- membrane depolarization opens both types of channels, but they respond independently and sequentially
1. sodium channels open first  initiates action potential  sodium channels become inactivated  loop of channel
protein moves  blocks ion flow through opening  inactivated until after membrane returns to resting membrane
potential and channels close
2. potassium channels open more slowly  remain open and functional until end of action potential
STAGES OF VOLTAGE GATED CHANNELS AND ACTION POTENTIAL
1. most voltage gated sodium channels are closed
2. stimulus depolarizes membrane  some gated sodium channels open  more Na+ diffuse into cell  further
depolarization opens more gated sodium channels  more Na+ diffuse into cell
3. rising phase: threshold is crossed  positive feedback brings membrane potential close to Ena
4. voltage gated sodium channels inactivate soon after opening  halts Na+ inflow
a. most voltage gated potassium channels open  rapid out flow of K+
b. falling phase: potential does ’t rea h E a a d ri gs back potential back toward Ek
5. undershoot: e ra e’s per ea ilit to K+ > rest  membrane potential closer to Ek than it is at resting
membrane potential  gated potassium channels eventually close  returns to resting membrane potential
- sodium channels remain inactivated during falling phase and early part of undershoot
o second repolarizing stimulus  it is unable to trigger action potential
- refractory period: downtime when second potential cannot be initiated
o limit of maximum frequency at which action potentials can be generated  ensures that all signals in axon
travel in one direction, from cell body to axon terminals
o refractory period due to inactivation of sodium channels, not to change in ion gradients
- differences in action potential frequency convey information about signal strength

o differences in time interval between action potentials are the only variable in transmission of information by
axon
- mutations in genes that encode ion channel proteins  disorders affecting nerves, muscles, brain, heart
o depends on where in body gene for protein is expressed
o myotonia: periodic spasming in muscles: mutations in voltage gated sodium channels
o epilepsy: mutations in sodium channels in brain  excessive synchronized firing of groups of nerve cells 
seizures
CONDUCTION OF ACTION POTENTIALS
-
1. Na+ inflow during rising phase creates electrical current that depolarizes neighbouring region of axon membrane
2. depolarization in neighbouring region is large enough to reach threshold  action potential reinitiated there
3. repeated many times along length of axon
4. magnitude and duration of action potential remain constant at each position (all or none event)
5. movement of nerve impulse from axon hillock to axon terminals  domino
- movement toward axon terminal: immediately behind travelling zone of depolarization caused by Na+ inflow = zone
of repolarization caused by K+ outflow
o repolarized zone: sodium channels remain inactivated
o inward current that depolarizes axon membrane ahead of action potential cannot produce another action
potential behind it  prevents action potentials from travelling back toward cell body
EVOLUTIONARY ADAPTATIONS OF AXON STRUCTURE
- resistance to electrical currently flow: inversely proportional: cross sectional area of conductor
- large diameter axon  less resistance to current of action potential
- giant axons (invertebrates): rapid behavioural responses such as muscle contraction that propels squid toward prey
- vertebrate axons: narrow diameters but action potentials at high speed
o electrical insulation: causes depolarizing current associated with action potential to spread farther along
axon interior  brings more distant regions to threshold sooner

-
o myelin sheath: electrical insulation surrounding vertebrate axons
▪ oligodendrocytes in CNS: type of glia producing myelin sheath
▪ Schwann cells in PNS: type of glia producing myelin sheath
▪ development: specialized glia wrap axons in many layers of membrane  mostly lipid  poor
conductor of electrical current
o nodes of Ranvier: voltage gated sodium channels restricted to gaps in myelin sheath in myelin axons
▪ extracellular fluid in contact with axon membrane only at nodes  action potentials not generated
in regions between nodes
▪ inward current produced during rising phase travels all the way to next node where it depolarizes
membrane and regenerates action potential
- salutatory conduction: action potential appears to jump along axon from node to node  opening/ closing of ion
channels occur at only limited number of positions along axon
o myelinated axon has a fast conduction speed
-
Concept 48.4 Neurons communicate with other cells at synapses
- electrical synapses: contain gap junctions which do allow electrical current to flow directly from one neuron to
another
o synchronize activity of neurons responsible for certain rapid, unvarying behaviours
- chemical synapses: involve release of chemical neurotransmitter by presynaptic neuron
o each terminal presynaptic neuron synthesizes neurotransmitter and packages it in multiple membrane
bounded compartments of synaptic vesicles
o arrival of action potential at axon terminal  depolarizes plasma membrane  opens voltage gated
channels  allows Ca2+ to diffuse into terminal
o Ca2+ concentration in terminal causes synaptic vesicles to fuse with terminal membrane  releases
neurotransmitter by exocytosis
o neurotransmitter released  diffuses across synaptic cleft (separates presynaptic neuron from postsynaptic
cell)  diffusion time is slow
o neurotransmitter bind to and activates specific receptor in membrane

-
- neural damage: inability of many neurons to reform synaptic connections lost when cells die from physical/ chemical
damage
GENERATED OF POSTSYNAPTIC POTENTIALS
- ligand gated ion channel: receptor protein that binds and responds to neuro transmitters at many chemical
synapses
o clustered in membrane of postsynaptic cell opposite to axon terminal
o i di g of eurotra s itter re eptor’s liga d  opens channel  specific ions diffuse across postsynaptic
membrane  postsynaptic potential  graded potential in postsynaptic cell
- some ligand gated ion channels are permeable to both K+ and Na+
o channel opens  membrane potential depolarizes between Ek and Ena
o brings membrane potential toward threshold
o excitatory postsynaptic potential (EPSP): depolarization brings membrane potential toward threshold
- some ligand gated ion channels are selectively permeable for only K+ or Cl-
o channels open  postsynaptic membrane hyperpolarizes
o inhibitory postsynaptic potential (IPSP): moves membrane potential further from threshold
- rapidly clear neurotransmitter molecules from synaptic cleft  limit duration of postsynaptic potentials
o some neurotransmitters: actively transported back into presynaptic neuron  repackaged into vesicles or
metabolized as fuels in glia
o some neurotransmitters: removed from synaptic cleft by simple diffusion or by enzyme that catalyzes
hydrolysis of neurotransmitter

-
SUMMATION OF POSTSYNAPTIC POTENTIALS
- magnitude of postsynaptic potential at one synapse varies with a number of factors including amount of
neurotransmitter released by presynaptic neuron
o as graded potential: postsynaptic potential becomes smaller with distance from synapse  by time a single
EPSP reaches axon hillock, it is too small to trigger an action potential in postsynaptic neuron
- 2 EPSPs occur a single synapse in rapid succession  posts apti euro ’s e ra e pote tial has ot retur ed to
resting membrane potential before arrival of second EPSP  EPSP adds together: temporal summation
- spatial summation: EPSPs produced nearly simultaneously by different synapses on same postsynaptic neuron can
also add together
- several EPSPs can combine to depolarize membrane at axon hillock to threshold through spatial + temporal
summation  postsynaptic neuron produces action potential
- summation in IPSP: 2 or more IPSP occurs nearly simultaneously at synapses in same region or in rapid succession at
same synapse  larger hyperpolarizing effect than single IPSP  also can counter effect of EPSP
-
- a o hillo k: euro ’s i tegrati g e tre  region where membrane potential at any instant presents summed
effect of all EPSPs and IPSPs
o membrane potential at axon hillock reaches threshold  action potential generated  travels along axon to
its axon terminals
o refractory period: neuron may produce another action potential, provided potential at axon hillock reaches
threshold once again
MODULATED SIGNALLING AT SYNAPSE
- synapses were receptor for neurotransmitter is not part of ion channel
o neurotransmitter binds to metabotropic receptor  activates signal transduction pathway in postsynaptic
cell involving second messenger

o second messenger systems: slower onset but last longer

▪ modulate responsiveness of postsynaptic neurons to inputs in diverse ways (e.g. altering number
of open potassium channels)
- signal transduction pathways modulate synaptic transmission
- cyclic AMP second messenger: neurotransmitter norepinephrine binds to metabotropic receptor 
neurotransmitter receptor complex activates G protein  activates adenylyl cyclase (enzyme that converts ATP to
cAMP)
o cAMP activates protein kinase A  phosphorylates specific ion channel proteins in postsynaptic membrane
 opens or closes
o amplifying effect of signal transduction pathway: binding of neurotransmitter molecule to a metabotropic
receptor can open or close many channels
NEUROTRANSMITTERS
- 5 groups of neurotransmitters: acetylcholine, amino acids, biogenic amines, neuropeptides, gases
-
- response depends on particular kind of receptor expressed by postsynaptic cell
o single neurotransmitter may bind to more than one different receptors
o can inhibit and excite
ACETYLCHOLINE
- vital for muscle stimulation, memory formation, learning
- vertebrates; 2 major classes of acetylcholine receptor
1. ligand gated ion channel
a. neuromuscular junction: motor neurons synapse with skeletal muscle cells
b. acetylcholine from motor neurons binds to receptor  ion channel opens  EPSP  terminated by
acetylcholinesterase (enzyme in synaptic cleft that hydrolyzes neurotransmitter)

2. metabotropic acetylcholine receptor: in vertebrate CNS and heart

a. acetylcholine activates signal transduction pathway
b. G proteins inhibit adenylyl cyclase and open potassium channels in muscle cell membrane
c. both effects reduce rate at which heart pumps  inhibitory effect in heart
- natural/ synthetic toxins disrupt neurotransmission by acetylcholine:
o nerve gas sarin inhibits acetylcholinesterase  buildup of acetylcholine to levels that trigger paralysis and
death
o certain bacteria produce toxin inhibiting presynaptic release of acetylcholine  botulism  muscles for
breathing fail to contract  Botox minimizes wrinkles by blocking transmission at synapses that control
facial muscles
AMINO ACIDS
- active in vertebrate CNS and PNS
- glutamate: common neurotransmitter
o binds to any ligand gated ion channels  excitatory effect on postsynaptic cells
o key role in formation of long term memory
- gamma aminobutyric acid (GABA): neurotransmitter at most inhibitory synapses in brain
o binding to GABA to receptors in postsynaptic cells  increases membrane permeability to Cl-  IPSP
o drug diazepam (Valium): reduces anxiety through binding to site on GABA receptor
- glycine: inhibitory synapses in parts of CNS outside of brain
o binds to ionotropic receptor that is inhibited by strychnine: rat poison
BIOGENIC AMINES
- synthesized from amino acids: e.g. norepinephrine made form tyrosine
o excitatory neurotransmitter in autonomic nervous system (branch of PNS)
o outside of nervous system: distinct but related functions as hormone as well as epinephrine
- dopamine made from tyrosine and serotonin (from tryptophan): released at brain  affect sleep, mood, attention,
learning
o drugs LSD an mescaline: produce hallucinatory effects by binding to brain receptors for these
neurotransmitters
- may play a role in nervous system disorders a d treat e ts: Parki so ’s disease la k of dopa i e i rai
o depression: treated with drugs that increase biogenic amines
o Prozac: enhances effect of serotonin by inhibiting its reuptake after release
NEUROPEPTIDES
- short chains of amino acids  neurotransmitters that operate via metabotropic receptors
o typically produced by cleavage of much larger protein precursors
- substance P: key excitatory neurotransmitter that mediates perception of pain
- endorphins: function as natural analgesics  decreases pain perception
o produced in brain in physical/ emotional stress (e.g. childbirth)
o relieve pain, decrease urine output, depress respiration, produce euphoria
o opiates bind to same receptor proteins as endorphins, opiates mimic endorphins and produce many of same
physiological effects
GASES
- some neurons in vertebrates release dissolved gases (NO) that act as local regulators
- sexual arousal: certain neurons in males release NO into erectile tissue of penis
o smooth muscle cells in blood vessel walls of erectile tissue relax  blood vessels dilate and fill spongy
erectile tissue with blood  erection
o Viagra: increases ability to achieve and maintain erection by inhibiting enzyme that terminates action of NO
- NO not stored in cytoplasmic vesicles but synthesized on demand
o NO diffuses into neighbouring target cells  change  broken down within few seconds

o NO works like many hormones, stimulates enzyme to synthesize second messenger that affects cellular
metabolism
- vertebrate body produces small amount of CO  neurotransmitter
o generated by hemeoxygenase enzyme
o regulates release of hypothalamic hormones in brain
o in PNS, acts as inhibitory neurotransmitter that hyperpolarizes plasma membrane of intestinal smooth
muscle cells
Concept 50.1 Sensory receptors transduce stimulus energy and transmit signals to the central nervous system
- sensory processes begin with stimuli  forms of energy
o converts stimulus to change in membrane potential  regulates output of action potentials to CNS
o does not always require large amount of stimulus energy
- e.g. he ole’s ose o ta ts o je t i tu el  touch receptors activated  transmit sensory info to brain 
brain integrate input and initiate one of two response pathways depending on whether food was detected
o motor output: either bite down with teeth or continue moving along tunnel
o
SENSORY PATHWAYS
- 4 basic functions: sensory reception, transduction, transmission, perception
SENSORY RECEPTION AND TRANSDUCTION
- sensory reception: detection of stimulus by sensory cells
o sensory receptor: sensory cell/ organ as well as subcellular structure that interacts directly with stimuli
▪ detect stimuli from outside (e.g. heat, light, pressure, chemicals)
▪ detect stimuli inside (e.g. blood P, body position)
- effect: open or close ion channels
o e.g. ion channels open/ close when substance outside cell binds to chemical receptor in plasma membrane
▪ resulting flow of ions across membrane changes membrane potential
- sensory transduction: conversion of physical/ chemical stimulus to change in membrane potential of sensory
receptor
- receptor potential: change in membrane potential
o graded potentials: magnitude varies with strength of stimulus
TRANSMISSION
- transmission of action potentials to CNS: initiated by transducing energy in stimulus into receptor potential
- some sensory receptors and specialized neurons whereas others are specialized cells that regulate neurons
1. neurons that act directly as sensory receptors: produce action potentials, have an axon that extends into CNS

2. non-neuronal sensory receptor cells: form chemical synapses with sensory neurons, respond to stimuli by increasing
rate at which afferent neurons produce action potentials
- response varies with stimuli of different intensities
o difference in magnitude of receptor potential  controls rate at which action potentials are produced
o receptor is sensory neuron: large receptor potential results in more frequent action potentials
o not sensory neuron: large receptor potential causes more neurotransmitter to be released  increases
production of action potentials by postsynaptic neuron
- sensory neurons spontaneously generation low rate action potentials  stimulus changes how often action
potential is produced (not on and off)
o frequency informs nervous system about strength of sensory stimulus
- stronger stimulus can trigger response by more receptors  more axons transmit action potentials
o decoded by nervous system as stronger stimulus
- processing can occur before, during, after transmission of action potentials to CNS
o integration of sensory info begins as soon as info is received
o integrated through summation as are postsynaptic potentials in sensory neurons that form synapses with
multiple receptors
PERCEPTION
- perception of stimuli: interpretation of sensory system input by the brain
o formed in brain and do not exist outside it (colours, smells, sounds, tastes)
- distinguishing different stimuli: depends on connections that link sensory receptors to the brain
o action potentials from sensory receptors travel along neurons that are dedicated to particular stimulus 
these dedicated neurons synapse with particular neurons in brain/ spinal cord
o brain distinguishes sensory stimuli (sight or sound) solely by path to brain along which action potentials
have travelled
AMPLIFICATION AND ADAPTATION
- 2 types of modification of transduction of stimuli by sensory receptors: amplification + adaptation
1. amplification: strengthening of sensory signal during transduction
a. e.g. action potential conducted from eye to human brain has about 100 000 times as much E as few photons
of light that triggered it
- amplification occurring in sensory receptor cells often require signal transduction pathways involving second
messengers
o include enzyme catalyzed reactions
o amplify signal strength through formation of many product molecules by single enzyme molecule
- amplification may occur in accessory structures of complex sense organ
o when pressure associated with sound waves is enhanced by factor of more than 20 before reaching
receptors in innermost part of ear
2. sensory adaptation: decrease in responsiveness
a. without it: you would be constantly aware of feeling every beat of heart etc.
b. also enables you to see, hear, smell changes in environment that widely vary in stimulus intensity

SINGLE CIRCULATION IN FISHES

- heart of 2 chambers: atrium + ventricle
- single circulation: blood passes through heart once in each complete circuit
1. blood in atrium  enters ventricles
2. contraction of ventricles  blood to arteries  gills
3. capillaries of gills: O2 diffuses into blood as CO2 leaves blood
4. blood in gills  rest of body  releases O2  returns to heart
- 2 disadvantages:
1. blood pressure drops as blood is delivered to rest of body  reduces efficiency of circulation
a. due to passing through gill capillaries
2. heart forced to rely upon deoxygenated blood for its own metabolic needs
o works well enough in fish that have relatively low metabolic demands
- double circulation: blood moving between heart and rest of body (systemic circuit) separated from blood that travels
between heart and respiratory surface (pulmonary circuit)
-
INCOMPLETE SEPARATION OF SYSTEMIC AND PULMONARY CIRCUITS IN AMPHIBIANS AND REPTILES
- frogs + other amphibians: heart with 3 chambers = 2 atria + 1 ventricle
- right atrium collects blood from body, left atrium collects blood from respiratory surfaces  both empty into ventricle
(but ridge separates blood from 2 atira)
- ventricle contracts  O2 blood from left atrium sent via systemic circuit to body
o no O2 blood from right atrium sent to respiratory surface of oxygenation
- pulmocutaneous circuit: circulatory system that supplies lungs and skin; respire through lungs and skin
o frogs adjust circuit  shunting blood to skin when underwater, or to lungs when breathing air
- reptiles: have a wall/ septum within single ventricle that separates pulmonary and system blood
o e.g. turtles, snakes, lizards: septum incomplete  permit some mixing of blood flows within ventricle
o e.g. crocodile: complete septum  efficiently separates 2 circuits
can control relative amount of blood flowing to lungs and body like amphibians

HOW AN AMPHIBIAN BREATHES

- positive pressure breathing: inflating lungs with forced airflow
- muscles lower floor of oral cavity  draws air into nostrils  floor rises  forces air down trachea  exhalation: air
forced back out by elastic recoil of lugs + by compression of muscular body wall
- courtship display: taking air several times without any release
HOW A BIRD BREATHES
- 2 features of ventilation  highly efficient
1. air over gas exchange surface in only one direction
2. incoming fresh air does not mix with air that already carried out gas exchange
- air sacs act as bellows that keep air flowing through lungs  gas exchange in parabronchi (same direction of air flow)
- 2 cycles of inhalation and exhalation
-

BLOOD COMPONENTS
- patient with myasthenia gravis: treatment with organophosphate insecticide?
o myasthenia gravis: antibodies that falsely recognizes receptors as foreign  blockage of receptor
o organophosphates: inhibit enzyme  inactivates acetylesterase  prolongs life of neurotransmitter 
alleviates symptoms
o yes  more probability of depolarization
-
- platelets: cell fragments of megakaryocytes
- fibrinogen: for blood clotting
BLOOD CLOTTING
1. platelets: full of actin for movement (no nucleus)
2. cut  platelets adhere together: changes shape with actin (no nucleus needed)
a. cut  do ’t take aspi i : a et lates e z e loo idase o espo si le fo p ostagla di s thesis
b. prostaglandin hormone: helps platelets adhere together
c. some calcium ions help platelets adhere together also
3. adhered platelets produce platelet factor: important for conversion of prothrombin (zymogen) into active thrombin
a. thrombin: endoprotease
4. other clotting factors (13) are also used
5. calcium ions also help conversion of prothrombin to thrombin
a. blood services use a chelator that mops up the calcium ions  prevents blood from clotting
6. thrombin hydrolyzes fibrinogen peptide bond  converts fibrinogen into fibrin
7. active fibrin produces fibrin threads (calcium ions involved as well)  Ca2+ function unclear
8. fibrin threads wind around platelets  becomes soft clot  red blood cells are caught up in soft clot
9. mature clot is created

- patie ts ith leedi g ul e s should ’t take aspi i

o blood clot is dissolved when no longer needed
- CASCADE REACTION
o cascade reaction: start with 1 thing  responsible for converting inactive clotting factor 2 to activate  etc.
o 13 clotting factors help prothrombin  thrombin
o defective clotting factor  decreased probability of blood clotting
- vitamin K is necessary for addition of carboxyl groups to clotting factors  more negative  can work with calcium
ions
PRACTICAL/ MEDICAL APPLICATIONS
GENETICS OF CLOTTING DISEASES – FACTOR XI
- located on X chromosome (hemophilia B)  e.g. Queen Victoria had a lot of children
KILLING RATS
- vitamin K must be converted to a reduced vitamin K (liver enzyme responsible for conversion)
- reduced vitamin K  important for making active clotting factors
- give rats warfarin  liver enzymes recognize warfarin as similar to vitamin K  liver enzyme binds to warfarin  will
not convert vitamin K into a reduced molecule  delays clotting
- rats start to have internal hemorridge  bleeds to death internally

- physicians can use warfarin for patients that have easily clotting blood
RED BLOOD CELLS erythrocytes

- carries oxygen to tissues
- bioconcave: increases surface area  allows easy diffusion
- no nucleus  can carry more proteins that carry oxygen
o red blood cells cannot divide (differentiates from stem cells)
- glycoproteins ABO in plasma membrane  blood type
o Rh glycoproteins included also

HEMOGLOBIN
- tetramer  2 beta globins and 2 alpha globins  has 4 heme groups with iron
- 300 million hemoglobins in each erythrocyte  10^9 oxygen molecules carried by each red blood cell
- fo ost pa t: he oglo i s ha e o ge o the do ’t
- one oxygen binds  change in conformation  easier for other 3 oxygen molecules to bind
- cooperativity to the binding
SPIROMETRY
- diagnosis/ monitoring of chronic obstructive pulmonary disease (COPD), asthma, cystic fibrosis etc.
-
MAMMAL RESPIRATORY SYSTEM
- circulatory system separates pulmonary and systemic circuits
- pulmonary circuit exposed o high partial pressure of Po2 at lungs
-
GASES AND GAS PRESSURE
AIR
- 21% oxygen, 78% nitrogen, 1% CO2 and other gases

- atmospheric pressure = pressure on body surfaces of animals measured in mmHg or kPa

- atmospheric pressure = sum of partial pressure (pressure exerted by each gas in air in proportion to their amounts)
o
o diffusion across cell membranes driven by partial pressure gradients
o Dalto ’s la : total p essu e = su of pa tial p essu es
IN CAPILLARY BEDS IN TISSUES
- tissues are using oxygen  low Po2 (cellular respiration)
- erythrocytes release O2 which diffuses into tissues
-
IN LUNGS
- Po2 in lungs, alveoli = 100 mmHg
- oxygen diffuses across membranes and picked up by hemoglobin
- CO2 is released because partial pressure is low (does not bind to the same site in hemoglobin)
CO2
-
- CO2 does not compete for oxygen sites  can be carried in plasma or red blood cells
- CO2 combines with water  carbonic acid (weak acid)  dissociates into bicarbonate ions and protons
o bicarbonate ions can act as buffers
o protons can be taken up by red blood cells  more acidic  oxygen comes off hemoglobin more easily
- temperature can also drive off oxygen from hemoglobin (high T)


- CO2 transported in 3 ways: fluid (not a lot), taken up by red blood cells (with hemoglobin but not on oxygen site),
combine with water and eventually to bicarbonate ions + protons  pH decrease somewhat so hemoglobin lets go
of oxygen
PARTIAL PRESSURE OF O2 AND CO2 AT POINTS IN CIRCULATORY SYSTEM
- at tissues: tissues use up oxygen  partial pressure of oxygen lowers to about 40 mmHg
- exhaled air: mixes with inhaled air and Po2 increases
- healthy human O2
Hb dissociation curve
o 100 = partial pressure of oxygen in alveoli
o curve: oxygen binds cooperatively  1 oxygen bound  easier to bind all 4
o tissues at rest: Po2 = 40  70 percent saturated
o strenuous exercise: Po2 = 30
o we carry more oxygen than we need  advantageous

- atmospheric pressure
decreases at higher elevations
o altitude sickness: shortness of breath, headache, heart racing
o climatization: adjust to altitude  increase # of red blood cells  erythropoiesis
- erythropoiesis  increase in hematocrit (red blood cells)
- people living at high altitudes: in addition to erythropoiesis  physically different
o large chest  increases chest size to carry more blood  more hemoglobin to deliver the oxygen to tissues
- native animals in high altitudes: lama (senor Rambo)
o
o curve for lama would be higher  hemoglobin is completely loaded with oxygen at lower partial pressure
o has a different type of protein  higher affinity for oxygen
- human fetus: no lungs filled with air
o steals oxygen from mother at the tissues  needs to complete loaded with oxygen at lower pressure
o human fetus curve = lama curve
o do not have beta subunit but rather gamma sub unit  can deliver oxygen from mom to fetus
- human hemoglobin 2 alpha, 2 beta
GLOBIN SYNTHESIS DURING HUMAN DEVELOPMENT
-
o epsilon  beta like species  gone in six weeks of conception

o
o gamma globin: gone soon after birth
-
o histones = + proteins  blank a region
o embryo stage: RNA polymerize ould ’t see those ge es
o development: polymerize can most easily find it
o epigenetics
BLOOD DISEASES
1. sickle cell anemia: caused by mutation  mutant hemoglobin aggregates at low Po2 which damages erythrocyte
membrane
a. forms folds  blood sickles  irreversibly damaged
b.
c. jams up capillary beds etc.
d.
e. gluten amino acid  affects shit 

f. hetrozygotes can live normally
g. distribution of mutant allele depends on whnere your ancestors came from  places where there is malaria
h. hetrozygote  advantage  more resistance to malaria  plasmodium does not grow anymore
i. plasmodium lives in red blood cells  uses up oxygen  some sickling of the cells

2. thalassemias: reduction in synthesis of alpha or beta goblins:

a. medeterranean populations  higher frequency of beta globin; beta globin in Asian regions
-
o symptoms that drive from fact that youre not delivering enough oxygen
ANEMIA
- too few red blood cells and reduce delivery of oxygen to tissues
-
CARBON MONOXIDE POISONING
- CO binds to sae site on hemoglobin (Hg) as O2 but with ~ 250x increase in affinity
- 1 molecule binds to Hb  remaining of O2 molecules are bound more tightly
- CO poisoning at ~ 100 ppm leads to hypoxia of tissues  how do you detect CO
- symptoms: not enough oxygen to the blood
- treatment: put them around more saturated oxygen levels/ oxygen chamber or give blood transfusion
- carbon monoxide poisoning partial pressure curve: shift to left  hemoglobin remains loaded up with oxygen  not
delivering to tissues
- red blood cells: interfere with open circulatory systems; white blood cells: 1/1000 of red blood cells
DEFENCE AND IMMUNITY

- adaptive defense: cellular response or humoral response  assisted my lymphocytes

- ancient defense system  found in most organisms
SPECIFIC ADAPTIVE DEFENSE MECHANISM
1. HUMORAL RESPONSE
- fluid, mediated in the fluid (not directly by proteins) but proteins in the lymph etc.  B cells
- B cells: found in the bone marrow; immature plasma cells  becomes plasma cells
-
<Week 16.3 Lecture Notes>
1. HUMORAL RESPONSE CONTINUED (HUMOR = FLUID)
- what takes place in fluid
- B cells (virgin/ naïve B cells)  mature into plasma cells/ mature B cells
CONVENTIONS
- all B cells have different specificity; numerous receptors covering B cells  only one type of receptors on each cell
- recognition: antigen-receptor reaction  starts cascade/ signal transduction
o division of B cells  cloning/ clonal selection  clonal specificity
▪ takes couple of weeks
- memory B cells:
o immunological memory

o plasma B cells: secrete antibodies
o
▪ tetramer held together by disulphide bridges
▪ 2 long polypeptides: heavy chain
▪ 2 short polypeptides: light chain
▪ variable region (purple)  antigen binding
o secreted antibody known as IgG (75%)
o IgM (Ig membrane  B cell receptor): B cell receptor
-
-
o immunoglobulin: distinct from globin family
AGGLUTINATION
-
o clumping of both foreign pathogens and the antibodies  easier for phagocytosis by white blood cells
▪ macrophages (type of phagocytes): big eaters

- dendritic cells: have branch points; McGill researcher discovered these  won a Nobel Prize
- *not coagulation
o natural killer cells (NK lymphocytes/ white blood cells):
▪ part of the ancient response (not specific)
▪ not dependent on the specificity
▪ natural killer cells recognize the FC region and knows that a cell is marked with antibody  non
specific
• FC region/ fragment crystallisable region: constant region, base of the Y
▪ makes protein perforin  lyses the cell through making a pore on the cell
o activation of complement: cascade reaction: protein  active protease
▪ 20 of these all in a row  depending on another  complement
▪ part of innate/ non specific response  can find in plants
-
o agglutination  lego do ut / membrane attack complex makes a pore on the cell  swelling and lysis

ANTIGEN – ANTIBODY COMPLEX
-
- antibodies connect adaptive immunity with innate response  link invading microbes and viruses to phagocytes,
complement proteins, natural killer (NK) cells
- hu o al espo se: does ’t i ol e the ells di e tl
IMMUNOGENETICS
- enormous diversity required?
-
LIGHT CHAIN ASSEMBLY
1. DNA is in pieces with number of variable regions + consecutive J regions + C region
- V region:
2. each region has a promoter on it, variable region codes for about 100 amino acids
3. palindrome at the end of region = transposable elements/ jumping genes  likely jumped in ancestral vertebral
genome  now able to develop immunoglobulins
- J region:
o palindrome sequence at the beginning
o about 20 amino acids
o at the end = splice site
- enhancer se ue e et ee J a d C egio : fi d the closest pro oter” to RNAs
- C region:
o has splice site
- region covered with blanket  cannot transcribe
1. B lymphocytes produce recombinase
a. *draw it like a pair of scissors  cuts AND REPAIRS

2. at random, puts V region next to J region  creates a protruding loop

a. palindromic repeat between them  recombinase cuts palindromic region  V region right next to J region
b. creates lost circular DNA (from protruding loop) + linear DNA where V is next to J  RNA polymerize
recognizes and transcribes
3. transcription: enhancer between J and C  sa s fi d the losest p o ote
4. primary transcript (preMRNA) produced (with poly A tail)
5. introns are spliced out between the J regions and the beginning of the C site
6. results in mature MRNA = V J C DNA
7. translation  into proteins
8. V + J = variable region in protein
9. C = constant region in protein
-
o recombinase found in lymphocytes puts the V and the J close together  creates sensible gene 
transcription  translation  VJ variable region + C constant region
GENE ASSEMBLY: novel joints and hypermutation together produce a huge number of different immunoglobulin light
chains
-
o novel joints: little bit of palindromic sequences left  extra amino acids  different variable region 
different specificity
o if V and J overlap  lost of extra amino acids  variable once again
o hypermutation: enzyme can convert cytosine to thymine etc.  point mutations  more mutations
▪ not important in humans, but important in chickens
▪ chickens depend on hypermutation to generate diversity
- ALLELIC EXCLUSION: only one chromosome is assembled  each B cell can only express one antigen  ONLY ONE
CHROMOSOME IS USED  ALLELIC EXCLUSION
o process not certain: one chromosome will start and if it comes up with decent looking assembly for RNA
polymerase  recombinase works on it

ALTERNATIVE C REGIONS
-
- alternative C regions give rise to other types of immunoglobulin classes
- 15000 different light chains 18000 different heavy chains = 10^7 different combinations + novel joints and
hypermutation = 10^9 different antibodies  evolution of vertebrates
Concept 42.1 Circulatory systems link exchange surfaces with cells throughout the body
- diffusion of O2 and CO2 is slow: time it takes for substance to diffuse is proportional to square of the distance
o solutions:
1. body size and shape that keep many cells in direct contact with environment  can thus exchange
materials directly with surrounding medium
a. only in certain invertebrates (e.g. cnidarians, flatworms)
2. i ulato s ste that o es fluid et ee ea h ell’s i ediate su ou di gs a d tissues he e
exchange with environment occurs
GASTROVASCULAR CAVITIES
- animals that lack distinct circulatory systems: e.g. hydras, jellies, other cnidarians
- gastrovascular cavity: functions in distribution of substances throughout body and in digestion
o opening at one end connects cavity to surrounding water
o fluid bathes both inner + outer tissue layers  exchange of gases + cellular waste
o only cells lining cavity have direct access to nutrients from digestion
▪ thin body wall  nutrients need to diffuse only a short distance into tissues
o e.g. h d a: thi a hes of gast o as ula a it e te d i to a i al’s te ta les

o e.g. jellies: gastrovascular cavity has much more elaborate branching patterns
▪
o e.g. planarians + most flatworms: combination of gastrovascular cavity and flat body  well suited for
exchange with environment
▪ flat body optimizes diffusional exchange  increases surface area and minimize diffusion distances
EVOLUTIONARY VARIATION IN CIRCULATORY SYSTEMS
- circulatory system minimizes distances that substances must diffuse to enter/ leave cell
GENERAL PROPERTIES OF CIRCULATORY SYSTEMS
- components: circulatory fluid + interconnecting vessels + heart (muscular pump)
o heart: uses metabolic energy to elevate hydrostatic pressure of fluid  flows through vessels back to heart
- circulatory system connects aqueous environment of body cells to organs that exchange gases, absorb nutrients,
dispose of wastes
o mammals: O2 from inhaled air diffuses across only 2 layers of cells in lungs and reaches blood
o oxygen rich blood  all parts of body, diffuses and enters fluid that bathes cells
- type: opened or closed, vary with regard to number of circuits in body, rely on pumps that differ in structure and
organization
OPEN CIRCULATORY SYSTEM
- open circulatory systems: circulatory fluid bathes the organs directly
o arthropods, most molluscs
-
- hemolymph = circulatory fluid/ interstitial fluid that bathes body cells
- contraction of heart  pumps hemolymph through circulatory vessels into interconnected sinuses (surrounding
organs)  chemical exchange between hemolymph and body cells
- relaxation of heart  draws hemolymph back in through pores (equipped with valves that close when heart contracts)
- body movements: help circulate hemolymph by periodically squeezing sinuses
- larger crustacean circulatory system (e.g. lobsters, crabs): more extensive system of vessels + accessory pump

- lower hydrostatic pressures  less costly than closed systems with energy
CLOSED CIRCULATORY SYSTEM
- closed circulatory system: blood is confined to vessels and is kept separate from interstitial fluid
o blood = circulatory fluid and distinct from interstitial fluid
- heart pumps blood into large vessels that brain into smaller ones  infiltrate organs  chemical exchange between
blood and interstitial fluid  exchange between interstitial fluid and body cells
- e.g. annelids (earthworms), cephalopods (squid, octopus) and all vertebrates have closed circulatory systems
- relatively high blood pressures  effective delivery of O2 and nutrients to cells or larger, active animals
o e.g. molluscs: closed system found in largest, most active species like squids and octopuses
- well suited to regulate distribution of blood to different organs
-
COMPARISON OF OPEN AND CLOSED CIRCULATORY SYSTEMS
- both systems widespread among animals  advantages to each system
1. open has lower hydrostatic pressures  less costly in energy than closed
2. open can serve other functions in invertebrates: e.g. spiders use hydrostatic pressure to extend legs
3. closed has high blood pressure  delivery of O2 and nutrients for larger, active animals
4. closed well suited to regulate distribution of blood to different organs
ORGANIZATION OF VERTEBRATE CIRCULATORY SYSTEMS
- cardiovascular system: closed circulatory system of humans and other vertebrates
o blood circulates to and from heart through vessels: total length of blood vessels in average human adult = x2
Ea th’s i u fe e e at e uato
- blood vessels:
1. arteries: carry blood away from heart toward capillaries to organs throughout body
2. arterioles: smaller arteries within organs (branched from arteries) and convey blood to capillaries
3. capillaries: microscopic vessels with very thin, porous walls
a. capillary beds: infiltrate very tissue  chemicals exchanged by diffusion between blood and
interstitial fluid around tissue cells
b. venules: small veins located in downstream end where capillaries converge  venules then converge
into veins
4. veins: vessels that carry blood from capillaries back to heart
5. portal veins: carry blood between pairs of capillary beds
a. hepatic portal vein: carries blood from capillary beds in digestive system to capillary beds in liver
b. blood in liver  hepatic veins  conduct blood toward heart
- muscular chambers:
1. atria: chambers that receive blood entering heart
2. ventricles: chambers responsible for pumping blood out of heart
FOUR-CHAMBERED HEARTS OF MAMMALS AND BIRDS

- left side of heart receives and pumps only O2 rich blood

- right side of heart receives and pumps only O2 poor blood
- separation  blood pressure independently regulated  reflects convergent evolution
Concept 42.2 Coordinated cycles of heart contraction drive double circulation in mammals
MAMMALIAN CIRCULATION
-
- pulmonary circuit:
1. contraction of right ventricle  blood to lungs via pulmonary arteries
2. blood flows through capillary beds in lungs  loads O2 and unloads CO2
3. O2 blood flows into left atrium via pulmonary veins
4. O2 blood flows into left ventricle  pumps O2 blood out of body tissues through systemic circuit
5. blood leaves via aorta  arteries  leads throughout boy
6. blood flows through aorta branching into coronary arteries  supply blood to heart muscle itself
7. branches flow into capillary beds in head and arms (forelimbs
8. aorta descends into abdomen  O2 blood to arteries  capillary beds in abdominal organs + legs (hind limbs)
9. capillaries: net diffusion of O2 from blood to tissues and CO2 into blood
10. capillaries rejoin into venules  convey blood to veins
11. oxygen poor blood from head, neck, forelimbs channeled into large vein superior vena cava
12. oxygen poor blood from trunk and hind limbs flow into inferior vena cava
13. vena cavae flow into right atrium  oxygen poor blood flows into right ventricle
THE MAMMALIAN HEART: A CLOSER LOOK

-
- two atria: relatively thing walls; serve as collection chambers for blood returning to heart from lungs and other body
tissues
o blood flows into ventricles while all heart chambers are relaxed
o some of the blood transferred by contraction of atria before ventricles begin to contract
- two ventricles: thicker walls and contract much more forcefully than atria
o left ventricle pumps to all body organs through systemic circuit; pumps same volume of blood as right ventricle
during each contraction
- contraction: pumps blood; relax: chambers fill with blood
- cardiac cycle: complete sequence of pumping and filling
o systole: contraction phase of cycle
o diastole: relaxation phase of cycle
- cardiac output: volume of blood each ventricle pumps/ minute
o determining factors:
1. heart rate (number of beats/ minute) (72 beats/ min)
2. stroke volume (amount of blood pumped by ventricle in single contraction) (70 mL average)
3. total volume of blood = stroke volume x heart rate (exercise increases as much as fivefold)

-
o 4 valves in heart prevent backflow and keep blood moving in correct direction (connective tissue)
o atrioventricular valve (AV): between atria and ventricles
▪ anchored by strong fibres preventing them from turning inside out
▪ pressure from powerful contraction of ventricles  closes AV valves  lood does ’t flo to at ia
o semilunar valve: where aorta leaves the left ventricle + where pulmonary artery leaves right ventricle
▪ pushed open by pressure from contraction of ventricles (relax  blood pressure in aorta closes
semilunar valves and prevent backflow)
o lub dup: fi st lu = e oil of lood agai st losed AV al es
▪ se o d dup = i atio s aused losi g of se ilu a al es
- heart murmur: abnormal sound caused by blood squirting backward through defective valve
MAINTAINING THE HEART’S RHYTHMIC BEAT
- some cardiac muscle cells are autorhythmic  contract/ relax without any signal from nervous system
- coordination of contractions in intact heart  autorhythmic cells located in wall of right atrium in superior vena cava
1. sinoatrial SA node/ pacemaker: sets rate and timing at which all cardiac muscle cells contract
a. produces electrical impulses like nerve cells  electrically coupled through gap junctions  impulses from SA
spread rapidly within heart tissue
2. impulses from SA spread through walls of atria  atria contract in unison
3. signal reaches other autorhythmic cells located in wall between left and right atria
4. atrioventricular AV node: impulses delayed before spreading to heart apex for atria to empty completely before
ventricles contract
5. signal conducted to heart apex and throughout ventricular walls by specialized structures of bundle branches and
Purkinje fibres

- sympathetic and parasympathetic divisions are responsible for regulation of SA node function
o sympathetic: speeds up pacemaker
o parasympathetic: division slows it down
- hormones secreted into blood influence pacemaker:
o epinephrine: flight or fight hormone secreted by adrenal glands  heart rate increase
- body temperature: increase in 1 centigrade raises heart rate by 10 beats/ min
FLUID RETURN BY THE LYMPHATIC SYSTEM
- loses 4 – 8 L of fluid from capillaries to tissue/ day

- lost fluid and proteins return to blood via lymphatic system
o network of tiny vessels intermingled among capillaries of cardiovascular system
o enters lymphatic system by diffusion  fluid lost by capillaries is called lymph
- lymph: similar to interstitial fluid; fluid lost my capillaries
o drains into large veins of circulatory system at base of neck  connection between lymphatic and circulatory
system  functions in the transfer of lipids from small intestine to blood
- movement of lymph: peripheral tissues  heart
o lymph vessels similar to veins  have valves that prevent backflow of fluid
o rhythmic contractions of vessel walls  draw fluid into small lymphatic vessels + skeletal muscle contraction
- disorders of lymphatic system:
o edema: swelling resulting from excessive accumulation of fluid in tissues
▪ severe blockage of lymph flow  swelling
o elephantiasis: parasitic worms lodge in lymph vessels  blocks uptake of fluids from extremities
- lymph nodes: organ that filters lymph by housing cells that attack viruses and bacteria along a lymph vessel
o honeycomb connective tissue with spaces filled with white blood cells  against infection, cells multiply 
lymph nodes become swollen and tender  lymph nodes can be examined for cancer patients to detect
spread of diseased cells (filtering, surveillance function)
Concept 42.4 Blood components function in exchange, transport, and defence
- fluid transported by open circulatory system continuous with fluid that surrounds all of body cells  same
- fluid in closed circulatory system highly specialized (e.g. blood of vertebrates)
BLOOD COMPOSITION AND FUNCTION
- plasma: vertebrate blood = tissue consisting of cells suspended in liquid plasma
o ions, proteins dissolved inside
o together with blood cells  function in osmotic regulation, transport, defence
o cellular elements = 45% of volume of blood, remainder = plasma

PLASMA
1. inorganic salts as dissolved ions = electrolytes (kept within narrow concentration ranges for homeostatic function)
a. some ions buffer blood  pH 7.4
b. salts: maintaining osmotic balance of blood
c. concentration of ions directly affects composition of interstitial fluid  vital role in muscle/ nerve activity
2. plasma proteins: buffers against pH changes, maintain osmotic balance between blood and interstitial fluid, contribute
to viscosity
a. immunoglobins/ antibodies: help combat viruses and other foreign agents invading body
b. other proteins: escorts for lipids (insoluble in water)  can travel in blood when bound to proteins
c. clotting factors: help plug leaks when blood vessels are injured (serum = blood plasma – clotting factors)
3. nutrients, metabolic wastes, respiratory gases, hormones
- much higher protein concentration than interstitial fluid (otherwise similar)
CELLULAR ELEMENTS
- two classes of cells in blood: red blood cells (transport O2), white blood cells (defence)
- platelets: fragments of cells involved in clotting process
1. erythrocytes/ red blood cells: most numerous blood cell (5 – 6 million red cells/ microliter)
a. main function: O2 transport  structure related to function
b. small disks that are bioconcave  increases surface area  enhances rate of diffusion of O2 across plasma
membrane
c. mature mammalian erythrocytes lack nuclei  more space for hemoglobin
d. hemoglobin: iron containing protein that transports O2
e. lack mitochondria and generate ATP by anaerobic metabolism (does not use the O2 they transport)
f. each contains 250 million molecules of hemoglobin  each hemoglobin binds to 4 molecules of O2  each
cell transport about a billion O2
g. O2 diffuses into erythrocytes  binds to hemoglobin  dissociates from hemoglobin in systemic capillaries
 diffuses into body cells
- sickle cell disease: abnormal hemoglobin polymerizes into aggregates  aggregates are large enough to distort
erythrocyte into elongated curved shape
o results from alteration in amino acid sequence of hemoglobin at single position
o significantly impairs function of circulatory system  lodge arteries/ capillaries  prevents deliver of O2 and
nutrients and removal of CO2 and wastes
o blood vessel blockage  organ swelling, pain
o sickled cells can rupture  reduces # of blood cells available  average life span of 20 days (1/6 of normal)
o rate of loss rate of regeneration in bone marrow
o short term therapy: replacement of erythrocytes by blood transfusion
o long term therapy: inhibiting aggregation of HbS
2. leukocytes: five major types of white blood cells/ leukocytes  fight infections
a. phagocytic: engulfs, digests microorganisms + debris from dead cells
b. lymphocytes: develop into specialized B cells + T cells that mount immune responses against foreign
substances
c. numbers increase temporarily whenever body is fighting infection
d. found outside circulatory system (unlike erythrocytes)  patrols both interstitial fluid and lymphatic system
3. platelets: cytoplasmic fragments of specialized bone marrow cells
a. no nuclei
b. structural and molecular functions in blood clotting
BLOOD CLOTTING
- break in blood vessel wall  exposes proteins that attract platelets and initiate coagulation
- coagulation: conversion of liquid components of blood to solid clot
- coagulant/ sealant circulates in inactive form of fibrinogen

- broken blood vessel  platelets release clotting factors  trigger reactions leading to formation of thrombin  fibrin
conversion  fibrin aggregates into threads  framework for clot
o thrombin: enzyme that converts fibrinogen to fibrin; also activates formation of more thrombin  positive
feedback
- hemophilia: disease characterized by excessive bleeding and bruising from even minor cuts and bumps  genetic
mutation that blocks step in clotting process
- anticlotting factors: prevent spontaneous clotting in absence of injury
o thrombus: blood clots form within blood vessel  blocks flow of blood
-
Concept 42.5 Gas exchange occurs across specialized respiratory surfaces
- gas exchange: uptake of molecular O2 from environment and discharge of CO2 to the environment
LUNGS
- lungs: localized respiratory organs with respiratory surface
o amphibian lungs are relatively small and lack extensive surface for exchange  relies on diffusion
o reptiles and all mammals depend entirely on lungs for gas exchange (except turtles)
MAMMALIAN RESPIRATORY SYSTEMS: A CLOSER LOOK
- system of branching ducts conveys air to lungs in thoracic cavity
- air enters through nostrils  filtered by hairs, warmed, humidified  pharynx, larynx  trachea/ windpipe past the
open glottis  vocal folds/ cords (larynx tensing produces sound)
- trachea branches into two bronchi leading to each lung  branch repeatedly into bronchioles
- epithelium lining the major branches: covered by cilia and thin film of mucus  traps dust, pollen  beating cilia
move mucus upward to pharynx where it can be swallowed into esophagus (mucus escalator)
- alveoli: site of gas exchange in mammals; air sacs clustered at tips of tiniest bronchioles
o oxygen entering alveoli dissolves in moist film lining their inner surfaces  diffuses across epithelium into
capillaries surrounding each alveolus
o net diffusion of CO2 occurs in opposite direction from capillaries across epithelium of alveolus and into air
o inflammation/ irreversible damage: when too much particulate matter reaches alveoli

▪ smoking: particulates from cigarette smoke  reduction in lung capacity

- surfactant: surfaces of alveoli covered by mixture of water, phospholipid, protein
o coats inner surface of lung  force that prevents alveoli from collapsing onto themselves
o premature babies: poorly developed lungs lacking enough surfactant  treatment of artificial surfactants
-
Concept 42.6 Breathing ventilates the lungs
- breathing: process that ventilates lungs  alternating inhalation and exhalation of air
HOW A MAMMAL BREATHES
- negative pressure breathing: pulling rather than pushing air into their lungs
- inhalation is always active and requires work: muscle contraction actively expands thoracic cavity  lowers air
pressure in lungs below that of air outside body  gas flows into nostrils and down breathing tubes of alveoli
- exhalation is usually passive: exhalation: muscles of thoracic cavity relax  volume reduced  air pressure in alveoli
forces air up breathing tubes and out of body
- diaphragm: sheet of skeletal muscle that forms bottom wall of cavity  contracting rib muscles expands rib cage by
pulling ribs upward and sternum outward
o contraction  expands thoracic cavity downwards

- double membrane surrounds lungs: inner layer adheres to outside of lungs, outer layer adheres to wall of thoracic
cavity; thin space of fluid separates layers  surface tension causes 2 layers to stick together  reduces friction
- exercise: muscles of neck, back, chest increase volume of thoracic cavity by raising rib cage
- tidal volume: volume of air inhaled/ exhaled with each breath (about 500 L in resting humans)
o vital capacity: tidal volume during max inhalation/ exhalation (3.4 L and 4.8L for men)
o residual volume: air remaining after forced exhalation
o aging: lungs lose resilience  residual volume increases at expense of vital capacity
- each inhalation mixes fresh air with oxygen depilated residual air  maximum Po2 in alveoli is less than
atmosphere
o maximum Po2 in lungs is less for mammals than birds (renew air in lungs with every exhalation)  mammals
function less well than birds in high altitude
CONTROL OF BREATHING IN HUMANS
- regulated by involuntary mechanisms  ensure that gas exchange is coordinated with blood circulation and with
metabolic demand
- controlled by medullar oblongata near base of brain  breathing control centre  establishes breathing rhythm
- breathing deeply: negative feedback prevents lungs from overexpanding
o inhalation  sensors detect stretching  send nerve impulses to control circuits in medulla  inhibits further
inhaling
- medulla uses pH of surrounding tissue fluid as indicator of blood CO2 concentraiton
o blood CO2 determines pH of cerebrospinal fluid (surrounding brain and spinal cord)
o CO2 in cerebrospinal fluid:

1. increased metabolic activity: lowers pH by increasing concentration of CO2 in blood  medulla detect pH
change  increases depth and rate of breathing  high until excess CO2 eliminated
2. O2 levels drop very low (e.g. high altitudes)  O2 sensors in aorta and carotid arteries in neck send signals to
breathing control centres  increases breathing rate
3. pons (next to medulla) regulates breathing  act in regulatory circuit with medulla or moderate output
- breathing control effective only if ventilation matched to blood flow through alveolar capillaries
o e.g. exercise: coordination couples an increased breathing rate  enhances O2 uptake and CO2 removal 
increased cardiac output
-

Concept 42.7 Adaptations for gas exchange include pigments that bind and transport gases
- blood molecules/ respiratory pigments facilitate exchange of gases through interaction with O2 and CO2
COORDINATION OF CIRCULATION AND GAS EXCHANGE
- partial pressures of O2 and CO2 vary in blood in different points
-
o loading and unloading of respiratory gases
- blood flowing from alveolar capillaries has a lower Po2 and higher Pco2 than air in alveoli
o CO2 diffuses down its partial pressure gradient from blood to air in alveoli
o O2 in air dissolves in fluid that coats alveolar epithelium and diffuses into blood
o in pulmonary veins: Po2 is raised and Pco2 is lowered  pumped through systemic circuit
- in tissue capillaries: gradients favour diffusion of O2 out of blood and CO2 into blood
o cellular respiration of cells near capillary removes O2 from and adds CO2 to interstitial fluid
o blood now returned to heart and pumped to lungs again
RESPIRATORY PIGMENTS
- low solubility of O2 in water  hard to transport in animals that rely of circulatory system to deliver O2
- respiratory pigments: proteins in which O2 is bound to and transported
o circulate with blood/ hemolymph are often contained within specialized cells
o greatly increase amount of O2 carried in circulatory system
o generally, has a distinctive colour  blue pigment hemocyanin (uses copper) found in arthropods, molluscs
o hemoglobin: many invertebrates and all vertebrates  contained in erythrocytes
HEMOGLOBIN
- 4 subunits each with a cofactor heme group that has an iron atom at its centre
- each iron minds to 1 molecule of O2  each hemoglobin can carry 4 molecules of O2
- binds O2 reversibly  depends on cooperativity between hemoglobin subunits
o O2 binds in 1 subunit  others change shape slightly  increases affinity for O2
o 4 O2 bound  one subunit unloads  other 3 subunits readily unload O2  associated shape change lowers
affinity for O2

-
o steep slope: slight change in Po2  causes emoglobin to load/ unload substantial amount of O2
▪ corresponds to range of Po2 found in body tissues
o cells working harder (exercise): Po2 dips in their vicinity as O2 is consumed in cellular respiration
▪ slight drop in Po2 causes relatively large increase in amount of O2 blood unloads
- production of CO2 in cellular respiration promotes unloading of O2 by hemoglobin in active tissues
o carbonic acid lowers pH of surrounding  decreases affinity of hemoglobin for O2
o Bohr shift: CO2 production is greater  hemoglobin releases more O2  support more cellular respiration
o
- high temperature reduces O2 affinity  favours unloading
o exercise: active muscles warm blood as it passes through muscle capillary beds  more O2 can be used
- red blood cells can change levels of cytoplasmic metabolites  mechanism to change O2 affinity of Hb
o increase level of 2, 3 – biphosphoglycerate (produced in glycolysis)  favours O2 unloading
- regulation of Hb in humans focused on response to changing internal conditions (e.g. exercise)
o animals surviving at low temperatures: possess Hb that is much better able to extract O2 from oxygen poor
environment
o te pe atu e is a othe fa to that affe ts a i al’s a ilit to o t ol O2 le els
CARBON DIOXIDE TRANSPORT
- hemoglobin helps transport CO2 and assists in buffering blood  preventing harmful changes in pH
o 7% of CO2 released by cells is transported in solution in blood plasma
o 23% binds to amino ends of hemoglobin polypeptide chain
o 70% transported in blood as bicarbonate ions (HCO3-)
- CO2 diffuses into blood plasma  diffuses into erythrocytes  reacts with water (with enzyme carbonic anhydrase)
 forms H2CO3  dissociates into H+ and HCO3-
o most of H+ binds to hemoglobin + other proteins  minimizes change in blood pH
o HCO3- diffuses into plasma
- blood through lungs: relative partial pressures of CO2 favour diffusion of CO2 out of blood  diffuses into alveoli 
amount of CO2 in blood decreases  shifts chemical equilibrium in favour of conversion of HCO3- into CO2
o enables further net diffusion of CO2 into alveoli
- Pco2 gradient is sufficient to reduce Pco2 by roughly 15% during passage of blood through lungs


Concept 43.1 In innate immunity, recognition and response rely on traits common to groups of pathogens
- immune system: enables an animal to avoid or limit many infections
- innate immunity: defence that is active immediately upon infection and is the same whether or not the pathogen has
been encountered previously
o outer covering (skin) etc.
o small present group of receptor proteins bind to molecules that are absent from bodies but common to a
group of viruses, bacteria, microbes
o binding activates internal defences
- molecular recognition: detection of nonself in which receptor molecules bind specifically to molecules from foreign
cells or viruses
- adaptive immunity/ acquired immune response: defence found only in vertebrates; produces vast arsenal of
receptors each of which recognizes a feature found only on particular part of particular molecule in a particular
pathogen
o activated after innate immune response and develops more slowly
-
- innate immunity found in all animals as well as plants
o invertebrates: repel and fight infection with only innate immunity
o vertebrates: innate immunity serves both as an immediate defence against infection and as foundation for
adaptive immune defences
INNATE IMMUNITY OF INVERTEBRATES
- insect exoskeleton: first line of defence against infections
o chitin: barrier against most pathogens
o chitin in intestine: blocks infection by many pathogens ingested with food
o lysozyme: enzyme that breaks down bacterial cell walls  further protects digestive system
- insect immune cells: hemocytes: travel throughout body in hemolymph (insect circulatory fluid)  can carry out
phagocytosis
o other hemocytes trigger production of chemicals that kill pathogens and entrap large parasites
o Plasmodium: parasite of mosquitoes that causes malaria
o hemocytes and other cells secrete antimicrobial peptides  inactivate or kill fungi/ bacteria by disrupting
their plasma membrane

- binding of immune cells: bind to molecules found only in outer layers of fungi/ bacteria
o fungal cell walls contain unique polysaccharides
o bacterial cell walls have polymers containing sugars  identity tags in pathogen recognition
- insect immune cells secrete specialized recognition proteins  binds to unique macromolecule of bacteria/ fungi
- innate immune responses are distinct for different classes of pathogens:
o e.g. Neurospora crassa fungus: infects fruit fly  pieces of fungal cell wall bind to recognition protein 
complex activates protein Toll (receptor on hemocytes)  signal transduction from Toll  synthesis of
antimicrobial peptides active against fungi
o e.g. Micrococus luteus bacteria: infection  different recognition protein activated  different set of
antimicrobial peptides effective against M. luteus
- synthesis of single type of antimicrobial peptide can provide effective immune defence in flies  can act against
different kinds of pathogens
-
INNATE IMMUNITY OF VERTEBRATES
- barrier defences, phagocytosis, antimicrobial peptides, natural killer cells, interferons, inflammatory response
BARRIER DEFENCES
- external epithelial surfaces of body block entry of many pathogens
- internalized external surfaces most vulnerable: e.g. lining of digestive, respiratory, urinary, reproductive tracts
o mucous membranes/ mucosa: certain cells secrete mucus  enhances defences by trapping microbes and
other particles
o e.g. trachea: ciliated epithelial cells sweep mucus and any entrapped microbes upward
o fluid secretions from saliva, tears, mucus  bathe tissues  washing action + inhibits colonizaiton
- body secretions: creates environment hostile to many pathogens
o lysozyme in tears, saliva, mucosal secretions  destroys cell walls of susceptible bacteria
o acidic environment of stomach  kills microbes
o secretions of oil, sweat gland  low ph enough to prevent growth of bacteria
CELLULAR INNATE DEFENCES
- phagocytic cells detect fungal/ bacterial components using several types of receptors (similar to Toll receptors)
- Toll-like receptor (TLR): binds to fragments of molecules characteristic of some pathogens
o TLR3 on inner surface of vesicles from endocytosis  sensor for double stranded RNA  nucleic
characteristics of some viruses
o TLR4 on immune cell plasma membranes  recognizes lipopolysaccharide  found on many bacteria
o TLR5: recognizes flagellin  main protein of bacterial flagella
- detection  phagocytic cell engulfs them  traps into vacuole  fuses with lysosome  destruction of invaders in
2 ways:
1. gases produced in lysosome poison engulf pathogens
2. lysozyme and other enzymes in lysosome degrade components of pathogens

-
- 2 types of phagocytic cells (in mammals):
1. neutrophils: circulate in blood; attracted by signals from infected tissues  engulf and destroy infecting
pathogens
2. macrophages: larger phagocytic cells; some migrate, some permanent in organs, tissues
a. some located in spleen where pathogens in blood become trapped
- other types of phagocytic cells: additional functions in innate defence
1. dendritic cells: populate tissues like skin tat contact environment  stimulate adaptive immunity against
pathogens they encounter and engulf
2. eosinophils: found beneath mucosal surfaces; low phagocytic activity; important in defending against
multicellular invaders (e.g. parasitic worms)
a. eosinophils discharge destructive enzymes
- natural killer cells: circulate through body; detect abnormal array of surface proteins (characteristic of some virus/
cancerous cells)
o release chemicals that lead to cell death  inhibits further spread of virus and cancer
- lymphatic system: network that distributes lymph throughout body
o macrophages in lymph node where they engulf pathogens that have flowed from interstitial fluid to lymph
o dendritic cells outside lymphatic system  migrate to lymph nodes after interaction with pathogens
o in lymph nodes: dendritic cells interact with other immune cells  stimulates adaptive immunity
ANTIMICROBIAL PEPTIDES AND PROTEINS
- pathogen recognition triggers production and release of variety of peptides and proteins that attack pathogens/
impede reproduction
- interferons (unique to vertebrate): proteins providing innate defence by interfering with viral infection =
o body cells upon infection secrete interferons  induce nearby uninfected cells to produce substances that
inhibit viral replication  limit cell to cell spread of virus  control viral infections like influenza
o some white blood cells secrete interferon that helps activate macrophages
o recombinant DNA technology to mass produce interferons to treat viral infection e.g. hepatitis C
- complement system: infection fighting system consisting of 30 proteins in blood plasma  circulate in inactive state
 activated by things on surface of microbe
o  biochemical reactions  leads to lysis (bursting) of cells
o also functions in inflammatory response

-
INFLAMMATORY RESPONSE
- inflammatory response: changes brought about by signalling molecules released upon injury/ infection
1. histamine: signalling molecule packed in densely packed vesicles/ mast cells found in connective tissue
2. histamine released at sites of damage
3. triggers nearby blood vessels to dilate  permits more blood to flow into region  more permeable
4. proteins and cells escape vessel and enter interstitial fluid surrounding cells
5. activated macrophages + neutrophils discharge cytokines
6. cytokines are signalling molecules that enhance immune response  promote blood flow to site of injury/ infection
7.  increased blood supply  redness, increased T
8. blood engorged capillaries leak fluid into neighbouring tissues  swelling

- during inflammation: cycles of signalling and response transform site

- activated complement proteins promote further release of histamine  attracts more phagocytic cells that enter
injured tissues and carry out additional phagocytosis
- enhanced blood flow to site helps deliver antimicrobial peptides
o accumulation of pus  fluid rich in white blood cells, dead pathogens, cell debris from damaged tissues
- severe tissue damage  response that is systemic
o cells in infected tissue often secrete molecules that stimulate release of additional neutrophils from bone
marrow
o more severe infection (e.g. meningitis, appendicitis): number of white blood cells increase several fold
- fever: things released by activated macrophages cause thermostat to reset to higher temperature  elevated
temperature may enhance phagocytosis and speed up tissue repair
- septic shock: overwhelming systemic inflammatory response  high fever, low blood pressure, poor blood flow
through capillaries
o most often in very old and very young
- chronic (ongoing) inflammation: C oh ’s disease + ulcerative colitis: unregulated inflammatory response disrupts
intestinal function
EVASION OF INNATE IMMUNITY BY PATHOGENS
- some pathogens can avoid destruction by phagocytic cells
- e.g. outer capsule surrounding bacteria interferes with molecule recognition and phagocytosis
o e.g. streptococcus pneumoniae: DNA can convey genetic information
- some bacteria resist breakdown within lysosomes after being engulfed
o e.g. bacterium that causes tuberculosis (TB)
▪ bacterium grows and reproduces effectively hidde f o od ’s i ate i u e defe es
Concept 43.2 In adaptive immunity, receptors provide pathogen-specific recognition
- vertebrates have unique adaptive immunity + innate immunity
- adaptive response relies on T cells and B cells  types of white blood cells called lymphocytes
- lymphocytes:
o originate from stem cells in bone marrow
o some migrate from bone marrow to thymus  lymphocytes into T cells
o B cells: remain and mature in bone marrow
o natural killer cells: remain in blood and become natural killer cells in innate immunity
- antigen: elicits response from B cell or T cell
- B cell or T cell binds to antigen (bacterial/ viral protein) via antigen receptor protein
o antigen receptor: specific enough to bind to just one part of one molecule from particular pathogen
o all antigen receptors made by single B or T cell are identical  immune system produces millions of different
antigen receptors
- infection by pathogen  triggers activation of B and T cells with antigen receptors specific for parts of that pathogen
o about 100 000 identical antigen receptors on surface of single B or T cell
- epitope: small accessible portion of antigen that binds to antigen receptor
o e.g. group of amino acids in particular protein
o single antigen has several different epitopes each binding a receptor with different specificity
- all receptors produced by single B cell or T cell are identical  they bind to same epitope
o each cell displays specificity for particular epitope  response to any pathogen producing molecules
containing same epitope
ANTIGEN RECOGNITION BY B CELLS AND ANTIBODIES
- B cell antigen receptor is a Y shaped molecule of 4 polypeptide chains
o 2 identical heavy chains
o 2 identical light chains with disulphide bridges linking chains together
o transmembrane region near one end of each heavy hai a ho s e epto i ell’s plas a e a e
o short tail region at end of heavy chain extends into cytoplasm

-
- constant C region: amino acid sequences vary little among receptors on different B cells
- variable V region: amino acid sequence varies extensively for each B cell
- asymmetrical binding site for an antigen: heavy chain V region + light chain V region = asymmetrical binding site
- 2 identical binding sites
1. binding of B cell antigen receptor to antigen  B cell activation
2. formation of cells that secrete soluble form of receptor
3. = antibody/ immunoglobulin (Ig)
4. antibodies: same Y shaped organization but secreted rather than membrane bound
5. antibodies rather than B cells actually help defend against pathogens  distinct functions
- antigen binding site for membrane bound receptor/ antibody: lock and key fit for particular epitope
o difference in amino acids  specificity
- B cell antigen receptors and antibodies bind to intact antigens in blood and lymph
-
ANTIGEN RECOGNITION BY T CELLS
- T cell: antigen receptor consists of 2 different polypeptide chains: alpha and beta chain linked by disulphide bridge
- ta s e a e egio that a ho s ole ule i ell’s plas a e a e ea the ase of T ell e epto

- variable V regions of alpha and beta chains together form single antigen binding site
o remainder of constant C regions
-
- T cell receptors bind only to fragments of antigens that are displayed or presented on surface of host cells
- MHC (major histocompatibility complex) molecule: host protein that displays antigen fragment on cell surface
1. pathogen or part of pathogen either infects or is taken in by host cell
2. enzymes in cell cleave antigen into smaller peptides  antigen fragment
3. antigen fragment binds to MHC molecule inside cell
4. movement of MHC molecule and bound antigen fragment to cell surface results in antigen presentation
5. antigen presentation: display of antigen fragment in exposed groove of MHC protein
6. encounters T cell with right specificity  antigen receptor on T cell can bind to both antigen fragment and MHC
molecule
7. T cell can participate in adaptive immune response
B CELL AND T CELL DEVELOPMENT
1. immense diversity of lymphocytes and receptors  immune system can detect pathogens never before encountered
2. adaptive immunity o all has self tole a e, la k of ea ti it agai st a i al’s o ole ules a d ells
3. cell proliferation triggered by activation  increases number of B and T cells specific for an antigen
4. stronger and more rapid response to antigen encountered previously  immunological memory
- receptor diversity and self tolerance arise as lymphocyte matures
o proliferation and memory occurs later after mature lymphocyte encounters and binds to specific antigen
GENERATION OF B CELL AND T CELL DIVERSITY
- immune system assembles many different receptors from much smaller collection of parts through combining
- immunoglobin (Ig) gene: encodes light chain of both secreted antibodies (immunoglobins) and membrane bound B
cell antigen receptors
o receptor light chain encoded by 3 gene segments: variable V segment, joining J segment, constant C segment
▪ V and J segment together encode variable region of receptor chain
▪ C segment encodes constant region
o light chain gene contains single C segment, 40 different V segments, 5 different J segments
▪ alternative copies of V and J segments arranged within gene in series
o 200 different ways of combining (40 V x 5 J x 1 C)
o number of different heavy chain combinations is greater  more diversity
o requires arranging DNA: early in B cell development: enzyme complex recombinase links one light chain V
gene segment to one J gene segment  eliminates long stretch of DNA between segments  forms single
exon that is part V and part J
o only one intron between J and C DNA segments  no further DNA rearrangement required
▪ J and C segments of RNA transcript joined when splicing removes intervening RNA

- recombinase: acts randomly  linking any one of 40V gene segments to any one of 5J gene segments
o heavy chains undergo similar rearrangement
- only one allele of light chain gene and one allele of heavy chain gene are arranged in each cell
o rearrangements are permanent and passed onto daughter cells when lymphocytes divide
- antigen receptors synthesized after rearrangement  transcribed and transcripts are processed for translation 
light chain and heavy chain assemble together  forms antigen receptor  each pair results in different antigen
binding site
-
Concept 43.3 Adaptive immunity defends against infection of body fluids and body cells

CELLULAR IMMUNE RESPONSE

- T cells mature in thymus
-
- many of cellular components in blood (e.g. T lymphocytes) originate in the bone marrow
-
- lymphoid stem cell  thymus  T lymphocytes
- monocytes  dendritic and macrophages
T CELLS/ LYMPHOCYTES
- receptor: dimer with alpha and beta polypeptide chain = variable region + constant region
o part of constant region anchored in membrane (transmembrane domain)
o anchored in membrane forever
o amino acid sequence in variable regions differ in different clones of T cells
o each variable region is encoded by various variable, diversity and joining gene pieces  assembled to
constant region

- T cell receptor: glued together like sheit
-
- cannot bind antigen unless they also bind to a major histocompatibility complex (MHC)/ hu a leuko te a tige s
(HLAs)
o identity tags found on cell body
o MHC I: found on most cells in body (except erythrocytes, platelets that lack nucleus)
▪ binding stabilized by CD8 (on killer T cells = cytotoxic T cells)
▪ CD8: cluster determinant 8 protein  stabilizes bond
-
o MHC II: found only on antigen presenting cells such as macrophages/ presentation cells, B cells, few other cell
▪ binding stabilized by CD4 (on helper T cells)
▪ CD4: clustered determinant cell  help T cells
CELL MEDIATED IMMUNITY
- macrophage: eats virus  display antigens from virus on the cell surface  immune system recognizes presence of
pathogen (Ashburner example about eggs and shit)
- virgin T cells/ naïve T cells: binds antigen stabilized by cluster determinant glycoprotein
- cascade of events  signal transduction events mediated by peptide hormones CYTOKINES
o produces population of memory T cells and helper T cells

-
HELPER T CELLS
1. binds to APC (macrophage): binding releases a chemical signal (peptide hormone cytokine = interleukin IL)
a. stimulates mitotic division of helper T cell (sometimes called T4 cell)
-
o reproducing and making more of themselves
2. binds B cells bearing B cell receptor and a bound antigen
a. when bound, interleukin released  stimulates B cells to divide and produce a clonal population of B cells
resulting in more plasma B cells and synthesis of specific antibodies
b.
3. helper T cell produces cytokines which stimulate killer T cells (cytotoxic T cells) to attack infected cells
a. killer T cells attack cells with specific antigen and MHC I with interaction stabilized by CD8
b. releases perforin (makes channels/ perforations in membranes of cells)  like natural killer cells
c.

4. helper T cell stimulates killer T cells by production of cytokines (ILs) to produce a clonal production of killer T cells and
memory killer T cells
a. production of more killer T cells
b. stimulates cell  population of T cells including some memory killer T cells (stays in circulation a longer time)
c. all produced cells have receptors that recognize the same antigen
d.
- new research:
NEXT STEP OF CELL MEDIATED IMMUNITY
- cytotoxic T cells circulate within body and look for specific pathogen
- kills cells by perforin through lysis (made by T cells and natural killer cells)

-
IMMUNOLOGICAL MEMORY
IMMUNE TOLERANCE
- body distinguishes between self and nonself components
- high diversity of lymphocyte also generates receptors binding to self
- mechanisms to prevent immune response to self:
1. clonal deletion during early development  cell recognizing T cells in thymus are destroyed by apoptosis =
cell death
2. clonal inactivation outside thymus: potential self reacting T cells become nonresponsive
a. cytokines will be released but would not divide
3. B cells undergo similar processes
AUTOIMMUNE DISEASE
-
o multiple sclerosis: no antibodies against myelin  T cell problem
▪ T cell receptors recognize myelin
- virus, bacteria can have genetics close to ours


Summary of the Immune System (KAPLAN)
8.1 Structure of the immune system
INNATE AND ADAPTIVE IMMUNITY

- innate immunity (nonspecific): defenses that are always active against infection but lack ability to target specific
invaders over others
o antimicrobial molecules
o various phagocytes: e.g. dendritic cells and macrophages  activate inflammatory response  secretes
proteins of cytokines that trigger influx of immune cells from blood
o phagocytes: e.g. monocytes (which can mature into macrophages) and neutrophils
- adaptive immunity (specific): defenses that target specific pathogen  slower but can maintain immunological
memory of infection for faster future attack
o B cells and T cells
▪ spawn memory cells that promptly eliminate invaders encountered before
o activated B cells: secrete antibody molecules that bind to antigens, specific components to a given invader 
destroy invader directly or mark it for attack by others
o T cells: recognize antigens displayed on cells
▪ some help activate B cells and other T cells
▪ others T cells directly attack infected cells
ANATOMY
- bone marrow: produces all leukocytes/ white blood cells that participate in immune system through hematopoiesis
o when B cells leave bone marrow  mature but naïve (not yet been exposed to antigen)
- spleen: blood storage and activation of B cells which turn into plasma cells to produce antibodies as part of adaptive
immunity
- humoral immunity: antibodies dissolve and act in blood (rather than within cells)  e.g. B cells and antibodies
- thymus: maturation site for T cells
- cell mediated immunity: coordinate immune system and directly kill virally infected cells  e.g. T cells
- lymph nodes: site for immune cells to communicate and mount attack, also site for B cell activation
- some immune tissue found close to digestive system: gut associated lymphoid tissue (GALT)  includes tonsils,
adenoids in head
o Pe er’s pat hes i s all i testi e, l phoid aggregates i appe di

LEUKOCYTES
- produced in bone marrow from hematopoietic stem cells
- divided into two groups of cells: granulocytes, agranulocytes  presence/ absence of granules in cytoplasm
o granules contain toxic enzymes and chemicals  released by exocytosis  effective against bacterial, fungal,
parasitic pathogens
o granulocytes: neutrophils, eosinophils, basophils
o agranulocytes: lymphocytes (antibody production, immune system modulation, targeted killing off infected
cells), monocytes (phagocytic in bloodstream)  become macrophages in tissues
8.2 The innate immunity system
NONCELLULAR NONSPECIFIC DEFENSES
- skin (integument) = first line of defense: physical barrier, defensins (antibacterial enzymes), sweat
- mucous membranes: lined with cilia in respiratory system, can produce lysozyme (tears, saliva)
THE GASTROINTESTINAL TRACT
- stomach secretes acid
- gut colonized by already existing bacteria  hard to invade
COMPLEMENT
- complement system: consists of # of proteins in blood  nonspecific defense against bacteria
- activation through: classical pathway (requires binding of antibody to pathogen) or alternative pathway (does not
require antibodies)
- complement proteins punch holes in cell walls  osmotically unstable (e.g. lysis)
- cannot be modified to target specific organism over others
INTERFERONS
- interferons: proteins that prevent viral replication  produced by infected cells
o cause nearby cells to decrease production of viral/ cellular proteins
o decrease permeability of cells  harder for virus
- upregulate MHC class I and MHC class II  increased antigen presentation + better detection of infected cells
- responsible for many flu like symptoms during viral infection
CELLS OF THE INNATE IMMUNE SYSTEM
MACROPHAGES (agranulocyte)
- resides (resident population) within tissues  derived from blood-borne monocytes
1. bacterial invader enters tissue  macrophage activation
2. macrophage phagocytizes invader through endocytosis
3. digests invader using enzymes
4. presents little pieces of invader (mostly peptides) to other cells using protein called major histocompatibility complex
(MHC)
5. MHC binds to pathogenic peptide (antigen) and carries cell surface  recognized by adaptive immunity cells
6. macrophages release cytokines: stimulate inflammation and recruit additional immune cells to area
- MHC molecules: class I and class II
o endogenous pathway: all nucleated cells in body display MHC class I molecules  only infected cells would
be expected to present nonself protein on surface  killed by cytotoxic T lymphocytes to prevent infection of
other cells
▪ binds antigens from inside cell
o exogenous pathway: MHC class II molecules displayed by professional antigen presenting cells e.g.
macrophages  pick up pathogens from environment, process the, present them on MHC II  activation of
both innate and adaptive immune ssytems

▪ antigens originated outside the cell

▪ professional antigen presenting cells: macrophages, dendritic cells in skin, some B cells, certain
activated epithelial cells
- macrophages and dendritic cells: have special receptors of pattern recognition receptors (PRR) e.g. toll-like receptors
(TLR)
o able to recognize category of invader  allows production of appropriate cytokines to recruit right type of
immune cells
o each immune cell has different weapons that can target particular group of pathogens
NATURAL KILLER CELLS
- natural killer cells (NK): nonspecific lymphocytes that are able to detect downregulation of MHC and induce apoptosis
in these virally infected cells
o cancer may downregulate MHC production  NK cells offer protection from cancer growth
GRANULOCYTES
- neutrophils, eosinophils, basophils, related mass cells
1. neutrophils: most populous leukocyte in blood, very short lived, phagocytic  target bacteria
a. follows bacteria using chemotaxis (sensing of certain products from bacteria)
b. can detect bacteria once they have been opsonized (marked with antibody from B cell)
c. dead neutrophil collections = pus during infection
2. eosinophils: bright red granules, involved in allergic reactions and invasive parasitic infections
a. activation: release large amounts of histamine (inflammatory mediator)  vasodilation + increased leakiness
of blood vessels
b. additional immune cells (macrophages, neutrophils) can move out of bloodstream into tissue  inflammation
which is useful against extracellular pathogens (bacteria, fungi, parasites
3. basophils: large purple granules, involved in allergic responses, least populous leukocyte in bloodstream
a. mast cells = closely related basophils (smaller granules, exist in tissues, mucosa, epithelium)
b. release large amounts of histamine in response to allergens  inflammatory response
8.3 The adaptive immune system
- humoral and cell mediated immunity
CELLS OF THE ADAPTIVE IMMUNE SYSTEM
- two types of lymphocytes: B cells, T cells  crated in bone marrow
o B cell matures in bone marrow and activated in spleen + lymph nodes
o T cells mature in thymus
HUMORAL IMMUNITY
- involves production of antibodies (as long as a week to become fully affective)  specific to antigens of invading
microbe
- antibodies produced by B cells
- B cells undergo hypermutation of its antigen binding region  trying to find best match for antigen  takes time
- clonal selection: only B cells that bind antigen with high affinity survive  mechanism for generating specificity
- naïve B cells (not exposed to antigen): wait in lymph nodes for antigen to come along  exposure  B cell will
proliferate and product 2 types of daughter cells
1. plasma cells: produce large amounts of antibodies
2. memory B cells: stay in lymph node awaiting reexposure to same antigen (may last lifetime)
a. recognition of antigen  immediately produce antibodies specific to pathogen  secondary
response (rapid, robust)  basis for vaccinations
o primary response: this initial activation step taking 7 – 10 days
ANTIBODY

- antibody/ immunoglobulins (Ig): can be present on surface of cell or secreted into body fluids
1. antibodies secreted into body fluids: three possibilities
a. opsonization: bind to antigen  may attract other leukocytes to phagocytize those antigens immediately
b. agglutination: antibodies may cause pathogens to clump together  large insoluble complexes that can be
phagocytized
c. can block ability of pathogen to invade tissues  neutralizes it
2. cell surface antibodies: binding of antigen to B cell  causes activation of cell  proliferation and formation of
plasma and memory cells
3. antibodies on surface of mast cell: degranulation (exocytosis of granule contents)
a. release of histamine and causing inflammatory allergic reaction
- Y shaped molecules made of 2 identical heavy chains + 2 identical light chains
o disulfide linkages + noncovalent interactions hold chains together
- antigen binding region at end of variable region/ domain at tips of Y
o specific polypeptide sequences that will bind only one specific antigenic sequence
- constant region/ domain: site where cells such as natural killer cells, macrophages, monocytes, eosinophils have
receptors for
- antibodies come in 5 different isotypes: different types can be used at different times during adaptive immune
response, for different pathogens, or in different locations of body  cells can change isotype production through
isotype switching
CYTOTOXIC IMMUNITY
- cell mediated immunity involving T cells that undergo positive/ negative selection
1. positive selection: maturing only cells that can respond to presentation of antigen on MHC cells (cells unable
to respond to presentation undergo apoptosis)
2. negative selection: causing apoptosis in cells that are self reactive (activated by proteins produced by
organism itself)
- thymosin (peptide hormone): facilitates maturation of T cells  mature but naïve
- exposure to antigen: T cells undergo clonal selection  only those with highest affinity for given antigen proliferate
TYPES OF T CELLS
1. helper T cells (Th): coordinate immune response by secreting lymphokines
a. lymphokines: capable of recruiting other immune cells (plasma cells, cytotoxic T cells, macrophages) 
increases their activity
b. HIV (human immunodeficiency virus): loss of helper T cells  prevents immune system from mounting
adequate response to infection  becomes acquired immunodeficiency syndrome (AIDS) where weak
pathogens can cause fatal infections
c. helper T cells repond to antigens presented on MHC II  presents exogenous antigens  most effective
against bacterial, fungal, parasitic infections (extracellular infections)
2. cytotoxic T cells (Tc): capable of directly killing virally infected cells by injecting toxic chemicals that promote apoptosis
into infected cell
a. respond to antigens presented on MHC I molecules  presents endogenous antigens  most effective
against viral + intracellular bacterial/ fungal infections (intracellular infections)
3. suppressor, regulatory T cells (Treg): express protein Foxp3
a. help tone down immune response once infection has been contained
b. turn off self reactive lymphocytes to prevent autoimmune disease  self tolerance
4. memory T cells: lie in wait until next exposure to same antigen
a. activation  robust, rapid response
RECOGNITION OF SELF AND NONSELF
- self antigens: proteins and carbohydrates present on surface of every cell of body
o normally signal to immune cells that cell is not threatening and should not be attacked
- hypersensitivity reactions:
1. autoimmunity: immune system attack cells expressing particular self antigens

2. allergic reaction: immune system misidentifies foreign antigen as dangerous when it is not
- T cells are educated in thymus: elimination of T cells that respond to self antigens  negative selection
- immature B cells that respond to self antigens are eliminated before they leave bone marrow
- most autoimmune disease can be treated with the administration of glycocorticoids (modified verions of cortisol) 
potent immunosuppressive qualities
Week 17 Textbook Notes
IMMUNODEFICIENCY DISEASES
- immunodeficiency: disorder in which immune system response to antigens is defective/ absent
o inborn immunodeficiency: genetic/ developmental defect in immune system
o acquired immunodeficiency: develops later in life following exposure to chemical/ biological agents
o increased susceptibility to certain cancers
- inborn immunodeficiency: defects in development of various immune system cells/ defects in production of specific
proteins
o e.g. antibody production defect or proteins of complement system
o depending on defect, innate or adaptive defences, or both may be impaired
- severe combined immunodeficiency (SCID): functional lymphocytes are rate or absent
o susceptible to infections like pneumonia, meningitis  death in infancy
o treatments: bone marrow/ stem cell transplantation
- drugs used to fight autoimmune diseases or prevent transplant rejection  suppress immune system 
immunodeficient state
- certain cancers suppress immune system
o e.g. Hodgki ’s disease: da ages l phati s ste
- acquired immunodeficiency syndrome (AIDS): caused by human immunodeficiency virus (HIV)
CANCER AND IMMUNITY
- adaptive immunity inactivated  frequency of cancers increases
o if immune system recognizes only nonself  fails to recognize uncontrolled growth of self cells
- viruses involved in about 15 – 20% of all human cancers
- immune system can recognize viral proteins as foreign  can act as defence against viruses that can cause cancer and
against cancer cells that harbour viruses
- hepatitis B virus: can trigger liver cancer
Concept 19.3 Viruses, viroids, and prions are formidable pathogens in animals and plants
VIRAL DISEASES IN ANIMALS
- viruses may damage / kill cells by causing the release of hydrolytic enzymes from lysosomes
o some cause infected cells to produce toxins that lead to disease symptoms
o some have molecular components that are toxic (e.g. envelope proteins)
- damage depends partly on ability of infected tissue to regenerate by cell division
o colds: epithelium of respiratory tract can efficiently repair itself from virus infection
o poliovirus: damage to nerve cells is permanent because these cells do not divide and usually cannot be
replaced
- vaccine: harmless variant or derivative of pathogen  stimulates immune system to mount defences against harmful
pathogen
o smallpox: eradicated by vaccination by WHO  narrow host range (only humans)
- antibiotics kill bacteria by inhibiting enzymes specific to bacteria but no effect on eukaryotic/ virally encoded
enzymes
o few enzymes that are encoded by viruses have provided targets for other drugs
- antiviral drugs resemble nucleosides and as a result interfere with viral nucleic acid synthesis
o e.g. azidothymidine (AZT) curbs HIV replication by interfering with synthesis of DNA by reverse transcriptase

▪ ultidrug treat e ts o ktails are ost effe tive: o i atio of 2 u leoside i i s a d a

protease inhibitor  interferes with enzyme required for assembly of viruses
▪


- trypanosomes spread by tsetse flies: causes sleeping sickness
o high mutation rate  antibodies become negligible
- gonorrhea: bacterium that causes venereal disease
o different pilus genes  high mutation rate
- foot and mouth disease: RNA virus infecting cattle, pigs. other cloven hoofed animals
o # of MHC I molecules getting to surface of cells (e.g. epithelial cells) is reduced to 50% via disruption of
secretory pathway by viral proteins
o killer T cells are not able to do their jobs without MHC I (e.g. 2001 UK eradication of cattle)
- plasmodium: parasite which causes malaria  multiplies within red blood cells
o in sickle cell anemia
-
o phenotype of baby: Rh+
o mixing of Rh- from mom and Rh+ of baby
o mom produces antibodies against Rh+ (recognizes it as foreign)  anti Rh antibodies
▪ maybe due to abortion, miscarriage etc.
o o ’s se o d hild: passi e i u ity  antibodies for Rh+ are taken by developing embryo  attacks red
blood cells of embryo
▪ Rh antibodies from mum can cross placenta  reduces # of erythrocytes  anemia
▪ symptoms: anemia, may die
▪ anti Rh+ antibodies would prevent production of Rh antibodies
o heterozygous advantage for Rh+ and Rh-: could live longer live, not susceptible to various diseases
IMMUNITY IN OTHER SYSTEMS: PLANTS
- both general and specific response
- deterrents (not induced response):
o e.g. ouabin  bounds Na+K+ atpase  prevents beetles from eating seeds)
o e.g. capcaisin: hot pepper receptors  protect plants from predators
- defenses against virus, bacteria, fungi, nematodes, protists, herbivores
EXPERIMENTS BY A.F. ROSS INFECTING TOBACCO PLANTS WITH TOBACCO MOSAIC VIRUS

1. inject plant with tobacco mosaic virus

2. a week later: injected leaf is dead
3. inject second leaf with virus and wait another week
4. leaf was okay  no virus damage  immune response to virus  protects second leaf
5. faster response than humans in this case
- intracellular immunity: R receptors for pathogens are specific for virus, bacterium etc.
o encoded by genes on the plant (already has R receptor for known pathogen)
o binds to pathogen  receptor changes conformation  signal transduction event
o release of peptide hormones etc.  salicylic acid etc.
o salicylic acid goes through circulatory system to destroy pathogen
o or metal group added to salicylic acid  sends signal via the air to plant nearby
o faster and efficient
INSECT IMMUNITY
-
- amino acids: insects can store the unlike humans
- he o ytes: i se ts do ’t ha e erythro ytes  no cell to transport oxygen (no hemoglobin in cell)  oxygen dissolved
in plasma
1. inject insect with e. coli  number of phagocytes in hemolymph increases
2. insect given LETHAL bacterium e.g. baccilas  phagocytes already present
- clotting: not highly regulated
1. cut  phagocytes congregate around  spills out contents of their cytoplasm
2. adheres to one another (using Ca2+ etc.)
3. cell fragments etc. build soft clot
4. phenyl oxidase is produced  phenyl oxidase produces melanin
5. melanin  seals off area
6. presence of pathogen  positive feedback  more melanin
- encapsulation:
1. parasite injects eggs in cell
2. phagocytes congregate around wasp egg
3. cells may burst/ spill out their content
4. cells produce phenyl oxidase  lays down melanin and seals off egg (no O2)
5. when eggs die, hemocytes can leave, hemocytes are right against egg
-
- insect immunity: innate and very effective

-
o fat body = liver in insects
1. foreign pathogen detected by cells
2. signal transduction events
3. activation of mediators e.g. kinases
4. produces anti microbial peptides
o has certain specificity but not as tight as humans
ENDOCRINE SYSTEMS: HORMONES AND CHEMICAL CONTROLS
RHODNIUS/ THE KISSING BUG
- vector for trypanosomes (like tste flies)  leads to Chagas disease
-
- 850 genes encoding coat proteins  hard to counteract, no vaccines  stroke, coma, heart attack etc.
- rhod ius kiss hu a lips  can produce feces during
o trypanosomes that can circulate around blood system etc.
- Sir Vincent Wigglesworth: study of rhodnius, vector of Chagas disease
o worked at Cambridge on insect physiology

EXPERIMENT WITH RHODNIUS AND SIR VINCENT WIGGLESWORTH

1. nymph stage of rhodnius (5th instar)
2. blood meal  28 days  becomes/ molt into adult
- regulation of molting: after 1 day of blood meal
1. Wigglesworth chopped off head of nymph
2. did ’t de elop  shit needs a head. no shit
1. blood meal: after 8 days chopped off head
a. 20 days later  perfectly normal adult without head (molted)
- blood meal + head (1 – 8 days) needed to molt
1. blood meal: after a day chopped off head
a. takes body of nymph without head (since 8th day)
b. glued body of nymph (since 1st day) with body of nymph (since 8th day)
c. two perfectly normal adults without heads (molted)
- Wigglesworth discovered that hormones from head after blood meal  would start process of molting  diffusible
substances (even from body of one nymph to another)  direct development
RHODNIUS CONTINUED
- hormones: reason for molting
-
1. blood feeding: digestive system swells with blood  stretch receptors send signals to brain
2. brain releases peptide hormone  goes through hemolymph
3. hormone picked up by receptors on prothoracic glands (behind brain)
4. prothoracic glands produce ecdysone hormone  molt
o about five days
1. brain peptide hormones bind to receptors of corpra allatum
2. endocrine glands corpra allatum: produces juvenile hormone (JH)
3. juvenile hor o e does ’t stop olt/ olti g hor o e  determines nature of the molt
a. high JH content  bigger nymph
b. low JH content  adult stage
o JH is a terpine  keeps insects juvenile (defense mechanisms for trees that control insects through keeping
them in juvenile stage, preventing them from laying eggs)
o mimics of JH can be used to preventing pests becoming reproductive adults  will die of old age and no eggs
REGULATION FO MOLTING DURING MOTH DEVELOPMENT

-
1. signal to brain  receptors in prothoracic gland  ecdysteroid
2. JH determines nature of molting
CLASSES OF HORMONES
WATER SOLUBLE
1. amines: derived from tyrosine/ tryptophan
a. dopamine, melatonin, can also be neurotransmitters
b. dopamine: controls mood as neurotransmitter or helps T cells to proliferate as a hormone
c.
2. peptide hormones: e.g. prolactin, but can also include larger proteins
a. can be neurotransmitters
b.
LIPID SOLUBLE
3. steroids: cholesterol derivatives, less soluble in water
a. ecdysone
b.

OTHERS
- e.g. juvenile hormones
- somewhat water soluble, lipid soluble
- sometimes receptors on membrane or inside cell or in nucleus
-
o part of blood clotting and aspirin
CASCADE REACTIONS WITH HORMONES
-
o one peptide hormone can activate 100s of adenylyl molecules
o which can activate 1000 molecules of camp
o which can activate 10000 protein kinase A etc.  amplification of signal
STEROID HORMONE ACTION

o sometimes hormones can turn off gene transcription  positive or negative

HORMONE RECEPTOR
1. only cells with appropriate receptors can respond to a particular hormone
2. receptors bind noncovalently and reversibly with hormone
3.
HORMONE CONTROL AND DIFFERENTIATION: MIKE ASHBURNER AND HIS CHROMOSOME PUFFS
-
- transcription is visualized
- ecdysone released  created puffs  puffs created to ecdysone  regulation
SALIVARY GLAND DISSECTION FROM FRUIT FLY LARVA
- salivary glands near head
THE CONTROL OF EARLY AND LATE PUFFS – REGULATION BY ECDYSONE
- ecdysone receptor is heterodimer

1. DNA binding domain is shown with ecdysone
2. complex represses glue genes (8)  no longer active
3. early genes/ response (6) are induced  early genes start to puff

4. late genes (100s) induced  early proteins induced late gene production
APPLICATION OF HORMONES
1. hormones and cheating in athletic performance:
a.
i. anabolic steroid: stimulates muscle cell nuclei to produce more mRNAs for muscle cell proteins
ii. muscle mass increases 10 – 20%
iii. proteins may change their activities  can change drainage of bile in liver  inhibits drainage 
problems with liver, toxicity
b. blood doping:
i. glycoprotein hormone  water soluble  receptors outside
ii. when there is not enough oxygen  receptors on bone

marrow allows stem cells to make more erythrocytes
iii. may make blood so thick that it wont be adequately delivered  heart attack etc.
c. 3 stimulants such as ephedrine (amines)
i. increases heart rate and blood pressure
ii. water soluble, receptors on membrane
iii. can breathe more oxygen in

2. hormones and behaviour – fish physiology

a.
b. specialized cells in the gills get rid of the excess salt:
i. peptide hormone natriuretic (Na sodium) peptides: come from brain and heart as endocrine
tissues
ii. fresh water  salt water stress: releases natriuretic hormones
iii. gills have receptors  hormone binding  upregulates sodium potassium ATPase  sodium ions
are pumped out of fish
iv. cystic fibrosis transmembrane transductance regulator (CFTR) pumps out excess Cl-
c. facilitated by steroids + peptide hormones
3. hormones and circulatory system: humans
a. in humans, natriuretic hormones are involved in osmoregulation as well as cardiovascular function
b.
c. decrease reabsorption of the sodium  increase volume of urine
d. blood volume is restored into normal amount
4. hormones and mineral balance: regulation of Ca2+ in humans

a.
b. UV light converts derivative of cholesterol into vitamin D (milk facilitates vitamin D production)
c. transported to liver  hydroxyl group added
d. transported to kidney  second hydroxyl group added
e. steroid hormone calcitrol is made  intracellular receptor in intestines
f. changes gene expression in intestines  takes up calcium from diet  various functions of calcium
- calcium deficiency:
o
o parathyroid gland produces peptide hormone parathyroid hormone
o travels in circulatory system and reaches the bone
o receptor on bones release calcium from bones
o parathyroid hormone can also go to kidney  akes sure e do ’t lose al iu olle ti g tu es i to uri e
o parathyroid hormone can also go to liver  stimulates liver and kidney to add hydroxyl groups to the vitamin
D
o highly regulated
o

Bio week 18 textbook notes endocrine system

- hormone: molecules secreted into extracellular fluid  circulate in hemolymph of blood  communicate regulatory
messages throughout body
o caterpillar: ecdysteroid hormone: stimulates growth of adult cells  programmed death of larval cells,
behaviours that bring about motionless pupal stage
- each hormone has specific receptors: only some cells have receptors for that hormone  elicits response only from
specific target cells (those that have matching receptor)
- endocrine system: function of chemical signalling by hormones  1 of 2 basic systems of communication and
regulation throughout body
o hormones secreted by endocrine cells regulate reproduction, development, energy metabolism, growth,
behaviour
o signalling by neurons can regulate release of hormones
o blood pressure affected by: epinephrine, norepinephrine, aldosterone
Concept 45.1 Hormones and other signalling molecules bind to target receptors, triggering specific response pathways
INTERCELLULAR COMMUNICATION
- two criteria: type of secreting cell, route taken by signal in reaching target
ENDOCRINE SIGNALLING
- maintains homeostasis, mediates responses to environmental stimuli, regulates growth and development
- hormones secreted into extracellular fluids by endocrine cells  reach distant target cells via bloodstream
- e.g. hormones coordinate responses to stress, dehydration, low blood glucose levels
- e.g. trigger behavioural, physical changes underlying sexual maturity + reproduction
-
PARACRINE AND AUTOCRINE SIGNALLING
- local regulators: molecules acting over short distances  reach target cells solely by diffusion
o e.g. cytokines: local regulators enabling communication between immune cells
- signalling by local regulators can be either paracrine/ autocrine
1. paracrine signalling: secreted cell affects nearby cells
-
2. autocrine signalling: secreting cell affects itself

SYNAPTIC AND NEUROENDOCRINE SIGNALLING

1. synaptic signalling: neurons secrete molecules/ neurotransmitters  diffuse a very short distance to bind to receptors
on target cells
-
a. synapse = space between neuron and its target cell
b. paracrine signalling if target cell is muscle
c. autocrine signalling if target were another neuron
2. neuroendocrine signalling: specialized neurons/ neurosecretory cells secrete molecules that diffuse from nerve cell
endings into bloodstream
a. neurohormones: molecules that travel through bloodstream to target cells
i. e.g. antidiuretic hormone/ vasopressin: hormone essential to kidney function and water balance
SIGNALLING BY PHEROMONES
- pheromones: chemicals that are released into external environment
- wide range of functions: defining territories, warning of predators, attracting potential mates
- e.g. luna moth: pheromones for mating
- e.g. pheromone traps: can assess density of insects such as emerald ash borer and spruce budworm
- synthetic pheromones mimic signals of females  lures insects into traps searching for a mate
ENDOCRINE TISSUES AND ORGANS
- endocrine glands: grouped endocrine cells
o e.g. thyroid, parathyroid glands of neck

- endocrine glands: secrete hormones directly into surrounding fluid

- exocrine glands: ducts that carry secreted substances out of body  into digestive tract or onto body surface
CHEMICAL CLASSES OF HORMONES
- 3 major chemical classes: polypeptides, steroids, amines
o polypeptide hormones:
▪ hydrophilic
▪ insulin: polypeptide hormone  2 polypeptide chains  formed by cleavage of one long polypeptide
chain
o steroid hormones (e.g. cortisol, ecdysteroid): lipids that contain 4 fused carbon rings
▪ all derived from steroid cholesterol
▪ hydrophic
o amine hormones: e.g. epinephrine, thyroxine  each synthesized from single amino acid of tyrosine
-
- hormones vary in solubility in aqueous and lipid rich environments
- hydrophilic/ polar hormones (e.g. polypeptides): readily dissolve in body fluids but cannot pass through lipid rich
plasma membranes of cells
- hydrophobic/ nonpolar hormones (e.g. steroids): cannot dissolve in body fluids  able to freely pass through cell
membranes
- amine hormones can be hydrophilic (e.g. epinephrine) or hydrophobic (thyroxine)
CELLULAR RESPONSE PATHWAYS
- difference between hydrophobic (lipid soluble) and hydrophilic hormones
o hydrophilic hormones cannot cross cellular membranes of secretory cell  secreted via exocytosis (can be
stored)
o hydrophobic hormones cannot be contained within membrane vesicles  synthesized on demand
- difference in solutibility:
o hydrophilic hormones dissolve freely in blood
▪ receptors on target cells are displayed outside
o hydrophobic hormones travel through blood attached to soluble carrier protein
▪ receptors for hydrophobic hormones reside inside cell
▪ receptors can function directly as transcription factors
- hydrophilic hormones can regulate gene expression through indirect effects that follow binding of hormone to
membrane receptor
PATHWAY FOR WATER-SOLUBLE HORMONES
1. binding of hydrophilic hormone to signal receptor proteins  cellular response
a. activation of enzyme/ change in uptake or secretion of molecules/ rearrangement of cytoskeleton
b. could cause proteins in cytoplasm to move into nucleus and alter transcription of specific genes
- signal transduction: series of changes in cellular proteins that converts extracellular chemical signal to specific
intracellular response

o typically involves multiple steps
-
- e.g. short term stress – epinephrine:
1. adrenal glands secrete epinephrine/ adrenaline
2. epinephrine reaches liver  binds to G protein coupled receptor in plasma membrane of target cells
3. binding of hormone  cascade of events involving synthesis of cyclic AMP as short lived second messenger
4. activation of protein kinase A by cyclic AMP  activation of enzyme required for glycogen breakdown +
inactivation of enzyme necessary for glycogen synthesis
5. liver releases glucose into bloodstream  fuel needed to respond to stress
o cell surface hormone receptors trigger sig. trans.

PATHWAY FOR LIPID-SOLUBLE HORMONES
- intracellular receptors for lipid soluble hormones perform entire task of transducting a signal within target cell
- hormone activates receptor  dire tly triggers ell’s respo se  usually change in gene expression
- steroid hormone receptors: in cytosol prior to binding to hormone
1. steroid hormone binds to receptor  hormone receptor complex forms  moves into nucleus

2. receptor portion of complex alters transcription of particular genes by interacting with specific DNA binding
protein or response element in DNA
- e.g. female reproductive function in vertebrates – estrogen:
o in female birds, frogs: estradiol (form of estrogen) has specific receptor in liver
a. binding  activates transcription of gene for protein vitellogenin
b. vitellogenin secreted after translation of messenger RNA
c. vitellogenin transported in blood to reproductive system  used to produce egg yolk
o
- thyroid hormone/ thyroid hormone receptor:
1. thyroid hormone receptor attaches to its target genes in absence of hormone  represses transcription
2. thyroxin enters cell  travels into nucleus to bind its receptor
3. receptor changes its shape  activates expression of gene
45.4 Endocrine glands respond to diverse stimuli in regulating homeostasis, development, and behaviour
PARATHYROID HORMONE AND VITAMIN D: CONTROL OF BLOOD CALCIUM
- fall in blood Ca2+ level  skeletal muscles begin to contract convulsively  tetany
- rise in blood Ca2+ level  precipitates of calcium phosphate can form in body tissues  widespread organ damage
- mammalian parathyroid glands: 4 structures/ glands embedded in thyroid play role in Ca2+ regulation
1. fall in Ca2+ level  glands release parathyroid hormone (PTH)
2. PTH raises level of blood Ca2+ by direct and indirect effects
3. in bone, PTH causes mineralized matrix to decompose and release Ca2+ into blood
4. in kidney, PTH directly stimulates reabsorption of Ca2+ through renal tubules
5. in kidney, PTH indirectly promotes conversion of vitamin D to active hormone
a. inactive vitamin D (steroid derived molecule) obtained from food/ synthesized in skin when exposed
to sunlight
b. vitamin D activation begins in liver, completed in kidneys  process stimulated by PTH
c. active vitamin D  acts directly on intestines  stimulates uptake of Ca2+ from food  augments
effect of PTH
d. rise in Ca2+ blood level  negative feedback loop inhibits further release of PTH from parathyroid
glands
- thyroid gland: calcium homeostasis
1. rise in Ca2+ levels  thyroid gland releases calcitonin
2. calcitonin inhibits bone resorption and enhances Ca2+ release by kidneys
3. calcitonin required in fishes, rodents for homeostasis; for humans: needed only during childhood for extensive
bone growth

- Ca2+ regulation

EVOLUTION AND DIVERSITY
ZIKA VIRUS
ZIKA FOREST: UGANDA

- Zika virus first identified in Uganda in Zika forest
o meeting of diverse ecotypes, ecosystems in Africa
o virus research centre by Rockefeller in Zika forest
- built high platforms/ towers: took animals in cages in different heights  viral vectors travelling at different heights
may infect differentially according to height
- 1947: Zika virus found (macac serum)  cultured virus in mouse brains
ZIKA PANDEMIC
- birthplace: somewhere in Uganda  spread rapidly, globally
- mosquito = vector
- microcephaly in children  abnormally small brains (lifelong condition)
-
1. Zika virus is spreading rapidly out from narrow equatorial band
2. ZIKV: arbovirus like dengue, yellow fever, chikanguya, West Nile
3. linked to microcephaly (abnormally small head) in child development and Guillain Barre syndrome
o immune system attacks peripheral nerves  paralysis in serious effects
o affi it for hildre ’s rai o pared to adult rai
o high viral levels i i fa ts’ brain  linkage between microcephaly and Zika
- arthropod borne virus (arbovirus): spread by ticks, mites, mosquitoes
- Brazil: favourable conditions for mosquito, zika also mutated in dangerous form
MICROCEPHALY
- microcephalics of Lahore and Leeds/Bradford provide insight to microcephaly
o large Pakistani community in Leeds  high incidence of microcephaly
o Lahore area in Pakistan also has high incidence of microcephaly
o practice of cousin – cousin marriage in culture: exposure of recessive genes (inbreeding)
- involves 8 genes (recessive genes) affecting brain growth
o 4 have been identified, all involving proteins necessary for neuroblast formation
o ¾ show hallmarks of extremely rapid evolutionary change in recent human history
o mystery on how it crosses placenta
o evidence of human to human transmission (e.g. sex)
FAMILY TREE OF ZIKA AND EVOLUTION
- vaccine of zika virus will be based on vaccine of yellow fever virus

- need to know where, how, secondary host, vectors, maintenance in host etc.
SEASONAL FLU
- flu viruses characterized as being type A, B, or C
1. type A: most mutable and epidemiologically dangerous
o strains are monitored closely and classified by Haemagglutinin and Neuraminidase proteins (surface proteins),
which can change to create antigen profiles that are novel to populations (changes quite rapidly)  but can
be readily sequenced for vaccines
- antigenic drift: caused by mutation
o caused by small mutations (e.g. point mutation)  changes amino acid etc.
o produces constantly changing antigen surface proteins
- antigen shift: caused by recombination between strains  bits of genome gets mixed
o different set of viruses circulating in different species  potential to infect another species  by change mixes
genome  dangerous
o special concern: recombination of strains native to other animals with those found in humans
o can cause major change in virus conferring a high degree of virulence and novelty
VACCINES
- FluNet: high frequency of H1N1 in 2016 in northern hemisphere
o swine flu virus
- must predict a year early for vaccine to be effective
- designing vaccines is based upon evolutionary predictions  probabilistic (educated guess)
o data on mutability of key surface antigens (HA, NA) and virulence of bug
o targets 3 different strains of any flu year: for 2016 
▪ H1N1 (California), H3N2 (Switzerland), B (Phuket, Yamagata virus)
- global travel, air traffic: modelling to improve estimates of spread of influenza
o flus mostly come from Asia (dense human populations + animals)
o vector must be taken into account (including humans in global travel)
PANDEMIC FLU
SPANISH FLU (H1N1) OF 1918, 1919
- origin unknown: possibly barracks in France, Kansas US camps, Chinese labourers brought in for WWI (virus from china)
- spread everywhere
- other of pa de i s: “pa ish : first reported it seriously (only one to do so because other countries were involved
with war)
o killed (not really) king Alphonso XIII etc.  killed people in their prime
- killed estimated 50 – 100 million people, sometimes within hours of infection
- up to 30% of people worldwide infected
- mortality rate of 15 – 34 year olds = 20x higher than any flu epidemic known
o flu typically kills thousands each year but usually those of 65+
o immunological prime  cytokine storm
- 3 – 5% of orld’s populatio died as a dire t result
- in the end, disappeared (killed itself)  ran its course from being very virulent (from own capacity to spread and
render patients sick)
- pandemics are characterized by waves
MORTALITY RATE OF PANDEMIC INFLUENZA VS. SEASONAL INFLUENZA

- age distribution of mortality differs between highly virulent pandemic strains of flu and seasonal flu
o due to evolving nature of immune response through our lives with age
o unlike seasonal flu, risk tends to grow with increasing intensity of immune response
o killed people because of the immune response it invoked (e.g. Spanish flu)  cytokine storm in people
suffering from flu
- pregnant women are at greater risk
- 100 days war: death rates was partially due to Spanish flu  ended WWI
BIRD FLU
- contraction from close contact with birds; human to human transfer is limited  bird virus may evolve for human to
human transfer
- has higher mortality rate than the Spanish flu
- antigenic shift may lead to capacity of human to human transfer
- H5N1 (avian flu): strain of influenza virus A (Orthomyxoviridae) negative sense, single stranded, segmented RNA virus
- limited human-human transmission  no evidence of recombination with human strains
- little human resistance and widespread endemic population in birds in Asia
MONITORING OF VIRUS
- phylogeographic approach: based on DNA or RNA or amino acid sequence  relate viruses
o determine how strong the nodes are and their probability of their relationship
H1N1 SWINE FLU
- mortality concentrated in old and young
- first case in California/ North America
- different dynamics from other flus
- nothing happened in 2010 after H1N1 pandemic: possibly change in human behaviour but no real answer
EVOLUTION STUDIES
1. understanding behaviour of organisms and their relationship with nature
2. significance of variation within populations
GALAPAGOS ISLAND
- island endemics: unique islands (even from island to islands  diversity)
DARWIN’“ VOYAGE
- 19th century: was made to study theology
- commissioned to go on voyage around the world (Beagle)
- studied geology  fossils and strata  relations of fossils to organisms in modern type
o shifting of plates etc.
- from island to island  great deal of variation (e.g. mocking birds)
o colonization and differentiation
o adaptive radiation into multiple organisms

-
DARWIN’“ BIG IDEA
- Alfred Russell Wallace codiscovered the principle of evolution
o admired Darwin: wrote a letter of his idea in 1858 describing his idea
o Wallace may have the discover of evolution (Darwin was afraid of his own idea)
1. there is variation within breeding groups (populations)  if affects survival of organisms  next generation may be
different from current generation
2. part of observed variation is heritable
3. variation influences fitness: some individuals are more successful in survival and reproduction than others are
EVIDENCE FOR EVOLUTION
- both historic, experimental, contemporary observations
1. evolution in action: direct observations
a. disease virulence + drug resistance of bacteria
b. artificial selection + experimental evolution: modify fruit fly environments and ir u sta es pla i g
Dar i
c. adaptation to anthropogenic change + biological invasions (can provide accidents in nature)
o evolution in a short time scale
2. adaptation: evidence of inherited qualities of phenotype that enhance fitness
a. reproductive success or organism: measurement of fitness = number of grandkids (direct offspring may be
sterile) or through relatives and enhancing reproductive success
3. homologies: related species share any of same parts but they are often used in different ways
a. e.g. organization of bones in mammals, birds, fishes etc.
4. fossils: organisms have changed dramatically over time represented (e.g. strata)
5. biogeography: geographic distribution of species provides evidence of evolutionary change
- F.C. Ho ell’s Early Man, The Road to Homo sapiens: implies linear transition from ancient to modern species and that
evolution is directed in some fashion
o evolution is not as linear as the illustration (subspecies of Homo etc.)

ARTIFICIAL SELECTION
1. measure phenotype of all individuals in population (e.g. height distributions of organism X)
2. breed those of a subset of the population
- e.g. breeding corn for increased oil yield:
o select on ovaries (kernels that we eat)  amplify through artificial selection
o
- e.g. cauliflower looking plant shit: Brassica oleracea (wild mustard)
o humans have selectively bred for particular characteristics: stems, leaves etc.
o same species (Brassica) but very different

o variability created from selective breeding
- e.g. domestic dogs:
o based upon DNA sequence, domestic dog is believed to be derived from a common ancestor shared with the
modern grey wolf and the extinct Taimyr wolf (30 – 40 thousand years ago)
o interbreeding with those species appears to have occurred through early period of domestication
o different shapes, physiology
PUSHING CHARACTERISTICS BEYOND NATURAL RANGE

- sometimes this is true: some kinds of traits have a limit: very simple genetic basis
- some traits through artificial selection leads to phenotypes outside the ancestral range limit
-
HOW SELECTION WORKS IN NATURE
- Malthus: believed that humans would deplete resources  outstripping resources

o populations of humans grow exponentially
o resources grow monotonically
o struggle for existence for limited resources  better adapted humans will be able to gain those resources
- e.g. soapberry bugs:
o found in southern Florida, and their beaks are a certain length fit for their nutrition (8 – 7 mm)
o flat podded golden rain tree fruit was brought into central Florida  soapberry bugs had shorter beaks in
these regions (6 – 9 mm) = rapid evolutionary change due to change in food
o
o genetic change over a short time
- phenotypic plasticity: phenotype changes due to change in environment (no difference in genes)
o between genetically identical species; plastic response; different phenotypes due to environment
o not adaptation: does not get passed to the offspring; response to environment
- e.g. Trinidad: guppies
o rivers are relatively undisturbed by humans, have multiple drainages into the ocean

o upper reaches are separated by barrier waterfalls from the lower reaches
o difference predators depending on location  fit

for prey localized in that area
ales eed to e less olou ful to hide f o p edatio

▪ there still may be another hypothesis possible for less colourful males in downstream
ENDLER’“ GREENHOU“E EXPERIMENT
- 3 different predator treatments

-
- evidence that predation by Crenicichla is limiting males in their colour spot presentation
o colour spots needed to attract females
- colour spots change towards matching gravel under high predation
BIO WEEK 19 TEXTBOOK NOTES
CHAPTER 22 DESCENT WITH MODIFICAITON: A DARWINIAN VIEW OF LIFE

- evolution: descent with modification  many species are descendants of ancestral species that were different from
present day species

o pattern of evolution consists of mechanisms that produce observed pattern of change  represent natural
causes of natural phenomena we observe
Concept 22.1 The Darwinian revolution challenged traditional views of a young Earth inhabited by unchanging species
SCALA NATURAE AND CLASSIFICATION OF SPECIES
- Aristotle first viewed species as fixed in a scale of nature = scala naturae  each form of life had its allotted rung
- Carolus Linnaeus, physician and botanist, developed the two part, binomial, format for naming species
1. adopted a nested classification system  grouping similar species into increasingly general categories
2. categorized according to pattern of creation  argued by Darwin for classification based on evolutionary
relationships
IDEAS ABOUT CHANGE OVER TIME
- Darwin found fossils: between superimposed layers of strata
- paleontology: study of fossils developed by Georges Cuvier, French scientist
o noted that older stratum  more dissimilar its fossils were to current life forms
o noted that some new species appeared while others disappeared in new strata
o catastrophism: principle that events in past occurred suddenly and were caused by mechanisms different
from those operating in the present (not evolution)
o each boundary between strata represented a catastrophe and confined to local regions
- Ja es Hutto : proposed that Earth’s geologi features ould e e plai ed gradual e ha is s operati g toda
- Charles Lyell: uniformitarianism: mechanisms of change are constant over time
o same geologic processes are operating today as in the past at the same rate
- Darwin: geologic change results from slow continuous actions  Earth is much older than bible states
-
LARMARCK’“ HYPOTHE“I“ OF EVOLUTION
- naturalists in 18th century suggested that life evolves as envrionments change
- Larmarck, French biologist:
1. use and disuse: idea that parts of body that are used extensively become larger and stronger while those that
are not deteriorate; e.g. giraffe stretching its neck to reach leaves of high branches
2. inheritance of acquired characteristics: organism could pass these modifications to its offspring

o thought evolution happens because organisms have innate drive to become more complex  rejected by
Darwin
o experiments show traits a ui ed y use du i g i di idual’s life a e ot i he ited i ay p oposed y
Larmarck
Concept 22.2 Descent with modification by natural selection explains the adaptations of organisms and the unity and
diversity of life
DARWIN’“ RE“EARCH
- Darwin was recommended by Henslow (botany professor) to Captain Robert FitzRoy for survey in ship HMS Beagle for
long voyage around world
THE VOYAGE OF THE BEAGLE
- Darwin observed that plants and animals in temperate regions of S. American closely resembled species in South
American tropics than in temperate regions of Europe
- Galapagos volcanic islands: birds he collected included finches + mocking birds  different species
o hypothesized that island had been colonized by organisms that have strayed from South American and then
diversified  new species on various islands
DARWIN’“ FOCU“ ON ADAPTATION
- adaptations: inherited characteristics of organisms that enhance their survival and reproduction in specific
environments
o fi hes’ arious eaks a d eha iours are adapted to specific foods available on their home islands
- natural selection: process in which individuals that have certain inherited traits tend to survive and reproduce at
higher rates than other individuals because of those traits
-
- Russel Wallace, British naturalist, first published the idea of evolution but thought Darwin did a more extensive job
THE ORIGIN OF SPECIES
- 3 broad observations about nature: unity of life, diversity of life, match between organisms and their environments
- in first edition: never used word evolution rather descent with modification
DESCENT WITH MODIFICATION
- organisms share many characteristics  unity of life
- unity of life due to descent of all organisms from an ancestor that lived in remote past
o thought that descendants of ancestral organisms lived in various habitats over millions of years 
accumulated diverse modifications/ adaptations that fit them to specific ways of life
o over long periods of time, descent with modification eventually led to rich diversity of life today
- e.g. Asian elephant, 2 African elephants:

o shared same line of descent until relatively recent split from common ancestor
o
o scientists estimate 99% of all species that have ever lived are now extinct
ARTIFICIAL SELECTION, NATURAL SELECTION, AND ADAPTATION
- artificial selection: modification of species over many generations by selecting and breeding individuals that possess
desired traits
-
- Dar i ’s o ser atio s a d i fere es:
1. observation 1: members of population often vary in their inherited traits
2. observation 2: all species can produce more offspring than their environment can support and many of these
offsprings fail to survive and reproduce
3. inference 1: individuals whose inherited traits give them a higher probability of survival and reproduction in a
given environment tend to eave more offspring than other individuals
4. this unequal ability of individuals to survive and reproduce will lead to accumulation of favourable traits in
population over generations
- orga is ’s herita le traits can influence not only its own performance, but also how well its offspring cope with
environmental challenges  advantages increase number of offspring to survive  traits favoured will likely appear
at a greater frequency in next generation
- natural selection resulting from factors such as predators, lack of food, adverse physical conditions can lead to
increase in proportion of favourable traits in a population
o advantageous variations will gradually accumulate in population and less favourable variations will diminish

-
NATURAL SELECTION: A SUMMARY
1. natural selection is a process in which individuals that have certain heritable traits survive and, because of those traits,
reproduce at higher rate than other individuals
2. over time, natural selection can increase match between organisms and their environment
3. if environment changes, or if individuals move to new environment, natural selection may result in adaptation to these
new conditions  sometimes gives rise to new species
- although natural selection occurs through interactions between individual organisms and their environment,
individuals do not evolve  population evolves over time
- natural selection can amplify or diminish only those heritable traits that differ among individuals in a population
o even if trait is heritable, if all individuals in population are genetically identical for that trait  evolution by
natural selection cannot occur
- environmental factors vary from place to place and over time  trait that is favourable in one place may be useless
in other places or times
o natural selection is always operating but which traits are favoured depends on context in which species
lives and mates
Concept 22.3 Evolution is supported by an overwhelming amount of scientific evidence
DIRECT OBSERVATIONS OF EVOLUTIONARY CHANGE
NATURAL SELECTION IN RESPONSE TO INTRODUCED PLANT SPECIES
- herbivores: adaptations that hep them feed efficiently on their primary food sources
- soapberry bugs: use hollow needlelike mouthpart to feed on seeds located within fruits of various plants
o Jadera haematoloma feeds on seeds of native plant, balloon vine in southern FLoria
o soapberry bugs in central Florida feed on goldenrain tree (balloon vine is rare)
o feed most effectively when their beak length closely matches depth at which seeds are found within fruit
▪ beak length shorter in populations that feed on goldenrain tree
o in populations feeding on introduced species in regions like Australia, natural selection would result in
evolution of longer beak length (because plants are larger in these areas)
THE EVOLUTION OF DRUG RESISTANT BACTERIA

- resistant strains of pathogens can proliferate very quickly

- Staphylococcus aureus: certain genetic strains of this species (methicillin resistant S. aureus MRSA) are formidable
pathogens  increase in virulent forms such as clone USA300 (flesh eating disease)
- 1943: penicillin became first widely used antibiotic
o by 1945: 20% of S. aureus strains were resistant to penicillin (had penicillinase that could destroy penicillin)
- 1959: methicillin used  deactivated protein that bacteria used to synthesize cell walls
o S. aureus populations exhibited variations in how strongly their members were affected by the drug
o some individuals able to synthesize cell walls using different protein that was not affected by methicillin
- some MRSA strains can exchange genes with members of their own and other species  multidrug resistant strains
1. natural selection is a process of editing, not creative mechanism
a. drug selects for resistant individuals that are already present in population
2. natural selection depends on time and place: favours those characteristics in a genetically variable population that
provide advantage in current, local environment
HOMOLOGY
- characteristics present in ancestral organism that are altered by natural selection in its descendants over time as they
face different environmental conditions
o related species can have characteristics that have an underlying similarity yet function differently
- homology: similarity resulting from common ancestry
ANATOMICAL AND MOLECULAR HOMOLOGIES
- e.g. forelimbs of all mammals show same arrangement of bones from shoulder to tips of digits even though these
appendages have very different functions  homologous structures
- homologous structures: structures that represent variations on a structural theme that was present in their common
ancestor: e.g. underlying skeletons of arms, forelegs, flippers, wings
-
- e.g. vertebrate embryos have a tail located behind anus + structures of pharyngeal (throat) pouches
o ultimately develop into structures of different functions (e.g. gills, ears, throat)
- vestigial structures: re a ts of features that ser ed a fu tio i orga is ’s a estors
o e.g. skeletons of some snakes retain vestiges of pelvis and leg bones of walking ancestors
- similarities at molecular level: all forms of life use DNA and RNA and the genetic code is essentially universal
- homologous genes may acquire new functions while others retain their original functions
o common genes that have lost their function
o inactive pseudogenes may be present simply because a common ancestor had them
HOMOLOGIES AND TREE THINKING
- e.g. tetrapods: vertebrate group of amphibians, mammals, reptiles
o all tetrapods have limbs with digits whereas other vertebrates do not

- all life shares deepest layer, and each successive smaller group adds its own homologies to those it shares with
larger groups  result of descent with modification from common ancestor
- evolutionary tree: diagram reflecting evolutionary relationships among groups of organisms
-
o each branch point represents common ancestor of all species that descended from it
o lungfishes and all tetrapods descended from ancestor 1
o mammals, lizards, snakes, crocodiles, birds descended from ancestor 3
▪ limbs with digits, amnion (protective embryonic membrane), feathers
o ancestor 2: limbs with digits present  found in all of descendants of that ancestor (tetrapods)
o ancestor 3: amnion present only in ancestor 3  shared only by some tetrapods (mammals and reptiles)
o ancestor 6: feathers only present in ancestor 6  found only in birds
o mammals positioned closer to amphibians than birds  but more closely related to birds because mammals
and birds share a more recent common ancestor (ancestor 3)
o ancestor 2: most recent common ancestor of birds and amphibians  mammals and birds equally related to
amphibians
A DIFFERENT CAUSE OF RESEMBLANCE: CONVERGENT EVOLUTION
- convergent evolution: independent evolution of similar features in different lineages
- e.g. marsupial mammals: distinct from another group of mammals, eutherians
o marsupials complete their development in external pouch
o marsupial sugar gilder is superficially very similar to flying squirrels (gliding eutherians in NA forests)
▪ sugar glider is much more closely related to kangaroos than to flying squirrels
- although they evolved independently from different ancestors  two mammals have adapted to similar
environments in similar ways
- analogous: analogous features share similar function but not common ancestry
o homologous features share common ancestry but not necessarily similar function
THE FOSSIL RECORD
- e.g. researchers found that pelvic bone in fossil stickleback fish became greatly reduced in size over time  reduction
in size of pelvic bone driven by natural selection
- fossils can shed light on origins of new groups of organisms
o e.g. cetaceans (whales, dolphins) closely related to even toed ungulates (deer, pigs, camels, cows)
o  prior to 50 – 60 million years ago, most mammals were terrestrial
o  formation of new species and origin of a major new group of mammals, cetaceans

- over time, descent with modification produced increasingly large differences among related groups of organisms,
ultimately resulting in diversity today
-
BIOGEOGRAPHY
- geographic distribution of organisms influenced by continental drift etc. from Pangaea
- islands generally have many species of plants and animals that are endemic: found nowhere else
o species closely related to species from nearest mainland or neighbouring island
o two islands with similar environments in distant parts of world tend to be populated not by species related
to each other but rather by species related to those of nearest mainland (despite different environment)
WHAT I“ THEORETICAL ABOUT DARWIN’“ VIEW OF LIFE?
- natural selection is the primary cause of observed pattern of evolutionary change is observed and tested in nature
- theory of evolution has been continually tested and accepted
o some changes: evolution may not always be a slow process; natural selection is not the only mechanism
responsible for evolution

ENDLER EXPERIMENT CONTINUED

- i ease i guppies’ spots ith la k of p edatio
1. females are selecting on males with bright colouration  puts males on risk of predation  trade off
2. predators have same sensitivity to light as those measured in females  tuned in to finding male guppies
- used streams in Trinidad as natural laboratories: transplanted guppies upstream
1. rapidly increase in colouration in males
-
- A1: another predator called i ulus pla es ale at isk of p edatio . At A1 zo e, the olou sta s o eut al. The
are worried about predation (trade off: attracting females with colour), but mostly not colourful. The predators will
look for males guppies. Ex. lower location containing alta and other predators (A1)
- A2: In a barrier waterfall, Rivulus lives in A2 zone, and through this experiment, it moved Guppies to the A2 zone
to see the Guppies’ eha iou . When Guppies see Rivulus in A2 zone, they are less colourful because they know
that Rivulus (predator) might eat them. changing body to keep them safe.
FOUR DECADES IN A NATURAL LABORATORY
- E dle ’s t a spla tatio s 이식 have been repeated by researchers many times now with twists:
1. bilateral movement of fishes between predation regimes 지배
2. communities of predators differ on N and S slopes of range
3. studies have shifted to understand how life history (defines organism in its growth, maturation, birth,
reproductive investment, survival, longevity, death etc.) strategies change:

-
▪ ot a ia e ut patte ; ot i eased ut ha ged :
▪ There might be variance in gene expression for 135 different loci and it is increasing the evolution.
▪ Evolutionary changes.
2. expression of genes on brain  behaviour change in different predation regimes
▪ over 100 different genes were expressed at a higher/ lower number than control
▪ phenotypically plastic response (not evolution, changes happen when it is forced by something like
guppies placed in A2 zone: same genotype produce different phenotype in different condition 
controversial 논란 whether it aided or impeded 지연하다 evolution
- Difference between guppies and gene expression (know that they are not same thing)
HOMOLOGY
- shared structures are evidence of common ancestry
1. e.g. mammalian forelimb illustrates how evolution repurposes and reshapes structures for wildly different
uses
2.
3. different structures for different purposes

▪ more fingers to support wing  more intrinsic and better aerodynamic performance
4. embryo would look similarity
- pentadactyl limb incorporated into various organisms:
1. from low fin fishes: fish that could move around in shallow waters, gasping air  adaptation to life on land
CONVERGENT EVOLUTION
EASTERN MEADOWLARK AND AFRICAN LONGCLAW
- resemblance (not through common ancestry): evolved due to environment, convergence
- diffe e t o ga is s sol i g si ila p o le s
CONVERGENT EVOLUTION

- when different taxa find similar solutions to the same evolutionary problem = covergence
- when similar taxa or populations adapt the same way, independently, = parallelism
- phenomena offer profound insights into functional basis of adaptation
VESTIGIAL STRUCTURES: loses its purpose  e . Hu a : Wisdo teeth do ’t eed it a o e / Bi ds: Wi gs i ds
that do ’t fly anymore)
-
- e.g. kiwi wings, goosebumps (faced with threat to look big)
- pseudogenes: duplicate genes no longer functional  ha ge a do l e ause the ’ e ot fu tio al  reactivation
may produce new variant they may be useful
SELECTION IS NOT PROGRESSIVE (depending on environments, sometimes it can be progressive and sometimes it can
be not progressive)e . Hu a if e a ’t speak a o e, e lose ou k o ledge of la guage, ho e e when we go
to school, we gain those knowledge again)lose/gain
- although organisms have become more specialized and complex, this does not imply some ultimate target or direction
to this change
1. organisms also frequently devolve
2. e.g. many parasite adaptations to independent life; vestigial structures
- adaptation predominantly occurs through character modification, and character loss
1. repurposing structures; most evolution happens from variations that pre-exist in a population
HOX GENE HOMOLOGIES
- molecular, genetic homologies throughout animal kingdom
- HOX genes determines segmental identity of animals
-
- paralogous: homologous genes formed via duplication
1. duplicated into gene families and modified and sometimes onto different chromosomes
- homeo domain: short region associated with HOX genes
- gene families may be potent material for shaping by natural selection
- mutant gene/ knocked out gene  wrong signal identities in structure  structures expressed in different parts

PHYLOGENY (Tree, Thinking)
-
- rapidly changing genes to compare hypermutating genes
- slow changing genes to compare ancient genes
- birds are technically dinosaurs: many dinosaurs were feathered
- Archae are closer to Eukaryotes than Bacteria
DARWIN’“ FINCHE“ OR PIGEON“
- some people say Darwin was interested in pigeons: a id pigeo fa
- breeders can select for a range of morphological features
- pigeons long been used as messengers (e.g. homing pigeons)
- pigeons with extraordinary evolution
- Darwin made phylogeny of pigeons: why was the wild type bird different from other pigeons  wanted to restore
rock dove from the other pigeons
-
-
GENES IN POPULATIONS
- evolution occurs through changes in gene pool/ gene frequencies of a population (because certain individuals in larger
groups are successful in reproducing)
- individuals vary in their success at survival and reproduction
1. heritable genetic basis to this variation (genetic polymorphism)  allele frequencies change in next
generation
2. not all variation is genetically based: environment, accidents, introduced variation
3. not call genetic variation is heritable: some variation is caused by gene to gene interactions that get broken
up by meiosis
- estimating:
1. how much of variation is genetically based vs. environmental variation (due to drought etc.)

-
1. movement of mean in next generation: need to know 1 and 2
- response R = heritability x strength of selection
▪ 1 = perfect heritability
BASIC QG
-
1. kids: average of mother and father
- traits underlain by many genes are referred to as quantitative genetic characters
- they do ’t sho si ple Me delia i he ita e as the see to le d i offsp i g a d ha e i o plete t a s issio
CORRELATION BETWEEN PARENTS AND OFFSPRING ESTIMATES HERITABILITY

-
o weak heritability: strong environmental role + weak genetics
o selected by environmental selection  gene frequency would not change
o human height: usually high heritability, weak heritability: environmental (lack of nutrition) may change height
▪ stable environment: human height has high heritability
- changes in gene expression is most likely to help the organism respond appropriately to changes in its environment
o changes in gene expression is always happening
o mutations in individuals within a lifetime usually lead to harmful effects
o evolutionary adaptation: benefit to environment over generations (not climatization)
QUANTIFYING VARIATION
-
o high heterozygosity  genetic diversity
- measurements: number of loci that have different alleles or number of alleles per loci
PARADOX OF VARIATION (genetictically mediated)
- natural selection (organisms have particular characteristics) relentlessly removes maladaptive variation
- natural observations and lab breeding experiments reveal rapid evolutionary responses, abundant variation in traits
directly affecting fitness
- even under lab controlled experiments, fruit flies had variation
- what sustains genetic variation in characters that affect fitness?

o
MUTATION SELECTION BALANCE
-
o selection purges harmful mutations, mutations counter this effect
BACTERIA, VIRUS MUTATION
-
- HIV: enormous populations in a small amount on infected human  pretty good chance of mutation that makes virus
more effective (has rapid evolution)

-
- took E. coli and cloned it into multiple copies (genetically identical)  used them to start 12 independent lines 
evolution from no variation (own mutation)
- froze ancestors, unfroze them and compared to newer generations to see evolutionary influence
- classical dynamics: growth  mutation  single growth then limit  mutation  growth then limit  staircase effect,
however
-
o multifold increase in fitness in A3 (rate of population increase): required 3 mutations that happens in a
particular sequence  ability to metabolize citrate
A3 MUTATION
- allows them to occupy a new environment (key

innovation)
- creationism vs. evolutionary biology: by chance, you can actually have a complex adaptation
o refer to slide 14
Bio Week 20 Chapter 23 Evolution of Populations Textbook Notes
- natural selection acts on individuals but evolutionary impact of natural selection is only apparent in changes in a
population over time
- e.g. red squirrels: offspring that are born earlier tend to be larger and better able to be independent when winter
approaches later in the year  higher survival rates and more likely to be successful in breeding the next year
o proportion of squirrels giving birth early in the spring increased from generation to generation
- microevolution: change in allele frequencies in a population over generations

- 3 main causes of frequency change:

1. natural selection
2. genetic drift: change events that alter allele frequencies
3. gene flow: transfer of alleles between populations
MUTATION: GOOD, BAD, UGLY
-
- survey frequency of inversion polymorphism (polytene chromosome in salivary glands of Drosophila)
o duplication after duplication  lots of gene product
- banding: represents density of chromatin  can read chromosome through staining
- high frequencies of distinctive chromosomes (generally from inversions)
- repair mechanism swaps order of genes (inversion)

(macromutation)  can link together two alleles at different loci (chiasma)  supergene
- link geographic location and indicators/ nature of chromosomes  adaptation at a particular location
CLINES

- lower latitudes to higher latitudes  mirror image of cline  adapted to environment

- couch potato allele: mutant that causes low activity and obesity
SEX: SHUFFLING THE DECK
-
o making diverse offspring so some organisms by luck reproduce successfully
o sex can take away the good gene combination that forms from natural selection
THE PROBLEM OF BLENDING
-
- ua titati e t aits do ot see to o e Me del’s ules  blur in F2
o Darwin thought pangenesis was at work: gemules and shit cuz hes dumb af
o however, le di g does ’t p o ide fo ge eti a iation (Darwin is dumb af)
-
o Yule thought because of blending, dominant allele over time came to a 3:1 ratio
- Regi ald Pu ett a d Godf e Ha old Ha d : uestio ed h do i a t allele did ’t a ifest a ¾ f e ue
o Hardy develops an equation
- clicker: characteristic underlain by few genes + simple additive effect rapid bounded and maximum
o unlike trait that is underlain by many loci + complicated genetic basis  not bounded

ALLELE AND GENOTYPE
- common allele = p
- allele frequencies must add to 1
- I thought BIOL102 was finished
- equilibrium genotype frequencies:
-
USING H-W
- e.g. find if something interesting is going on such as selection for specific trait

-
GENETIC DISEASES
- q = 0.01 (1/100) carry allele for PKU
-
Concept 23.1 Genetic variation makes evolution possible
- variations in heritable traits is a perquisite for evolution
GENETIC VARIATION
- genetic variation: differences among individuals in the composition of their genes/ other DNA segments
o phenotype: product of inherited genotype and many environmental influences
o e.g. bodybuilders alter their phenotypes but do not pass their huge muscles onto the next generation
o only genetically determined part of phenotype can have evolutionary consequences
- without genetic variation, evolution cannot occur
VARIATION WITHIN A POPULATION
1. discrete characters: either-or- asis e.g. ea h pla t of Me del’s pea pla t ha e flo e s that a e eithe pu ple o hite
a. many are determined by single gene locus with different alleles that produce distinct phenotypes
2. quantitative characters: vary along a continuum within a population
a. usually results from influence of two or more genes on a single phenotypic character
- need to describe how much genetic variation there is in particular population

o measure at whole gene level (gene variability)

o measure at molecular level of DNA (nucleotide variability)
- average heterozygosity (gene variability): average percentage of loci that are heterozygous
o survey protein products using gel electrophoresis: cannot detect silent mutations that alter DNA sequence of
gene but not amino acid sequence of protein
o PCR based methods + restriction fragment analyses: can take into account silent mutations into their count
- nucleotide variability: comparing DNA sequences of two individuals in a population and then average the date from
comparisons
- gene variability tends to exceed nucleotide variability: difference at only one of the thousands of nucleotides in a
gene can be sufficient to make two alleles of that gene different  increases gene variability
VARIATION BETWEEN POPULATIONS
- geographic variation: differences in genetic composition of separate populations
- e.g. house mice: in certain populations, some of chromosomes have been fused
o however, patterns of fused chromosomes differ from one population to another
o patterns of fused chromosomes differ from one population to another
o phenotypic effects on mice seem to be neutral as they leave genes intact on the chromosome level
o variation between these populations appears to have resulted from change events (drift) rather than natural
selection
- cline: graded change in character along a geographic axis
o can be produced by gradation in environmental variable (e.g. temperature on frequency of cold adaptive allele
in mummichog fish
o probably result form natural selection: otherwise no reason to expect associate between environmental
variable and frequency of allele  selection can only operate if multiple alleles exist for given locus

-
SOURS OF GENETIC VARIATION PG. 505
- mutation, gene duplication produce new alleles and new genes
- sexual reproduction can result in genetic variation as existing genes are arranged in new ways
FORMATION OF NEW ALLELES
- new alleles can arise by mutation
- multicellular organism: only mutations in cell lines that produce gametes can be passed to offspring
- plants and fungi: many different cell lines can produce gametes
- most animals: majority of mutations occur in somatic cells and are lost when individual dies
- phenotypes generally provide close match to their environment
o unlikely that new mutation that alters phenotype with improve it
- mutations in eukaryotic organisms in noncoding regions are often harmless
- mutant allele may on rare occasions actually make its bearer better suited to environment  enhances reproductive
success
ALTERING GENE NUMBER OR POSITION
- genes are duplicated due to errors in meiosis (e.g. unequal crossing over), slippage during DNA replication, or activities
of transposable elements  source of variation
- duplications of large chromosome segments (chromosomal aberrations) are often harmful
- duplications of smaller pieces of DNA may not be harmful
- gene duplications that do not have severe effects can persist over generations  accumulation of mutations 
expanded genome with new genes that may take on new functions
- e.g. remote ancestors of mammals had a single gene for detecting odours that has since been duplicated many times
 enables them to detect faint odours and to distinguish among many different smells
o mice olfactory receptor genes > human olfactory receptor genes  more important to mice than humans
RAPID REPRODUCTION
- prokaryotes typically have short generation spans so mutations can quickly generate genetic variation in populations
- e.g. HIV has a generation span of about two days
o its RNA genome has a higher mutation rate because of the lack of RNA repair mechanisms
o drug cocktails are used: less likely that multiple mutations conferring resistance to all drugs will occur in a
short time
SEXUAL REPRODUCTION

- unique combinations of alleles that each individual receives from its parents
- sexual reproduction shuffles existing alleles and deals them at random to produce individual genotypes
- crossing over, independent assortment of chromosomes, one inherited from each parent, trade some of their alleles
by crossing over
- sexual reproduction rearranges existing alleles into fresh combinations each generation
Concept 23.2 The Hardy-Weinberg equation can be used to test whether a population is evolving
- presence of genetic variation does not guarantee evolution
GENE POOLS AND ALLELE FREQUENCIES
- population: group of individuals of same species that live in same area and interbreed, producing fertile offspring
o isolated populations most likely exchange genetic material only rarely
- gene pool: consists of all copies of every type of allele at every locus in all members of population
- fixed allele: if only one allele exists for particular locus in population = fixed in gene pool
- homozygous/ heterozygous: two or more alleles for particular locus in population
- each allele has a frequency in population
- (p) represents frequency of one allele and (q) represents frequency of other allele
o frequency = number of particular allele/ number of total allele
THE HARD WEINBERG PRINCIPLE
- determine what the genetic makeup of a population would be if it were not evolving at that locus  compare with
data rom real population
o no differences: real population is not evolving
o differences: real population may be evolving
HARD-WEINBERG EQUILIBRIUM
- Hardy-Weinberg principle: frequencies of alleles and genotypes in a population will remain constant from generation
to generation provided that only Mendelian segregation and recombination of alleles are at work  Hardy Weinberg
equilibrium
- consider combination of alleles in all of crosses in a population
- wildflower example:
1. population of 500 flowers: red p = 0.8, red q = 0.2
2. for 1000 total copies of flower colour gene: 800 red alleles + 200 white alleles
3. probability that egg or sperm contains red or white allele is e ual to f e ue of these alleles i i
4. each egg/ sperm has 80% chance of containing red allele and 20% chance of containing white allele
5. calculate frequencies of three possible genotypes assuming random union of sperm and eggs
6. two red alleles: p x p = 0.8 x 0.8 = 0.64  64% of plants in next generation will have genotype RR
7. two white alleles = 0.2 x 0.2 = 0.04  4% of plants will have WW
8. heterozygotes: 0.8 x 0.2 = 0.16 = 16% must multiply by two (each allele can be from sperm or egg) = 32%
9. 100% = 64% + 4% + 32%: at a locus with two alleles, 3 genotypes will appear in the following proportions
- population is in Hardy Weinberg equilibrium only if genotype frequencies are such that the actual frequency of one
homozygote is p2, the actual frequency of other homozygote is q2, actual frequency of heterozygotes is 2pq
- epeated shuffli g of a populatio ’s ge e pool o e ge e atio s a ot i itself ha ge the f e ue of o e allele
relative to another

-
CONDITIONS FOR HARDY-WEINBERG EQUILIBRIUM
1. no mutations: gene pool is modified if mutations alter alleles or if entire genes are deleted or duplicated
2. random mating: if individuals mate preferentially within a subset of the population, such as their close relatives
(inbreeding), random mixing of gametes does not occur, and genotype frequencies change
3. no natural selection: differences in survival and reproductive success of individuals carrying different genotypes can
alter allele frequencies
4. extremely large population size: smaller the population, the more likely it is that allele frequencies will fluctuate by
change from one generation to the next (genetic drift)
5. no gene flow: by moving alleles into or out of populations, gene flow can alter allele frequencies
- population can be evolving at some loci, yet simultaneously be in Hardy-Weinberg equilibrium at other loci
- some populations evolve so slowly that the changes in their allele and genotype frequencies are difficult to distinguish
from those predicted for nonevolving population

APPLYING THE HARDY-WEINBERG PRINCIPLE

- e.g. estimating percentage of population carrying allele for inherited disease
- e.g. phenylketonuria (PKU): metabolic disorder that results from homozygosity for recessive allele
o symptoms can be avoided with diet low in phenylalanine
1. assume not new PKU mutations are introduced and people neither choose their mates on basis of whether or
not they carry this gene nor generally mate with close relatives
2. mutation rate for PKU gene is low, population is large etc.  therefore conditions are good assumptions
3. q^2 = frequency of homozygotes
4. q = (1 baby/ 10 000 births)^1/2 = 0.01
5. frequency of dominant allele = 1 – q = 0.99
6. frequency of carriers: 2pq = 2 x 0.99 x 0.01 = 0.0198
o harmful recessive alleles at this and other loci can be concealed in a population because they are carried by
healthy heterozygotes
Concept 23.3 Natural selection, genetic drift, and gene flow can alter allele frequencies in a population
- 3 mechanisms that alter allele frequencies directly and cause most evolutionary change: natural selection, genetic
drift, gene flow
NATURAL SELECTION
- selection results in alleles being passed to next generation in proportions that differ from those in present generation
- e.g. fruit fly D. melanogaster: developed resistance to insecticides due to strong selective force of DDT
- natural selection can cause adaptive evolution: evolution that results in better match between organisms and their
environment
GENETIC DRIFT
- genetic drift: chance events can cause allele frequencies to fluctuate from one generation to the next, especially in
small populations
- unpredictable changes in allele frequencies caused by change events associated with survival and reproduction
- chance events that occur during fertilization: e.g. by change alone, every egg and sperm pair that generated offspring
could happen to have carried red allele and not white allele
THE FOUNDER EFFECT
- founder effect: few individuals become isolated from larger population  establishes new population whose gene
pool differs from source population
o e.g. few members of population are blown by storm to new island
- relatively high frequency of certain inherited disorders among isolated human populations
o e.g. Tristan da Cunha: small islands in Atlantic Ocean
▪ one of colonists carried recessive allele for retinitis pigmentosa  4 descendants of colonists on island
had retinitis pigmentosa  frequency of allele that causes disease is ten times higher on the island
than where founders came from
THE BOTTLENECK EFFECT
- bottleneck effect: severe drop in population size
o by chance alone, certain alleles may be overrepresented among survivors others may be underrepresented
and some may be absent
o recovery  still may have low levels of genetic variation for long period of time = legacy of genetic drift that
occurred when population was small
o human actions sometimes create severe bottlenecks for other species
FIELD STUDY: IMPACT OF GENETIC DRIFT ON THE GREATER PRAIRIE CHICKEN
- number of greater prairie chickens plummeted due to hunting and conversion of these prairies to farmland

- few surviving birds had low genetic variation and much less than 50% of their eggs hatched
- genetic variation and increase in frequency of harmful alleles due to genetic drift during bottleneck
- researchers measured the baseline estimate of how much genetic variation was present before population shrank:
had lost nine alleles that were present in museum specimens
- fewer alleles per locus than pre bottleneck populations
- drift had reduced genetic variation, may also have increased frequency of harmful alleles
- treatment: add 271 birds from neighbouring states  new alleles entered population and egg hatching rate improved
to over 90%
EFFECTS OF GENETIC DRIFT: A SUMMARY
1. genetic drift is significant in small populations
a. chance events tend to alter allele frequencies more substantially in small populations
2. genetic drift can cause allele frequencies to change at random
a. unlike natural selection: genetic drift causes allele frequencies to change at random over time
3. genetic drift can lead to loss of genetic variation within populations
a. can eliminate alleles from population  influence how effectively population can adapt to change
4. genetic drift can cause harmful alleles to become fixed
a. alleles a e lost o fi ed ha e: populatio ’s su i al a e th eate ed e.g. g eate p ai ie hi ke
GENE FLOW
- gene flow: transfer of alleles into or out of population due to movement of fertile individual or their gametes
- e.g. insects carrying pollen from plants of another population may fly to pollinate plants in original population
o modifies flower allele frequencies in next generation
1. tends to reduce genetic differences between populations
2. gene flow can result in two populations combining into single population with common gene pool
- e.g. Parus major (great tit): females born in eastern population survive twice as well as females born in central
population regardless of where females eventually settle and raise offspring
o thought that females born in eastern population are better adapted to life on island than females born in
central population
o two populations are connected by high levels of gene flow (mating)  would reduce genetic differences
o unequal amounts of gene flow from mainland: birds with mainland genotypes survive and reproduce poorly
on Vlieland, and in eastern population, selection reduces frequency of these genotypes
o central population: gene flow from mainland is so high  overwhelms effects of selection
o females born in central population have many immigrant genes  reduces degree to which members of that
population are adapted to life on island
-
3. gene flow can transfer alleles that improve ability of populations to adapt to local conditions
o e.g. gene flow resulted in worldwide spread of several insecticide resistant alleles in mosquito Culex pipiens
(vector of West Nile virus etc.)
▪ these alleles increased because they provided insecticide resistance  transferred to new
populations and their frequencies increased as a result of natural selection
4. gene flow has become an important agent of evolutionary change in human populations

o humans move much more freely about the world than in the past
o mating is more common between members of populations that had little contact before  alleles and fewer
genetic differences between these populations
Concept 23.4 Natural selection is the only mechanism that consistently causes adaptive evolution
- outcome of natural selection is NOT RANDOM
- natural selection consistently increases frequencies of alleles that provide reproductive advantage and thus leads to
adaptive evolution
A CLOSER LOOK AT NATURAL SELECTION
RELATIVE FITNESS
- e.g. barnacle that is more efficient at collecting food than its neighbours have greater stores of energy  able to
produce larger number of eggs
- relative fitness: the contribution an individual makes to gene pool of the next generation relative to contributions of
other individuals
- natural selection is subjected to the whole organism, not the underlying genotype  selection acts more directly
on phenotype than on genotype
o acts on genotype indirectly via how genotype affects phenotype
DIRECTIONAL, DISRUPTIVE, AND STABILIZING SELECTION
- natural selection can alter frequency of distribution of heritable traits in 3 ways depending on which phenotypes in a
population are favoured
o directional, disruptive, stabilizing selection
1. directional selection: conditions favour individuals exhibiting one extreme of phenotypic range  shifts populatio ’s
frequency curve for phenotypic character in one direction or the other
o o o he populatio ’s e i o e t ha ges o he e e s of populatio ig ate to e ha itat
o e.g. increase in relative abundance of large seeds over small seeds led to increase in beak depth in Galapagos
finches
2. disruptive selection: conditions favour individuals at both extremes of phenotypic range over individuals with
intermediate phenotypes
o e.g. black bellied seedcracker finches: small billed birds feed mainly on soft seeds whereas large billed birds
specialize in cracking hard seeds
i. intermediate sized bills are relatively inefficient at cracking both types of seeds  lower relative
fitness
3. stabilizing selection: acts against both extreme phenotypes and favours intermediate variats
o reduces variation and tends to maintain status quo for particular phenotypic character
o e.g. birth weights of most human babies: babies who are either much smaller or much larger suffer higher
rates of mortality
- selection favours individuals whose heritable phenotypic traits provide higher reproductive success than do traits
of other individuals

-
THE KEY ROLE OF NATURAL SELECTION IN ADAPTIVE EVOLUTION
- fit adaptations can arise gradually over time as natural selection increases the frequencies of alleles that enhance
survival and reproduction
o as proportion of favourable traits increases  math between a species and its environment improves 
adaptive evolution
- adaptive evolution can be continuous: environment may change over time  continuous natural selection
- genetic drift and gene flow can increase frequencies of alleles that improve the match between organisms sand their
environment but neither does so consistently
o genetic drift: cause frequency of slightly beneficial allele to increase, but can also cause frequency of such
allele to decrease
o gene flow: may introduce alleles that are advantageous or disadvantageous
- natural selection is the only evolutionary mechanism that consistently leads to adaptive evolution
SEXUAL SELECTION
- sexual selection: form of selection in which individuals with certain inherited characteristics are more likely than other
individuals to obtain mates
o can result in sexual dimorphism: difference between two sexes in secondary sexual characteristics (e.g. size,
colour, ornamentation, behaviour)

1. intrasexual selection: selection within same sex; individuals of one sex compete directly for mates of the opposite sex
o e.g. single male may patrol group of females and prevent other males from mating with them  defends its
status by defeating smaller, weaker, less fierce males in combat
o psychological victor in ritualized displays that discourage would-be competitors but do not risk injury that
would reduce his own fitness
o sometimes among females (e.g. ring tailed lemurs, broad nosed pipefish)
2. intersexual selection: mate choice; individuals of one sex (usually females) are choosy in selecting their mates from
the other sex
o hoi e depe ds o sho i ess of ale’s appea a e o eha iou
o ale’s sho i ess a ot see adaptive in any other way and may in fact pose some risk
o e.g. bright plumage may make male birds more visible to predators
▪ but if such characteristics help male gain a mate, and if this benefit outweighs risk from predation,
both bright plumage and female preference for it will be reinforced because they enhance overall
reproductive success
o females prefer male traits that are correlated with good genes: both male trait and female preference for it
should increase in frequency
THE PRESERVATION OF GENETIC VARIATION
- neutral variation: differences in DNA sequence that do not confer a selective advantage or disadvantage
o variation is also found at loci affected by selection
- tendency for directional and stabilizing selection to reduce variation is countered by mechanisms that preserve or
restore it
DIPLOIDY
- diploid eukaryotes: considerable amount of genetic variation is hidden from selection in form of recessive alleles
- recessive alleles less favourable than dominant counterparts or harmful in current environment can persist by
propagation in heterozygous individuals
- latent variation is exposed to natural selection only when both parents carry same recessive allele and two copies end
up in same zygote  rare if frequency of recessive allele is low
- heterozygote protection maintains huge pool of alleles that might not be favoured under present conditions but which
could bring new benefits if the environment changes
BALANCING SELECTION
- balancing selection: occurs when natural selection maintains two or more forms in population
- includes heterozygote advantage and frequency dependent selection
Heterozygote Advantage
- heterozygote advantage: heterozygote individual at particular locus have greater fitness than do both kinds of
homozygotes (heterozygous in genotype)
- natural selection maintains two or more alleles at that locus
- if phenotype of heterozygote is intermediate to phenotypes of both homozygotes, heterozygote advantage is a form
of stabilizing selection
- e.g. locus in humans that codes for beta polypeptide subunit of hemoglobin
o homozygous: certain recessive allele at locus causes sickle cell disease  damage
o heterozygotes: not enough blood cells become sickled to cause sickle cell disease
▪ protected against most severe effects of malaria  body destroys sickled red blood cells rapidly,
killing parasites they harbour (nut not affecting parasites in normal blood cells)
▪ in tropical regions: selection favours heterozygotes over homozygous dominant individuals who are
more vulnerable to malaria and over homozygous recessive individuals who develop sickle cell disease
▪ frequency of sickle cell allele highest in Africa

-
Frequency-Dependent Selection
- frequency dependent selection: fitness of phenotype depends on how common it is in population
- e.g. scale eating fish (Perissodus microlepis) in Africa: attack other fish from behind, darting into remove free scales
from prey
o some are left mouthed (recessive), some a right mouthed (dominant)
o left outhed fish atta k p e ’s ight fla k
o ight outhed fish atta k p e ’s left fla k
o prey species guard against attack from whatever phenotype of scale eating fish is most common in the lake
o selection favours whoever mouth phenotype is least common
o frequency of left and right mouthed fish oscillates over time  balancing selection keeps frequency of each
phenotype close to 50%
-
WHY NATURAL SELECTION CANNOT FASHION PERFECT ORGANISMS
1. selection can act only on existing variations
o natural selection favours only the fittest phenotypes  new advantageous alleles do not arise on demand
2. evolution is limited by historical constraints
o evolution does not scrap ancestral anatomy and build each new complex structure from scratch
o each species has a legacy of descent with modification from ancestral forms
o evolution co opts existing structures and adapts them to new situations
3. adaptations are often compromises
o humans: versatile hands and flexible limbs  prone to sprains dislocations etc.
▪ structural reinforcement compromised for agility
4. chance, natural selection, and the environment interact
o environment at particular location may change unpredictably from year to year  limits extent to which
adaptive evolution results in close match between organism and current environmental conditions

THE MODERN SYNTHESIS
-
- g adual : graded, smooth (not slow)
- saltationism: idea that populations have steady state for long time then undergoes sudden changes  alleles largely
affected
- Julian Huxley: wrote book Evolution: laid out ideas that came from a bunch of evolutionary biologists
-
o however, punctuated equilibrium: has been supported with some evidence
▪ once species appear in fossil records, they will become stable, showing little net evolutionary change
(no gradual speciation)
o neutralist theory/ movement: evolution is more about random change and caused by genetic drift of mutant
alleles that are neutral (not by natural selection)
o epigenetics etc.
MALARIA
PLASMODIUM
-
- plasmodium: has more than one host, primary (human) and secondary (mosquito) hosts

- malaria in Rideau Canal and Kingston

- Plasmodium falciparum is the most common species that causes most serious cases of malaria
INFECTION FROM MOSQUITOES
- merozoites circulate in blood and lives in RBCs  multiply by both asexually
o multiply sexually inside mosquito
o parasite bites another person etc. etc.
SICKLE CELL
- recessive allele; harmful effect on homozygous patients
- sickle cell allele in heterozygous patients  resistance to malaria
o first thought thalassemia was in high frequency in malaria infected regions
▪ homozygous: anemic symptoms etc.
-
JBS HALDANE
- Chippindale loves him (academic grandfather)
SICKLE CELL ANAEMIA BY ANTHONY ALLISON

-
- found high frequency of S allele in areas of malaria  pretty much the same except for few areas
-
o heterozygotes (carriers) suffer from less adhesion by the parasite to the blood cells  less capable for malaria
to complete life cycle
o i hi its pa asite’s a ilit to ultipl i li e
o red blood cells are destroyed in which parasites host in
- benefit of being a heterozygote outweighs risk of being homozygous

-
o balancing effect (stable equilibrium): heterozygote advantage  stabilizing selection
o frequency dependent natural selection
ANTI MALARIA TRAITS CANCEL OUT
- two anti malarial traits cancel each other out
- negative epistasis
- thalassemia + sickle cell allele  cancels protective effect
-
- where there are thalassemia genes, sometimes not sickle cell genes  for malaria resistance
-
o subtractive: not clearly understood why there is cancellation
- overlaps: due to people not interbreeding between cultures
LIFE CYCLE OF PLASMODIUM

-
- females bite (not males): need protein meal to produce eggs
- separate infections from separate female mosquitoes  competition between strains of plasmodium  competition
between itself inside human body  less gametocytes produced than they could
GENETIC DRIFT
o
- small population sizes  allele frequencies can change in response to random events
o fixations and extinctions possible
o heterozygosity can also decrease

- relative stability with large population; fixation vs. extinction

FOUNDER EFFECT
- change
FOUNDER FLUSH VS. BOTTLENECK
-
- founder event: new habitat could also lead to more diversification + unique opportunities to radiate into multiple
forms
- bottle neck: down to small size and recovers with different allelic frequencies
o e.g. northern elephant seal: heavily hunted  recovery  genetic diversity is dramatically lower than s. seals

- *A1A1 instead of AA
o heavy inbreeding possible  genetic revolution
o *chance of two individuals that go to the island being A1A1 = 0.66 = probability of losing A2
▪ rare allele lost 2/3 of the time due to founder effect
▪ loss in heterozygosity and genetic richness
- commonly lose less frequent alleles in founder effect and bottlenecks
- prairie chicken (Tympanicus cupuid) bottle neck example: decrease in alleles per locus and percentage of eggs hatched
o introduce other populations  introduce new variations  increase genetic diversity
o restoring only the habitat did no good  da age as al ead do e  extinction vortex  needs to introduce
individuals from other populations
o single male is successful in mating with every female in population through ritualistic displays
▪ effective population size may decrease if males are less than females
o conservation of prairie chicken
- extinction vortex:
o pg. 1332: consaguinance: CONSANGUINEOUS

-
SEX THE COSTS
-
- not all organisms have separate sexes (hermaphroditic) + many sexes may sometimes be beneficial
- most multicelled sexual organisms have two sexes  problem:
o why does it take two sexes to make offspring
TWO FOLD COST
-
1. parents have successfully passed themselves on

2. grandoffspring: only ¼ related to original parents
-
CLONES WIN, FAST
-
o if female due to mutation can asexually reproduce (single female)  twice the reproductive rate  does ’t
produce two different offspring
o sexually reproductive females disappear soon + males become rarer etc.
o what is the purpose of males then?
SEX: PAYING BACK THE COSTS

-
o advantages of sex
o variations in environment: must make offspring genetically different  bet hedging
o without sex, parasites may have more harmful effects
- H.J. Muller:
o
o over generations, offspring will almost certainly be same or worse than mothers through clonal reproduction
o recombination  by chance, gametes may have no mutations even though the two parents have mutations 
less mutant offspring than themselves
o Le ski’s E. oli: a utatio s e e eeded fo A3 to e a le to eta olize itrate  sexual reproduction
may have allowed this mutation to take place faster
▪ faster beneficial mutations in the same genome  better individuals/ evolution faster
o ruby in the rubbish: good mutations can escape from bad backgrounds
- G. C. Williams:

o
o oyster model: bet hedging idea, throwing out different offspring
o sex kicks in under stress  o ga is s k o that it’s ti e to se up
▪ offspring may be better next year and the year after that
o offspring may suffer from environment  decides to sex  recombinant that is better
THE RED QUEEN
-
- found that there is an equal extinction probability in all of the organisms whether they were successful or relatively
new arisen lineage
- nobody is safe: organism is preyed  more abundant, successful prey = more exploitation from other organisms
o the e’s alwa s so ethi g that will t to kill ou  a ’s a e
- evolution: organism vs organism
CURTIS LIVELY: RUNNING WITH THE RED QUEEN

-
- parasites have capacity to out evolve us (e.g. plasmodium)  humans have to keep changing their immune system
SEXUAL REPRODUCTION VS. SEXUAL REPRODUCTION
- asexual reproduction has a 2-fold advantage over sexual reproduction
o sexual organisms generally rely on two separate sexes: dependent on each other for reproductive output
SEX AND MUTATION: H. J. MULLER
-
- Muller believed that mutation was a negative process for multicelled organisms:
o mother dividing asexually can only make offspring that are genetically worse than herself  as mutations
de elop, the e’s o mechanism to purge those mutations
o genetic drift: losing genotype in finite populations  least fit genotypes may be lost in asexual population
- recombination helps recover less mutant, fitter genotypes in populations in sexually reproductive organisms 
stops the ratchet  advantage to sexual reproduction against accumulation of mutations
- sex may combine beneficial mutations:
o e.g. Le ski’s E. oli: lo al ep odu tio , afte 60 000 ge e atio s  citrate metabolizing mutation

▪ if sexual reproduction/ recombination occurred in E. coli, these mutations in several different

individuals may be recombined into one cell  brings together beneficial mutations  population
would adapt more rapidly compared to asexual reproduction (clonal interference)
- clonal interference: asexual organisms; when two or more different beneficial mutations arise independently in
different individuals  mutations cannot join to form organism carrying both of them  compete against each other
 loss of one of them  fate of fitness are effected for other variations in population
- if good utatio happe ed i i di idual li eage of lo fit ess ut it as ’t the est, it ould still be lost like other
poor genomes to extinction with no means of escaping (for asexual organisms due to clonal interference) (J.R. Peck)
SEX AND UNCERTAINTY: G.C. WILLIAMS
-
- some organisms have sexual process that is not the main type of reproduction:
o e.g. malaria: asexual reproduction predominates
o e.g. Daphnia: divide asexually in growing season (spring  fall)  can grow more rapidly in large numbers
and million different clones
▪ natural selection: by the end of the season, only 3 or 4 predominate populations in lakes
▪ at the end of season: they recombine in sexual process and mix up genotypes
- heterogonic life cycle: free living stage of life cycle of an organism that also has parasitic stage
o have sexual reproduction occasionally  enough to stop the ratchet and stop harmful mutations etc.
o asexual reproduction when they need to grow
- if genotype is not working in current condition  better to recombine sexually with another
o stress inducing the sexual reproductive mode
THE RED QUEEN HYPOTHESIS: LEIGH VAN VALEN

- Red Queen hypothesis: organisms must constantly adapt, evolve, and proliferate not merely to gain reproductive
advantage but also simply to survive while pitted against ever-evolving opposing organisms in an ever changing
environment
o explains constant extinction rates observed in paleontological record of competing species (coevolution)
o explains advantage of sexual reproduction as opposed to asexual reproduction
- organism becomes successful and abundant  becomes better target for opposing organism  under competition
from other opposing organisms
- pointless evolution: evolution between biotic factors (maybe coevolution)
RUNNING WITH THE RED QUEEN EVIDENCE: CURTIS LIVELY
- the Red Queen Hypothesis:
1. where sexual and asexual forms of the same organism coexist around the same zone, asexuals harbour more parasites
a. e.g. asexual Heteronotia geckoes in Australia, pupfish in Arizona: found to harbour many more mite
ectoparasites than sexually reproducing forms
b. parasites have dialed in number of clones  sexual species are more resilient
2. where parasites are more abundant in environment, sexual forms outcompete asexuals
a. e.g. NZ mudsnails, Potamapyrgus antipodarum: predominantly asexual females except in shallow lake waters
where ducks feed
- New Zealand mudsnails: found in fresh water; natural enemy = parasite microphallus
o
o microphallus grows in ducks, released as eggs, feeds on snails by castrating gonads and killing them, snails
release cysts  picked up by ducts as they feed
o shallow water: where you find sexual form of Potamapyrgus antipodarum  where ducks are pooping and
releasing eggs that infect snail  asexual snails would not be able to survive in this environment with parasite
o deep water: only asexual snails  they have the advantage here because parasites are limited
-
- when you get a clone, its inevitably driven down back to extinction or low frequencies
o
o
o lo e’s su ess is sho t li ed lo e that ises i shallo ate s ha e
▪ sexual parents often produce clonal offspring
- clones make great invaders: NZ mudsnail is evasive in North America; can breed rapidly as clones because their natural
deterrent (parasite) is not present

o
3. particular asexual genotypes have short term success before becoming rare
a. cycles of rise and fall in frequency – short term success of particular clones – over time within populations
(snails)
b. local adaptation of disease to host: parasites do best with hosts from same area (snails)
WHY TWO SEXES
ORIGINS OF ANISOGAMY: sexual reproduction involving fusion of two dissimilar gametes
- in most sexual species, one mating type produces large and nitrified gametes, whilst the other makes small gametes
virtually devoid of cytoplasm
1. SAFE SEX HYPOTHESIS
- in isogamy: gametes are same sized: fusion of gametes into zygote  has enough energy to grow and look after itself
after being provisioned
- endosymbiosis of primitive mitochondrion (textbook pg. 119 – 20, 552 – 553) from Rickettsia bacterium  created
e o ous o fli t et ee host ell a d its e guest
o primitive mitochondrion was a disease/ parasite that established itself in some Archaea
- sex would promote spread of more infectious strains of bacterium from cell to cell via cytoplasm fusion and sharing
o sex becomes a great vehicle for bacterial transmission: cell to cell fusion between isogametes in sexual
reproduction
o if host ell had a e dos io t that was e efi ial a d was ’t as i fe tious  becomes resident and forms
mutualistic relationship (like mitochondria; domesticated)
▪ when isogametes are shared with one that is infected with the bad strain  nasty bacteria will win
battle and ruin mutualistic relationship
- early Eukaryote that had more cooperative endosymbionts would have competitive edge growing asexually
o but such a relationship would be vulnerable to invasion and displacement by nasty bacteria
- ga etes that do ’t a ept toplas f o othe , just u lei, just DNA:
o e.g. fungi, sperm going into egg
▪ sperm mitochondria are carefully removed/ avoided (very few exceptions)
o resulting zygote is small  poor survival probability
o gain advantage of sex from DNA, but disadvantage in gaining energy
o gain advantage in maintaining cooperative relationship of endosymbiont  grow asexually and dominate
with good genotypes, but disadvantage in gaining energy
o  gamete producer will make its gametes larger
o selection will favour a gamete producer that makes smaller gamete that can find the big gametes
(endosymbiotic team gamete)
- one sex keeps its cytoplasm, other gamete producer produces gametes that are small and less nutritified  no
cytoplasm with only flagella to find those well nourished gametes  big pay off
FEMALE FIRST HYPOTHESIS: SAFE SEX

o creation of oocytes that can supply nourishment to zygote  opportunity for another gamete producer to
produce smaller gametes
- origin of eukaryotes
o eukaryotes and Archaean are closely related more than bacteria
o Rickettsiales are bacteria that infect cells and grow in cytoplasm (parasite)  origin of mitochondria
MALE FIRST: DEADBEAT DADS
- if everyone makes isogametes (isogamy):
o if o e i di idual akes heape s alle ga etes i a la ge a ou t  high fertilization frequencies but low
zygote survival probabilities  this gamete producer is parasitizing other individuals  parasitic male theory
- parasitic male theory: one gamete producer forces other gamete producers to enlarge gametes in response
o tradeoff between size and number: some play numbers game, some play quality game (variation)
o variation between size and survival
o ancestrally: two medium sized cells produced a fair zygote
▪ if one gamete producer cheats and makes smaller gametes  lower zygote survival probability 
drives disruptive process  disruptive process: other gamete producer enlarges its gamete in
response
▪ other way around: one enlarges its gametes and puts lots of energy in (egg), another one producing
medium sized gamete does not have an advantage for its medium size
- generating disruptive selection: one playing numbers game will drive the other to play quality game vice versa
-
o medium sized gametes is losing strategy: either undernourished or overnourished
o isogamy is unstable because it can lead to cheating
SEX AND MULTICELLULARITY

POWER STRUGGLE
- the more complicated and larger an organism gets  the more fuel/ energy it takes to nourish itself (e.g. freespawning
organisms) = energy had to be in the egg
- zygote needs more nourishment to grow to point where it can acquire energy for itself
- gender differentiation:
o one sex produces inexpensive gametes in huge numbers
o one sex produces energetically costly, small number gametes  more careful who fertilizes it
o characteristic role of females being discriminate and males being indiscriminate in mate choices
- e.g. volvocene algae/ group: resembles particular single celled free living algae
o have both sexual and asexual reproduction in response to stress
o increase in size and complexity

o how multicellularity arose: rise of anisogamy from isogamy  oogamete
-
CONFLICT BETWEEN THE SEXES
- separate sexes that are dependent on each other  organisms which can be physiologically different trying to
maximize their outcome  conflict: arms race + tug of war between sexes
- females and males are in disagreement about mating
- about controlling access to the eggs (precious resource)
ARMS RACE
- one sex has adaptation to exploit the other  other sex evolves defense against exploitation

- Red Quee p o ess

1. direct conflict over mating: Locke Rowe, Goran Arnqvist
a. pond striders/ water striders: above image, male is trying to mount female against her wishes
b. sexual dimorphism:
ale’s appe dage is o e g izzl  uses it to grab into female by penetrating through eyeball
i. + specialized hair structures + adhesive pads  forces fertilizaion
c. in response: female striders are larger, have spines + other defenses against males to control mating
2. sexual conflict in Drosophila: Bill Rice
a. Drosophila is a promiscuous species: practice of having casual sex frequenty with different patners or being
indiscriminate  sexual conflict is always greater in promiscuous species than monogamy  advantage to
males who can gain many mates
b. in monogamy: female reproductive = male reproductive success in true monogamy  eliminates sexual
conflict
c. Drosophila has tricks (like other organisms) for their reproductive success:
i. harass females by following them, chase them, buzz wing at them  reduces female lifespan and
reproductive output
ii. mating: males have spine that anchors them during mating  wounding and potential infection
transmission (harming effect from mating)
iii. seminal fluid: he i al o ktail ith to s of fu k i the spu k a d demon in the semen
1. Rice allowed males to adapt to particular strain of females: those females became better at
courting and inducing egg lays of females and booting other sperm from other males
-
- Drosophila: chemical warfare:

o
▪ changes conformation of oviduct etc.  beneficial for male
▪ introduces chemicals that decrease female interest with other males
▪ proteins that modify composition of epicuticle of female  changes olfactory appearance  makes
her less attractive to other males
▪ against postcopulatory sexual selection competition: males release chemicals in seminal fluid that
help expel other sperms or incapacitate those sperms (second male will leave 80% of sperm)
- postcopulatory sexual selection: competition between sperm of different males in female
▪ toxicity of seminal fluid: reduces female survival  side effect and not adaptation
Bio Week 21 Textbook Notes
APICOMPLEXANS

- apicomplexans: protist in a clade that includes many species that parasitize animals
o some cause human disease
o parasites spread through their host as tiny infectious cells of sporozoites
o one end (apex) of the sporozoite cell contains complex of organelles specialized for penetrating host cells and
tissues
o recent data show that apicomplexans retain a modified plastid (apicoplast) most likely of red algal origin
- both sexual and asexual stages for apicomplexans
- life cycle often requires two or more host species for completion
PLASMODIUM
- parasite that causes malaria, lives in both mosquitoes and humans
- insecticides that reduced carrier populations of Anopheles mosquitoes and by drugs that killed Plasmodium in humans
were used
o  emergence of resistant varieties of both Anopheles and Plasmodium  resurgence of malaria
- plasmodium lives mainly inside cells  hidde f o host’s i u e s ste  hard to find vaccines
- like trypanosomes, Plasmodium continually changes its surface proteins

Concept 46.1 Both asexual and sexual reproduction occur in the animal kingdom
- sexual reproduction: fusion of haploid gametes forms a diploid cell, zygote
o female gamete = egg = large nonmotile cell
o male gamete = sperm = smaller, motile cell
- asexual reproduction: generation of new individuals without fusion of egg and sperm
o most asexual animals: reproduction relies entirely on mitotic cell division
- for most animals: reproduction is primarily or exclusively sexual
o few all-female species: reproduction is exclusively asexual  e.g. bdelloid rotifer + certain species of whiptail
lizard (Aspidoscelis)
MECHANISMS OF ASEXUAL REPRODUCTION
- fission: separation of parent organism into two individuals of approximately equal size
- budding: new individuals arise from outgrowths of existing ones
- e.g. stony corals: buds form and remain attached to parent  result in colony more than 1 m across consisting of
thousands of connected individuals
- some invertebrates: e.g. sponges; release specialized groups of cells that can grow into new individuals
-
- fragmentation + regeneration: breaking of body into several pieces followed by regrowth of lost body parts
o if more than one piece grows and develops into complete animal  reproduction
o e.g. certain annelid worms: can split their body into several fragments each regenerating complete worm in
less than a week
o e.g. numerous sponges, cnidarians, bristle worms, sea squirts
- parthenogenesis: asexual reproduction in which egg develops without being fertilized
o e.g. certain species of bees, wasps, ants
o progeny can be either haploid or diploid
▪ haploid progeny  offspring develop into adults that produce eggs or sperm without meiosis
• e.g. honeybees, males (drones) are fertile haploid adults that arise by parthenogenesis
• e.g. female honeybees are diploid adults that develop from fertilized eggs
▪ 1/1000 species of vertebrates use parthenogenesis where females had been kept completely isolated
from males of their species but nevertheless produced offspring
SEXUAL REPRODUCTION: AN EVOLUTIONARY ENIGMA
EVOLUTION
- ½ females produce sexually, ½ females produce asexually
o two offspring of asexual female will both be daughters that will each give birth to 2 more reproductive
daughters
o ½ of se ual fe ale’s offsp i g ill e ale

▪ number of sexual offspring will remain same at each generation because both male and female are
required to reproduce  asexual condition will increase in frequency at each generation but sex is
maintained
- advantage of sex: unique combinations of parental genes formed during meiotic recombination and fertilization
o may enhance reproductive success of parents when environmental factors such as pathogens change
relatively rapidly
o beneficial gene combinations  speed up adaptation  rate of beneficial mutations is high and population
size is small
o shuffling of genes  allows population to rid itself of sets of harmful genes more readily
- asexual reproduction advantage: advantageous in stable, favourable environments because it perpetuates successful
genotypes faithfully and precisely
-
REPRODUCTIVE CYCLES
- animals conserve resources, reproducing only when sufficient energy sources or stores are available and when
environmental conditions favour the survival of offspring
- ovulation: release of mature eggs, occurs at midpoint of each reproductive cycle
o e.g. ewes (female sheep): cycle generally occurs only during fall and early winter and length of any resulting
pregnancy is 5 months  most lambs are born in early spring when their chances of survival are optimal
- reproductive cycles are controlled by hormones, which in turn are regulated by environmental cues
o climate change can decrease reproductive success
- reproductive cycles found among animals that can reproduce both sexually and asexually
o e.g. water flea (Daphnia): female can produce eggs of two types  one egg requires fertilization, other
develops by parthenogenesis
▪ favourable environment  asexual reproduction
▪ environmental stress  sexual reproduction
- reproductive cycle among animals that only reproduce asexually:
o e.g. genus of fishes, amphibians, reptiles: complex parthenogenesis that involves doubling of chromosomes
after meiosis, producing diploid offspring
o e.g. 15 species of whiptail lizards in Aspidoscelis: no males but courtship and mating behaviours are typical of
sexual species of same genus
▪ during breeding season, one female of each mating pair mimics male
▪ each member of pair alternates roles two or three times during season
▪ individual adopts female behaviour prior to ovulation when level of female sex hormone estradiol is
high, then switches to male-like behaviour after ovulation when level of progesterone is highest

▪ ovulation more likely to occur in individual mounted during critical time of hormone cycle: isolated
lizards lay fewer eggs than those that go through motions of sex
▪ parthenogenetic lizards evolved from species having two sexes and still require certain sexual stimuli
for maximum reproductive success
VARIATION IN PATTERNS OF SEXUAL REPRODUCTION
- blurring strict distinction between male and female  overcoming challenge for finding sexual partner
o e.g. sessile (stationary) animals: barnacles
o e.g. burrowing animals: clams
o e.g. some parasites: tapeworms
o lack of locomotion  limited opportunity to find mate  hermaphroditism
- hermaphroditism: each individual has both male and female reproductive systems
o produces as both a male and a female, any two individuals can mate
o each animal donates and receives sperm during mating (e.g. sea slugs)
o sometimes capable of self fe tilizatio : allowi g a fo of se ual ep odu tio that does ’t e ui e a
partner
- e.g. bluehead wrasse (Thalassoma bifasciatum), coral reef fish: live in harmens each consisting of a single male and
several females
o lone male dies  female wrasse undergoes sex reversal (change in sex)
o transformed individual is producing sperm instead of eggs
o largest (usually oldest) female in harem undergoes sex reversal  larger size may be more important for
males than females in ensuring successful reproduction (defense against intruders)
- e.g. some oysters: undergo sex reversal
o individuals reproduce as males and then later as females when their size is greatest
o # of gametes produced increases with size much more for females than males  sex reversal in this direction
maximizes gamete production  enhanced reproductive success
o oysters are sedentary animals and release gametes into surrounding water rather than mating directly 
releasing more gametes  more offspring
Concept 46.2 Fertilization depends on mechanisms that bring together sperm and eggs of the same species
- fertilization: union of sperm and egg  can be external or internal
- external fertilization: female releases eggs into environment where male fertilizes them
1. moist habitat: required for external fertilization  prevents gametes drying out + allows sperm to swim to
eggs
2. correct timing
o spawning: individuals clustered in same area release gametes into water at same time (can be triggered by
chemical signals or environmental cues (T, day length) can cause whole population to release gametes at one
time)
o e.g. palolo worm: times its spawning to both season and lunar cycle
▪ spring (moon in last quarter): palolo worms break in half  releases tail segments engorged with
sperm/ eggs  rise to ocean surface  burst in vast numbers (milky with gametes)  sperm quickly
fertilize floating eggs
o non synchronous fertilization across population: individuals may exhibit specific mating behaviours leading to
fertilization of eggs of one female by one male (courtship)
o courtship behaviour:
1. allows mate choice
2. increases probability of successful fertilization by triggering release of both sperm and eggs
- internal fertilization: sperm deposited in or near female reproductive tract and fertilization occurs within tract
o enables sperm to reach egg efficiently even when environment is dry
o requires cooperative behaviour that leads to copulation + sophisticated and compatible reproductive systems
o male copulatory organ delivers sperm
o female reproductive tract often has receptacles for storage and delivery of sperm to mature eggs

o production of fewer gametes but survival of higher fraction of zygotes  eggs fertilized internally 
sheltered
- pheromones: chemicals released by one organism that can influence physiology and behaviour of other individuals
o small volatile or water soluble molecules that disperse into environment and are active in tiny amounts
o mate attractants etc.
ENSURING THE SURVIVAL OF OFFSPRING
- internal fertilization has mechanisms that provide greater protection of embryos and parental care of young
- internally fertilized eggs of species of terrestrial animals: adaptations that protect against water loss and physical
damage during external development
- birds and other reptiles + monotremes (egglaying): zygote consist of eggs with calcium, protein containing shells and
several internal membranes
- fishes and amphibians: only have gelatinous coat and lack internal membranes in eggs of fishes
- marsupial mammals (e.g. kangaroos, opossums): spend only short period in uterus  embryos crawl out  complete
fetal de elop e t atta hed to a a gla d i othe ’s pou h
- eutherian (placental) mammals (e.g. humans): remain in uterus throughout fetal development  nourished by
othe ’s lood suppl th ough pla e ta
- some fishes, sharks: complete development internally although typically embryo and mother lack connection for
nutrient exchange
- newborn is not yet capable of independent existence:
o e.g. gastric brooding frogs (Rheobatracus): during reproduction, female frog would carry tadpoles in her
stomach until they underwent metamorphosis and released out of mouth as frogs
-
GAMETE PRODUCTION AND DELIVERY
- sexual reproduction in animals relies on sets of cells that are precursors for eggs and sperm
o cycles of growth and mitosis increase  amplify number of cells available for making sperm and egg
- simplest systems do not even include discrete gonads (e.g. palolo and most other polychaete worms Annelida)
o eggs and sperm develop from undifferentiated cells lining coelom (body cavity) for Annelida
- gonads: organs that produce gametes in most animals
- depending on species, gametes may shed through excretory opening, or, swelling mass of eggs may split portion of
body open and spilling eggs into outside
- elaborate reproductive systems: sets of accessory tubes and glands that carry, nourish, protect gametes
o e.g. most insects: separate sexes with complex reproductive systems
▪ males: sperm develop in pair of testes  passed along coiled duct to two seminal vesicles
▪ mating: sperm ejaculated into female reproductive system
▪ eggs develop in pair of ovaries and conveyed through ducts of uterus
▪ eggs fertilized in uterus and expelled for development outside body

-
o sperathecae: sacs in which sperm may be stored for extended periods
o female releases male gametes from spermatheca only in response to appropriate stimuli  fertilization occurs
under conditions likely to be well suited to embryonic development
- variations:
o nonmammalian vertebrates: digestive, excretory, reproductive systems have common opening to outside =
cloaca: structure that was present in ancestors of all vertebrates probably
o mammals: generally lack cloaca and have separate opening for digestive tract
o most female mammals: separate openings for excretory and reproductive systems
o most vertebrates: uterus is partly or completely divided into two chambers
o humans and other mammals that only produce 1 or few young at a time: uterus is a single structure (also in
birds and many snakes)
o male reproductive systems differ mainly in copulatory organs:
▪ most fish: simply release sperm outside without aid of copulatory organ
▪ some fish: use pelvic fins that fold together to produce channel for sperm transfer
▪ most reptiles: simply empty cloaca to release sperm but have penis like structures that insert into
female reproductive tract
- monogamy: sustained sexual partnership of two individuals: relatively rare among animals including most mammals
- mechanisms that enhance reproductive success of male with particular female and diminish chance of female mating
successfully with another partner:
o e.g. some male insects transfer secretions that make female less receptive to courtship  reduces likelihood
of mating again (e.g. Drosophila melanogaster)
o e.g. female fruit flies play a major role in determining reproductive outcome of multiple mating

-
Chapter 51 Animal Behaviour
- behaviour: action carried out by muscles under control of nervous system in response to stimulus (based on
physiological systems and processes)
o subject to natural selection over time
Concept 51.1 Discrete sensory inputs can stimulate both simple and complex behaviours
- Niko Ti e ge ’s fou uestio s i u de sta di g eha iou :
1. what stimulus elicits behaviour, what physiological mechanisms mediate response
2. ho does a i al’s e pe ie e du i g g o th a d de elop e t i flue e espo se
3. how does behaviour aid survival and reproduction
4. hat is eha iou ’s e olutio a histo
o proximate causation: how behaviour occurs/ modified
o ultimate causation: why behaviour occurs in context of natural selection
- behavioural ecology: study of ecological and evolutionary basis for animal behaviour
FIXED ACTION PATTERNS
- Ti e ge ’s e pe i e t:
o fish tanks containing threespined sticklebacks (Gasterosteus aculeatus)
o male sticklebacks (with red bellies) attack other males invading nesting territories
▪ male sticklebacks also behaved aggressively when red truck passed in front of tank
▪ ed olou of i t ude ’s u de side p o okes attack behaviour  fixed action pattern
- fixed action pattern: sequence of unlearned acts directly linked to simple stimulus (trigger = sign stimulus)
o essentially unchangeable and once initiated usually carried to completion
- sign stimulus: external cue
MIGRATION
- environmental stimuli are a trigger + provides cues that animals use to carry out those behaviours
- e.g. many birds, fishes, other animals use environmental cues to guide migration (regular, long distance change in
location)
- some animals track thei positio elati e to su a d adjust fo su ’s positio elati e to Ea th hi h ha ges
throughout day) by means of circadian clock
o circadian clock: internal mechanism that maintains 24 hour activity rhythm/ cycle
o e.g. migrating birds orient differently relative to sun at distinct times of day
- nocturnal animals: use North Star which has constant position in night sky
- e.g. homing pigeons and cloudy days:
o placing small magnet on head of homing pigeon  prevents it from returning efficiently to its roost
o pigeo s a se se thei positio elati e to Ea th’s ag eti field the e a igate ithout sola ues
- heads of migrating fishes and birds contain bits of magnetite  Ea th’s ag eti field a affe t ag etite o tai i g
structures  transmission of nerve impulses to brain
o o ag eti field effe t o photo e epto s i e e a i als see ag eti field
BEHAVIOURAL RHYTHMS
- circadian clock: circadian rhythm with daily cycle of rest and activity that affects behavioural physiology
o normally synchronized with light and dark cycles of environment but can maintain rhythmic activity under
constant environmental conditions (e.g. hibernation)
- circannual rhythms: behavioural rhythms linked to yearly cycle of seasons

o influenced by periods of daylight and darkness (artificial environ. with extended daylight  induce
outofseason migration)
- e.g. William Rowan experiment: depending of different light cycles, crows flew in different directions corresponding
to what they would do in normal conditions that had those particular light cycle
ANIMAL SIGNALS AND COMMUNICATION
- signal: stimulus transmitted from one animal to another
- communication: interactions between individuals = transmission + reception of signals
FORMS OF ANIMAL COMMUNICATION
- Drosophila melanogaster: courtship constitutes stimulus-response chain
o stimulus response chain: response to each stimulus is itself the stimulus for the next behaviour
1. male identifies female and orients body toward hers
2. male sees and turns toward female  visual communication
3. fl ’s olfa to s stem detects chemicals released into air
4. females detect odours emanating from exoskeleton/ cuticle of males  chemical communication:
transmission and reception of signals in form of specific molecules
5. male approaches and taps female with foreleg  tactile communication (touching)
6. he i als i fe ale’s a do e a e t a sfe ed to ale  chemical conformation
7. male extends and vibrates wing producing specific courtship song  auditory communication
8. copulation
-
- von Frisch experiment: honeybee Apis melifea: uses da e la guage that etu i g fo age s use to i fo othe
bees about distance and direction of travel to food sources
o food source is close to hive: returning bee moves in tight circles while wangling abdomen from side to side =
round dance  motivates follower bees to leave hive
o food source far: waggle dance = half circle swing and straight run  communicates both direction and distance
of food source in relation to hive
▪ some clever ass angle measurement dance
▪ greater distance to food source = dance with longer straight run, more abdominal waggles/ run

PHEROMONES
- pheromones: communicative odours/ tastes emitting chemical substances (many mammals, insects, reproduction)
- e.g. chemical communication when female fruit flies attract males during courtship
- not limited to short distance signalling
- e.g. male spruce budworm moths: have receptors that an detect pheromone from female from kms away
o moths are together  pheromones also trigger specific courtship behaviours
- e.g. honeybee colony: queen produces pheromones  daughte s, o ke s, ai tai hi e’s so ial o de
o queen substance (pheromone): attracts workers to queen  inhibits development of ovaries in workers 
attracts males (drones) to queen during her mating flights out of hive
- e.g. alarm substance of fish: injured fish  skin cells release chemicals  conspecifics detect substance  exhibit
fright response  more vigilant, form tightly packed aggregations
o not pheromones because they are released (only when damaged) and not secreted
- form of o u i atio that e ol es is losel elated to a i al’s lifest le a d e i o e t: e.g. ats, ole ates usi g
olfactory and auditory signals
- stimuli activate sensory systems  processed in CNS  result in motor outputs that constitute behaviour
Concept 51.3 Selection for individual survival and reproductive success can explain most behaviours
FORAGING BEHAVIOUR
- foraging: activities an animal uses to search for, recognize, and capture food items (subject to natural selection)
EVOLUTION OF FORAGING BEHAVIOUR
- Drosophila melanogaster fruit fly: variation in forager (for) gene dictates foodsearch behaviour of fruit fly larvae
o enzyme encoded by forager locus is more active in for(R) larvae than in for(s) larvae and has properties typical
of enzyme in signal transduction pathway  larvae can travel nearly twice as far while feeding
o larvae maintained for many generations at low density foraged over shorter distances than those kept at high
density
o for(s) allele had increased in frequency in low density populations whereas for(R) allele had increased in high
density group
OPTIMAL FORAGING MODEL
- optimal foraging model: natural selection should favour foraging behaviour that minimizes costs (risks) of foraging
and maximizes benefits (of nutrients)
- North western crow (Corvus caurinus) by Reto Zach: the higher the crow flies, the greater the force with which the
whelk (prey) strikes the rocks  flying higher = consuming more energy
o Zach determined that height of 5m is optimal  crows fly to height 5.23m
- optimal foraging model reflects selective forces shaping evolution of behaviour
BALANCING RISK AND REWARD
- predation risk can affect foraging behaviour
- mule deer (Odocoileus hemionus): risk of predation differed greatly across uniform foraging areas
o major predator = mountain lion = at forest edges and only small number in open areas and interiors  mule
deer feed predominantly in open areas  reflects large variation in predation risk and not smaller variation
in food availability (food is constant throughout)
MATING BEHAVIOUR AND MATE CHOICE
MATING SYSTEMS AND SEXUAL DIMORPHISM
- promiscuous mating: relationship in which mating occurs with no strong pairbonds or lasting relationships
- monogamous: one male mating with one female
- polygamous: individual of one sex mating with several of other  most often involve single male (polygyny) and
sometimes polyandry (single female)
o generally dimorphic with males being showier and often larger
o polyandrous: dimorphic but females are generally more ornamented and larger

- sexual dimorphism: extend to which males and females differ in appearance

MATING SYSTEMS AND PARENTAL CARE
- male that stays with and helps single mate may ultimately have more viable offspring than it would by going off to
seek additional mates (most birds are monogamous)
o for birds with young that can feed and care for themselves almost immediately after birth, males derive less
benefit from staying their partner  polygyny
- mammals: lactating female is often only food source  males play no role in raising young
o some species protect females and young (lion): male or small group of males typically takes care of harem of
females at same time
- e tai t of pate it : ale othe tha fe ale’s usual ate a ha e fathe ed that of fe ale’s offsp i g  certainty
of paternity is relatively low in most species with internal fertilization because acts of mating and birth are separated
over time
o  male parental care is rare in bird and mammal species
o males of many species with internal fertilization engage in behaviours that appear to increase their certainty
of paternity (e.g. guarding females, removing any sperm from female reproductive tract before copulation,
introducing large quantities of sperm that displace other sperm)
- high certainty of paternity when egg laying and mating occur together (external fertilization)
o  parental care in aquatic invertebrates, fishes, amphibians is at least likely to be by males as by females
o parental care occurs in only 7% of species with internal fertilization but in 69% of species with external
fertilization among fishes and amphibians
- parental behaviour correlated with certainty of paternity exists because it has been reinforced over generations (n.s.)
SEXUAL SELECTION AND MATE CHOICE
- degree of sexual dimorphism within a species results from sexual selection, a form of natural selection in which
differences in reproductive success among individuals are a consequence of differences in mating success
- sexual selection:
o intersexual selection: members of one sex choose mates on basis of characteristics of other sex
o intrasexual selection: involves competition between members of one sex for mates
Mate Choice by Females
- stalk-eyed flies: their eyes are at tips of stalks which are longer in males than in females
o courtship male approaches female headfirst
o females are more likely to mate with males that have relatively long eyestalks
o ornaments such as long eyestalks in these flies and bright colouration in male birds correlate in general with
ale’s health a d italit
- zebra finches: mate choice influenced by imprinting
o both male and female zebra finches normally lack any feather crest on their head
o researchers taped long red feather to forehead feathers of either or both zebra finch parents 2 days before
chicks opened eyes
o females raised by ornamented male parent preferred ornamented males as their own mates  female
finches apparently take cues from their fathers in choosing mates
- mate choice copying: behaviour in which individuals in population copy the mate choice of others
o e.g. Poecilia reticulata: when female guppy chooses between males with no other females present, female
almost always chooses male with more orange colouration
▪ if female guppy observed model courting a male with less extensive orange markings, she often copied
preference of model female  female chose male that had been presented in association with model
female rather than more orange alternative
▪ mate choice behaviour typically did not change when difference in colouration was large  mate
choice copying can mark genetically controlled female preference below certain threshold of
difference
- female that mates with males that are attractive to other females increase probability that her male offspring will also
be attractive and have high reproductive success

-
Male Competition for Mates
- male competition may involve agonistic behaviour, often ritualized contest that determines which competitor gains
access to a resource such as food or mates  outcome determined by strength/ size  psychological consequence
- behavioural and morphological variation in males is extremely high in some vertebrate species
- in some species sexual selection led to evolution of alternative male mating behaviour and morphology
- game theory to analyze where more than one mating behaviour can result in successful reproduction
APPLYING GAME THEORY
- often, fitness of behavioural phenotype is influenced by other behavioural phenotypes in population  game theo.

- game theory: evaluates alternative strategies in situations where outcome depends on strategies of all individuals
involved
- e.g. side-blotched lizard: males have orange, blue, yellow throats and each is associated with different pattern of
behaviour  orange throat males are most aggressive and defend large territories that contain many females
o blue throat males are territorial but defend smaller territories and fewer females
o yellow throats are nonterritorial males that mimic females and use sneaky tactics
o mating success of each male type is influenced by relative abundance of other types (frequency dependent
selection)
o each type of male lizard has advantage over one of the other two types
o blue throats are abundant  defend few females in their territories from advances of yellow throats
▪ blue throats cannot defend against hyperaggressive orange throats
o orange throats become abundant  larger number of females in each territory provides opportunity for
yellow throats to have greater mating success
o yellow throats become more frequent but give way to blue throats
- relative performance, not absolute performance, is key to understanding evolution of behaviour

Concept 24.4 Speciation can occur rapidly or slowly and can result from changes in few or many genes
THE TIME COURSE OF SPECIATION
PATTERNS IN THE FOSSIL RECORD
-
- punctuated equilibria: describes periodic apparent stasis punctuated by sudden change (other species do not show
punctuated pattern  change more gradually over long period)
o punctuated pattern indicates speciation occurred relatively rapidly
- species whose fossils changed more gradually: cannot tell exactly when new species formed since information about
reproductive isolation does not fossilize (probably gradual speciation)
SPECIATION RATES
-
- Helianthus anomalus wild sunflower: rapid speciation production; originated by hybridization of two other sunflower
species
o anomalus is reproductively isolated and ecologically different; two parent species and hybrid all have same
number of chromosomes
o natural selection could produce extensive genetic changes in hybrid populations over short periods of time 
appear to have caused hybrids to diverge reproductively from parents
- new species can arise rapidly once divergence begins
- time interval: time that elapses before populations of newly formed species start to diverge from one another plus
time it takes for speciation to be complete once divergence begins
o varies considerably: could be millions of years before nearly formed species will itself give rise to another spec.
o orgnisms do not have speciation clock causing them to produce new species at regular time intervals
o speciation begins only after gene flow beween populations is interrupted perhaps by changning
environmental conditions or by unpredictable events such as storms

STUDYING THE GENETICS OF SPECIATION

- few cases, evolution of reproductive isolation is due to change in single gene
o e.g. Japanese snails  change in single gene  mechanical barrier to reproduction (change in genitalia orient.)
o e.g. monkey flower Mmulus cardinalis and M. lewisii: due to small number of genes  isolated by several
prezygotic and postzygotic barriers
▪ hummingbirds prefer red flowered M. cardinalis and bumblebees prefer pink fowered M. lewisii
▪ pollinator choice is affected by at least two loci in monkey flowers: yellow upper (yup) locus influences
flower colour  M. lewisii plants with M. cardinalis yup allele received more visits from hummingbirds
than did wild type M. lewisii
▪ M. cardinalis plants with M. lewisii yup allele received more visits from bumblebees than did wild type
M. cardinalis
▪ mutation at single locus can influence pollinator preference and hence contribute to reproductive
isolation in flower monkeys
- speciation with large numbers of genes/ interactions: hybrid sterility between two subspecies of Drosophila
pseudoobscura results from gene interactions among at least 4 loci
o postzygotic isolation in sunflower hybrid zone influenced by at least 26 chromosome segments
o few or many genes can influence evolution of reproductive isolation and hence emergence of new species
FROM SPECIATION TO MACROEVOLUTION
- as speciation occurs again and again  differences accumulate  become more pronounced  formation of new
groups of organisms that differ greatly from their ancestors
- as one group of organisms increases in size by producing many new species  another group of organisms may shrink,
losing species to extinction
- all these may lead to evolutionary changes documented in fossil records


BIOLOGICAL SPECIATION
-
- biological species concept: can interbreed with each other
o cannot test with asexual species, cannot test with fossils
o hybrid may live but may be sterile/ partially sterile
o similar species but do not interbreed
MALLARD AND BLACK DUCK: ANAS PLATYRYNCHUS VS. ANAS RUBRIPES
- co-occur in North America but do not interbreed; hybrids are viable fertile
- separated by breeding habits etc. grey areas in speciation definition
-
SEX CHROMOSOMES AND FERTILITY: HALDANE’“ RULE AND THE MULE
- mule = offspring of horse vs. donkey  one of the sexes is infertile
o XY sex is the infertile offspring  Haldane made a rule about this
o heterogametic sex is the one that is infertile
- incompatibility of the XY chromosomes etc.

- mule = donkey jack vs. horse mare
- mule = donkey jack (male) x horse mare (female); more common
- hinny = horse stallion (male) x donkey jennet (female)
o really hard to get stallions to mate with jennets  more unusual
SETTINGS FOR SPECIATION
- divergence in allopatry: physical isolation
o barrier between physical regions
- sympatry/ parapatry:
o sympatry: ranges overlaps  no barrier to gene flow
▪ may be common (had many skeptics)
o parapatry: allopatric ranges touch and where populations meet: potential for gene flow to happen

-
o separation of populations: divergence possibly due to adaptations on different environments, genetic drift
o genetic differences accumulate  postzygotic isolation
o postzygotic isolation: after the zygote forms
▪ zygote does not survive very well or infertile offspring
▪ reduced fitness of hybrids
o  could lead to prezygotic isolation: discrimination against breeding with the other species do better than
those that cannot discriminate
▪ individual that selects its own species does better than mating with other species = reinforcement
• mate choice helps prevent reduced fitness of offspring
-
o divergence (allopatry etc.)  sexual conflict etc.
o  leads to prezygotic isolation arising first: incompatible mating signals (e.g. conflict has modified their
genitalia): isolation before mating
o  could lead to postzygotic isolation since gene flow is limited between the two populations  hybridize less
and less well
RING SPECIES: GREENISH WARBLERS
- shows that speciation can occur with possibility with gene flow between populations
- one of few known systems of ring type distribution: believed that they originated from south and has spread
northward in both directions (usually live in high altitudes)
o adapted at lower altitudes but further north where it is still cooler
o used to be continuous by deforestation has made some parts unsuitable
o spread around the Tibetan plateau to the east and the west in simultaneous fashion
- in Siberia: potential hybrid zone: but birds do not hybridize
o cline of genetic variation: most dissimilar at Siberia (meeting zone): differentiation south to north
- southern birds (ancestral) have simple song form, north birds have complex song forms
o complicated songs in both species of greenish warblers in Siberia but quite different  females will not accept
the song of the other subspecies
- similar birds, bar on its wings are different: P. t. virdanus vs. P. t. plumbeitarsus
- continuous distribution yet gene does not flow in meeting zone

SPECIOSITY (ADAPTIVE RADIATION): CICHLIDS

- what makes them so speciose and diverse: radiating into multiple forms (adaptive radiation)
o territorial: defends own territory
o adaptable, unique mouthparts: pharyngeal jaws (inside of their throat: crack things)  can eat wide variety
of food sources  successful
o body forms can be variable (lability in body form)
o exhibit strong mate choice: strong chromatic, bright ornamentation allows both mate choice and species
discrimination
▪ run off from fertilizers and chemicals in Riff Lakes  nutrification  algae blooms, cloudy waters etc.
 cichlids cannot see each other  cannot avoid hybridization  merges together (diversity declines)
o many reproductive strategies/ breeding strategies: cooperative breeders (nesters, moothbrooders), free
spawners, many strategies in between
o flexibility in life style etc.  cichlids are very diverse
- species flocks (diversity of species) of lake Malawi:
o
o scale eaters/ fin eaters: often sided, specialized to be righties or lefties  prey look over the particular side
more  negative frequency dependence
o mouthbrooder paedophage: stealing young out of other fishes mouths
SYMPATRIC SPECIATION? IN LAKE MALAWI: HELPED BY FRAGMENTATION OF HABITAT
- bathymetry: alternating substrate (boulders etc.)
- fishes are territorial  do not move that much  long established community between rocks
- brood young: young do not disperse all over the place
- Malawi is deep: cichlids would not cross the open water  do not move along coast  isolation
o west side isolated from east side; deep and anoxic below 250m
o sympatric speciation? same like but probably more fragmentation than expected
RADIATION OF CICHLIDS IN CAMEROONIAN VOLCANO LAKE
- small and simple crater lakes: nothing blocking gene flow
- colonized by single species  differentiation into different species within lakes based upon breeding habits etc.
- ability to differentiate in rapid pace: sympatric speciation
- mini species flocks in tiny crater lakes: 9+ monophyletic species  sympatric speciation
SPECIATION MACHINE: RICE AND SALT
- speciation machine: allowed animals to start off in common chamber but move to one of eight different
environmental circumstances: geotaxis, dark/ light, acetaldehyde (disliked)/ ethanol (liked)
- flies are expected to: go up, light chamber, ethanol
o limited resources in favourable chamber
o some odd flies go to different disfavoured chambers  become successful  become more represented

-
- punishes the common strategy  strong divergence, discrimination against one another in 25 generations, strong
habitat preferences  selection created from a common chamber  speciation process
CLICKER QUESTION
- what process/ factor appears to be most important in determining male success: negative frequency dependence
o what is rare is most favoured: seems to be most important in determining male success
- why do fruit fly male seminal fluids shorten female lifespan: incidental: males are really competing with other males
TRAIN OF SPERM: COOPERATION OF SPERM
- beetles: promiscuous, sperms hook together to form trains
- only the head sperm can fertilize

JUMPING SPIDERS: VARIETY IN SAME SPECIES
-
SKY ISLAND SPIDERS SPECIATION
- all live close to each other, but they have diversity
- evidence of rapid divergence between populations: Sky islands of Arizona and northern desert of Mexico: relatively
rush but around them is desert
o through desertification  habitat at tops of mountains are maintained (more precipitation, cooler
temperatures than valley below)
- habitat was once continuous  same species fragmented into different terrestrial islands: example of population that
has gone into allopatry by habitat fragmentation
- males vary wildly: elaborate drumming songs, court female with elaborate displays etc.
- females: plain brown spider (not exotic) but males have diverged dramatically  possibly sexual conflict (chase away
selection model), sexual selection of sort
- mitochondrial DNA of females: identical
- sexual selection/ conflict model  if females reject spiders of different populations because they look different
o (if they come into contact)

-
HABITAT DIFFERENTIATION: RHAGOLETIS (MAJOR CROP PEST)
- fragmentation because of two different food sources
- apple maggot fly: native to hawthorn fruits; had jumped hosts to apples (that were introduced) from hawthorns: host
shift (like balloon vine)
- take same species from apples and hawthorns  genetically differentiated, strong specificity to resource/ fidelity to
resource, mate on the fruit: preference of mating with hawthorn populations and apple populations
- prezygotic isolation then postzygotic isolation: prezygotic isolation reinforces postzygotic isolation
-
SOURCES OF SELECTION IN RHAGOLETIS
- if they breed: insect does not survive the winter as an adult  goes into diapause
- apples fruit before hawthorns do: insects have to grow to certain point to get into diapause state
o diapause too early: warm spell will wake them up before spring
o diapause too late: die of freezing
o window of time in fall where it is optimal to diapause
- flies that grow on apples: have to grow more slowly to try to heat the same target
- flies that grow on hawthorn: have to grow more rapidly to pupate and diapause before frost
- hybrids are strongly discriminated against: intermediate developmental times  disastrous for fly
o hawthorn: diapause too late; apple: diapause too early  disastrous
o strong potential for reinforcement for mate choice to discourage hybridization with other race

-
HYBRID ZONES: CONTACT AFTER ISOLATION AND DIVERGENCE
- diverged species come into contact
- if hybrid species have reduced fitness (e.g. maggot fly): creates opportunity for reinforcement: positive assortative
mating: like mating with like is better  do not form hybrids that are deleterious
- fitness
- test for reinforcement

- drosophila that are genetically diverged by genetic distance (divergence of DNA sequence)
o species encounter each other: may or may not hybridize
▪ high prezygotic isolation: do not hybridize
▪ low prezygotic isolation: do hybridize
- allopatric species: greater genetic distance  greater prezygotic isolation
- sympatric species: high prezygotic isolation even in short genetic distance
o evidence that reinforcement can happen in these species when it has to when they encounter each other
ALLOPATRIC SPECIES VS. SYMPATRIC SPECIES
- willingness to interbreed: prezygotic isolation: linear relationship

- as genetic distance increases for sympatric species: clustered on left hand corner
o genetic difference is small  high degree of prezygotic isolation
o high cost of hybrid for sympatric species
o reinforcement at prezygotic level: smart animals avoid hybridization even before mating happens
HYBRID ZONE: STABILITY
- reinforcement can happen with low fitness hybrids in the hybrid zone: may lead to disappearance in hybrid zone from
prezygotic isolation
- slight fitness reduction: gene flow into hybrid zone  persistence of low level hybridization
- equally good or better fitness of hybrid: zone expands with extensive gene flow  two species become continuum
o clinal variation across the range because of homogenization of species  may completely homogenize or
sustain it
-
ECOTONES AND HYBRID ZONES: SPECIAL CASE OF HYBRID ZONES
- two species that have ranges that intersect in ecotone that differs environmentally
o different habitat (e.g. high altitudes where hybridization happens)
- ecotone: habitat that differs from normal ranges/ conditions

- different habitats for either species  third species may emerge from the ecotone
- advantage of hybrids over the parents only in ecotone  advantage in ecotone: hybrids are superior, gene flow, etc.
HYBRID ZONE/ ECOTONE EXAMPLE IN CHOROTHIPPUS P. PARALLELUS VS. C. P. ERYTHROPUS
- grasshoppers in Europe
- France to Spain  met up in Pyrenees mountain: expect to see cline of gene variation
o changes in gene frequency and morphological differences

- look for evidence of clines: intersecting clines of different characteristics

o expect to see a cline with an allele that is common in one species and not common in other species
o e.g. number of pegs on legs to make singing songs
o character display a cline and a steep change in hybrid zone (sharp clines)
o morphological characters seem to coincide  probably hybrid zone
o hybrid zone is narrow: cost to hybridization
- expect to see cline in physical characters: clines in graph
o confluence of different characteristics
o hybrid zone: intermediacy: slight cost to hybridization but gene flow sustaining the pattern on graph
o
INSTANT SPECIATION: POLYPLOIDIZATION
- unreduced gametes mating with unreduced gametes  fuse together  possibly tetraploid zygote (even multiplier)
AUTOPOLYPLOIDY: ULTIMATE SYMPATRIC SPECIATION
- unreduced gametes fertilize  fuse together  tetraploid zygote (even multiplier)  can make even gametes
o gametes with twice as many chromosomes but balanced: common in plants (self fertilization)
- tolerate inbreeding: might persist by self fertilization with tetraploid offspring  capable of growing up and self
fertilizing: reproductively isolated from other diploids (would result in triploid zygote  unbalanced and sterile)
- tetraploids arise if few tetraploids start a small population  reproductively isolated from diploids around them
o e.g. pla ts: pol ploids are see to do etter at e d edges ra ge li its of e iro e ts here it’s old et .
o tetraploids are usually hardy and survival well
-
- triploids are universally sterile  barrier to hybridization between diploids and tetraploids

- tetraploids can do really well on marginal/ stressful conditions: mechanism where you get an instant reproductive
isolation between offspring and parent species
ALLOPOLYPLOIDY
- possibility for one species producing an unreduced gamete
o normal gamete by other species
o hybridization into unbalanced genotype (normally sterile)
o by chance if it is fertile: it can transfer all of its chromosomes into that zygote
- repeated event  gamete fertilizes with normal gamete  adds in rest of species genome
- produces new species: viable fertile hybrid = allopolyploid (e.g. 2n = 10)
-
- eventually getting balanced genotype
- happens not infrequently in plants
CLAWED FROGS: POLYPLOIDIZATION
- African clawed frogs are noted for polyploidization events
- clawed frogs in Xenopous and Silurana: multiple ploidies (stable ploidies)
- complex system of hybrids and polyploids

- diversity partially comes from allopolyploidy  isolates them from other species
- can tolerate so many copies of chromosomes (other species have trouble with extra copies of chromosomes)
TAXONOMIC ASSOCIATIONS IN POLYPLOIDIES
- polyploidies in agricultural systems: sterile but vigorous, fruits without seas, shellfish with desirable characteristics
- in nature: common in plants (flowering and bryophytes), not as common in vertebrates
o polyploidization events in ancestors of vertebrates  multiplication of HOX genes
-
- economically important in agriculture (e.g. oysters for meat)
- Japanese Giant Salamander: giant polyploids (protected in Japan, not in China)
o huge stream dwelling polyploid salamanders, predators
HETEROCHRONY
- spe iatio affe ted de elop e tal pro esses: e ode o
- heterochronic changes in growth can impact organism:
o complex developmental program in organisms
o changing timing of certain events will mess up developmental program
o heterochronic genes will affect the timing of developmental events
- cascade of genes being activated earlier or later  impact on ultimate organism (e.g. paedomorphosis)
- neotony/ paedomorphosis: maintenance of juvenile features in the adult
o female humans tend to be more neotenic in their features
PAEDOMORPHIC SALAMANDERS
- instead of going into metamorphosis: juvenile grows up without metamorphosis into sexually mature adult
o animal is aquatic
o accomplished through simple genetic switch  cascade change in developmental program
- take organism in neotenic form and induce them to go into metamorphosis chemically
- changes in timing/ timing of development
- shifts in timing of developmental events can lead to major change sin morphology at maturity
- changes in genes that affect timing: could have massive impact on end of development

PAEDOMORPHOSIS: SALAMANDER
- close relatives that have metamorphosis into terrestrial from aquatic (lose gills etc.)
o some species mature sexually into adults but still look like juvenile with juvenile features  paedomorphisis
- can be manipulated to go through metamorphosis
-
- small genetic changes  huge developmental changes
- gradualism vs. punctualism (e.g. heterochronic change)
HUMAN PAEDOMORPHOSIS/ NEOTONIZATION BY BOLK (1920S)
- humans may have evolved with this process
- many traits retained from juvenile states in our primate ancestors
- young chimpanzees (evidence)
o brow ridges (less pronounced), projection of mouth/ jaws (not allometric), foramen magnum exit (straight up
and down)  changes as it develops into adult
- humans evolved rapidly from neotonization: maintenance of juvenile features that are already there, timing in
developmental events  allowing us to change rapidly
-
- in humans: resembles middle of development of juvenile
o developmental into adult chimpanzee may have stopped at some point  retention of incephalizaiton  by
not going through transformation leading to shrinkage of cranial case
- relative volume of brain to body has increased compared to ancestors

-
- humanoid skull in juvenile chimp  comparable to humans: stopped midway along the differentiation path
- SELECTION FOR INCEPHALIZATION: POSITIVE ALLOMETRY FOR BRAIN SIZE  may have led to paedomorphosis or
other way around
- e.g. skull of macaque: human brains are relatively big because muscle attachment zones do not have to be as big as
those in gorillas and chimpanzees (allows massive jaws to move, gorillas do not prepare food  whole lot of time
chewing/ processing food)
o human loss of big jaw muscles may be due to/ allowed for cooking  allowing us to lose those features
- e.g. key gene in human evolution/ molecular footprints: myosin gene MYH16  mutation/ knocked out in past
o found in all of our relatives MYH16 gene in active form: became inactivated in our lineage somewhere in
evolutionary past
o MHY16 critical to development of jaw muscles  inactivation/ mutation results in loss of muscle mass 
smaller jaw muscles
o may have facilitated evolution of language; related to food manipulation and cooking?
-
- comparing sequences using molecular clock technique  estimate loss of function time  2.4 million years ago
o coincident with incephalization of humans
- loss of MYH16 correlates with fossil records: beginning of cephalization  human
- dN/dS: measurement of strength of selection: non synonymous changes (not silent in codon)/ synonymous (silent)
o low: characteristic is conserved in evolutionary time
o after 2.4 million years: dN/dS = 1.0  after i activatio , does ’t atter if utatio occurs
o after gene was silenced  should be no selection (pseudogene)
- chimpanzee muscles are stronger and faster due to MYH16

- dN/dS: changes in codon that causes amino acid change  nonsynonymous changes (dN)
o change in nonsilent codon but codes for same amino acid  no change (dS)
o look at ratio between those that affect change in amino acid vs. ones that do not
o rapid evolutionary change: high dN/dS, nonsynonymous changes
o conserved gene by evolution: low dN/dS  new mutations are generally deleterious and removed by selection
▪ mostly synonymous changes (nonsynonymous is selected out)
o strong natural selection affecting gene product: dN/dS is large
- inactivation of MYH16  pseudogene: same ratio of nonsynonymous to synonymous: gene has been knocked out
BAUPLAN BY ED LEWIS
- bauplan = body plan, differ from group to group
- HOX genes:
- 4 wings instead of 2
- morphogenetic radiance: whole family of HOX genes
-
- hunchback and gradient: hypothesized morphogenetic gradients  tells ells hat the ’re supposed to e, gradie ts
helping to determine what segmental identity is

- won Nobel Prize

- identifying HOX like genes, comparing between different organisms
- HOX genes are ancient in all living animals
BLASHKO LINES
- mutations that cause skin pigmentation to differ from segment to segment = blashko lines
- indicates our segmental identity
-
-
- fruit fly vs. shrimp:
-
o 3 pairs of legs many legs switched on
- manipulating UBX can lead to suppression or nonsuppression for legs in drosophila abdomen
o UBX fro Arter ia i to Drosophila: produ tio of rudi e tar leg here the ’re ot supposed to e
- UBX gene: split into two major clades
o transformed drosophila with artermia UBX genes  hybridization  embryo had many limbs
SIMPLICITY AMID CHAOS

-
- HOX genes have evolved as part of conserved structure through things like polyploid events and gene duplication,
chromosome duplication  evolution of greater duplicated family  flexibility in body plan
- new regions in genome through polyploidy
Concept 53.4 Life history traits are products of natural selection
- life history: traits that affe t orga is ’s s hedule of reprodu tio a d sur i al; e tails 3 ai aria les: he
reproduction begins (age at first reproduction or age at maturity), how often organism reproduces, how many
offspring are produced per reproductive episode
EVOLUTION AND LIFE HISTORY DIVERSITY
- e.g. Pacific salmon: hatches in headwaters of stream and then migrates to open ocean where it requires time to
mature  eventually returns to freshwater stream to spawn  produces eggs in single reproductive opportunity
before it dies  semelparity
- semelparity: one shot pattern of big bang reproduction
o occurs in some plants e.g. agave/ century plant: generally grow in arid climates with unpredictable rainfall and
poor soils  grows for years, accumulates nutrients until there is wet year  sends up large flowering stalk
 produces seeds  dies = adaptatio to aga e’s harsh desert environment
- iteroparity/ repeated reproduction: organisms produce relatively few but large offspring each time they reproduce
 they provision offspring better
- semelparity vs. iteroparity: survival rate of offspring and likelihood that adult will survive to reproduce again
o survival rate of offspring low (typically in highly variable/ unpredictable environments)  semelparity
favoured (adults less likely to survive in such environments so producing large numbers of offspring should
increase probability that at least some of those offspring will survive)
o dependable environments: iteroparity may be favoured where adults are more likely to survive to breed again
and where competition for resources may be intense  few relatively large, well provisioned offspring
- intermediates between semelparity and iteroparity: oak trees, sea urchins: can live long, but repeatedly produce
relatively large numbers of offspring
TRADE OFFS AND LIFE HISTORIES
- trade off between reproduction and survival: e.g. Artic islands eiders: females less likely to survive to next breeding
season if they produce many young
- selective pressures influence trade off between number and size of offspring
-  young are subject to high mortality rates  produce large numbers of relatively small offspring

o e.g. plants in disturbed environments: produce many small seed, only a few may reach suitable habitat
o small size may increase chance of seedling establishment by enabling seeds to be carried longer distances to
broader range of habitats
o animals that suffer high predation rates: tend to produce large numbers of offspring
- extra investment by parent  i reases offspri g’s ha es of sur i al
o e.g. walnut and Brazil nut trees provision large seeds with nutrients that help seedlings become established
o primates generally bear only one or two offspring at a time: parental care and extended period of learning in
first several years of life for offspring fitness
o in habitats with high population densities
- K – selection: selection for traits that are sensitive to population density and are favoured at high densities
o operate in populations living at a density near the limit imposed by their resources (carrying capacity, K) where
competition among individuals is stronger
- r – selection: density independent selection: selection for traits that maximize reproductive success in uncrowded
environments
o maximizes r, the per capita rate of increase, and occurs in environments in which population densities are well
below carrying capacity or individuals face little competition  found in disturbed habitats
o e.g. weeds growing in abandoned agricultural field = r selected organisms
Concept 53.5 Factors that regulate population growth are density dependent
- farmers may want to reduce abundance of insect pests/ stop growth of invasive weed
- conservation ecologists may need to know what environmental factors create favourable feeding/ breeding habitats
for endangered species
POPULATION CHANGE AND POPULATION DENSITY
- birth, death, immigration, emigration change
- if immigration and emigration offset each other  population grows when birth rate exceeds death rate and declines
when death rate exceeds birth rate
- density independent: birth rate or death rate that does not change with population density
o e.g. mortality of dune fescue grass: due to physical factors that kill similar proportions of local population
regardless of its density e.g. drought stress when roots of grass are uncovered by shifting sands
- density dependent: death rate that rises as population density rises as is a birth rate that falls with rising density
o e.g. reproduction of dune fescue declines as population density increases because water or nutrients become
more scarce
MECHANISSMS OF DENSITY – DEPENDENT POPULATION REGULATION
- feedback regulation can apply to population dynamics: negative feedback between population density and rates of
birth and death
o density-dependent regulation provides that feedback  halting population growth through mechanisms that
reduce birth rates or increase death rates
- e.g. survival of bighorn lambs on Ram Mountain varies with population size: many adult sheep competing for food if
mothers provide less milk  smaller lambs are less likely to survive
- increased densities cause population growth rates to decline by affecting reproduction, growth, survival


-
POPULATION DYNAMICS
- population dynamics: fluctuations from year to year or place to place: influenced by many factors and affect other
species: e.g. fluctuations in fish pop. influence seasonal harvests of commercially important species
STABILITY AND FLUCTUATION
- bighorn sheep on Ram Mountain: population grew for 15 yrs, declinded for two decades
o as sheep numbers increase, population growth slows because food becomes limited and fewer lambs survive
winter
o immune systems become weakened and sheep become more susceptible to parasites and disease
o specialized predation by cougars also contributed to recent decline of sheep  must rely on immigrants from
nearby bighorn populations to repopulate area
- moose population on Isle Royale Island in Lake Superior: first moose grew quickly, then starvation caused numbers to
decline; wolves arrived on island after  predation would reduce large fluctuations in moose density/ help stabilize
population  two major increases and collapses
o wolves initially helped bring about decline of moose population; disease accidently introduced by human
visitors then caused wolf numbers to collapse  moose population grew quickly but crashed once more due
to food shortage made worse by harsh winter
o i reedi g lo ge eti di ersit are slo i g olf populatio ’s re o er urre tl
POPULATION CYCLES: SICENTIFIC INQUIRY
- some populations undergo regular boom and bust cycles
- 10 year cycling of snowshoe hares and lynx in Canada and Alaska: lynx = predators that specialize in prettying on
snowshoe hares  lynx numbers are expected to rise and fall with numbers of hares
o but hare numbers rise and fall in 10 year cycles:
o food shortage hypothesis: when hares become abundant, they overexploit winter food resources and
starvation causes decline in abundance  hare population recovers once vegetation grows back
o predatio h pothesis: hare le is dri e hare’s i tera tio ith predators: l o ere ploits hare  drives
numbers very low  predator population declines  hare population recovers

-
o scientists supplied some plots with hares with extra food and on some plots predators were excluded with
electric fence: hares became more abundant on plots with extra food but populations continued to cycle in
much the same way as unfed control populations  hare cycle is not due to food limitation alone
o scientists attached radio collars to some of hares  discovered that almost 90% of hare deaths were due to
predators: by reducing predator numbers  hare numbers declined much more slow
o overexploitation by predators seemed to be essential part of hare cycle
- complex predator prey interactions: food shortage for prey may increase impact of predators
o snowshoe hare: hares caught by predators were usually more malnourished than rest of population
o indirect effects of prey: causing changes in physiology and behaviour rather than directly killing them  stress
from having predators around can cause snowshoe hares to produce smaller/ even stillborn young
-
IMMIGRATION, EMIGRAITON, AND METAPOPULATIONS
- metapopulation: group of spatially separated populations that sometimes go extinct and are connected by migration
o often in environments where discrete patches of suitable habitat are surrounded by unsuitable habitat
o e.g. populations of collared pika live in crevices among loose talus rocks, rarely venture far off
▪ alpine environment is harsh  pika population sizes tend to be small
▪ populations frequently go extinct and must be re-established by individuals dispersing from other
populations
- Glanville fritillary: butterfly found in 500 meadors across Aland Islands but potential habitat is much larger (4000
patches)  new populations of butterfly regularly appear and existing populations become extinct  balance of
extinctions and recolonizations

-
Concept 53.6 The human population is no longer growing exponentially but is still increasing rapidly
- no population can grow indefinitely
THE GLOBAL HUMAN POPULATION
- human population is an exceptional case: increased relatively slow until 1650: currently populationg rows by more
than 1 million people each week  8.3 – 10.9 billion people on Earth by year 2050
o rate of growth began to slow during 1960s  human population has departed from true exponential growth
into a constant rate  fundamental changes in dynamics due to diseases and voluntary population control
o
REGIONAL PATTERNS OF POPULATION CHANGE
- in stable regional human population: birth rate equals death rate (disregarding immigration and emigration)
o
- demographic transition: movement from high to low  tends to accompany industrialization and improved living
conditions; associated with increase in quality of health care and sanitation as well as improved access to education
- number of births in population depends on number of women of reproductive age  uses Total Fertility Rate =
expected children/ woman/ lifetime
o economic, social, political factors influence rate and timing of decline in birth rate
- in industrialized nations: populations are near equilibrium with reproductive rates near replacement level of 2.1
children/ female

o in many industrialized countries, total reproduction rates are below replacement  populations will
eventually decline if no immigration and birth rat does not change
- reduced family size = key to demographic transition
o social change and rising educational and career aspirations of women  encourage women to delay marriage
and postpone reproduction
o delayed reproduction  helps decrease population growth rates towards society with zero population growth
AGE STRUCTURE
- age structure: relative number of individuals of each age in population
o graphed as pyramids
o pyramid is bottom heavy in counties where birth and death rates are high
o spindle shaped age structure: fewer young people than middle aged people
▪ obvious bulge (45 – 65) = baby boom generation
▪ Ca ada’s populatio still e pe ted to gro a little fro i igratio
o declining but still moderately high birth rate + death rate comparable to Canada = India = country in transition
- age stru ture diagra s predi t populatio ’s gro th tre ds + illu i ate so ial o ditio s
- increasing population of retired boomers  stress on universal healthcare and pension programs
-
INFANT MORTAILITY AND LIFE EXPECTANCY
- infant mortality = number of infant deaths/ 1000 live births
- life expectancy at birth = predicted average length of life at birth
-  differences reflect quality of life faced by children at birth and influence reproductive choices
o high infant mortality  parents likely to have more children to ensure that some reach adulthood
-
GLOBAL CARRYING CAPACITY
ESTIMATES OF CARRYING CAPACITY
- Anton van Leeuwenhoek: discoverer or protists; estimated carrying capacity as 13.4 billion

- difficult to estimate: some use cures like that produced by logistic equation to predict future maximum
o others generalize from existing maximum population density and multiply number by area of heritable land
o others base estimates on single limiting factor such as food and consider variables
LIMITES ON HUMAN POPULATION SIZE
- ecological footprint: summarizes aggregate land and water area required by each person, city, nation to produce all
resources it consumes and to absorb all waste it generates
o add up all ecologically productive land and divide by population = 2 ha/ person
▪  except conservation lands  1.7 ha/person (in Canada or US = 10 ha/ person)
o can use energy: energy use differs greatly for person in developed and developing nations
▪ US is 30x more energy than in central Africa
- combination of resource use/ person and population density determines global ecological footprint
- so far, technological improvements in agriculture have allowed food supplies to keep up with global population growth
o if everyone ate as much meat as the wealthiest people, less than half of the present world population could
be fed by current food harvest
Concept 54.1 Community interactions are classified by whether they help, harm, or have no effect on the species
involved
- interspecific interactions: interactions with individuals of other species in the community: competition, predation,
herbivory, symbiosis (parasitism, mutualism, commensalism), facilitation
- +/- for predation = positive effect on survival and reproduction of predator population and negative effect on that of
prey population
- mutualism = +/+; positive interactions are ubiquitous and their contributions to community structure are on point
- 0 = population is not affected by interaction is any known way
COMPETITION
- interspecific competition: -/- interaction that occurs when individuals of different species compete for resource that
limits their growth and survival
- e.g. lynx and foxes in northern forests of Alaska and Canada compete for prey such as snowshoe hares
COMPETITIVE EXCLUSION
- Paramecium Aurelia and Paramecium caudatum by G. F. Gause: cultured species under stable conditions, adding a
constant amount of food each day
o when Gause grew them separately  each population grew rapidly and levelled at carrying capacity
o grew the cultures together  P. caudatum became extinct in culture
o P. Aurelia had competitive edge in obtaining food  2 species competing for same limiting resources cannot
coexist permanently in the same place
- even a slight reproductive advantage will eventually lead to local elimination of inferior competitor  competitive
exclusion
ECOLOGICAL NICHES
- ecological niche: su of spe ies’ use of ioti a d ioti resour es i its e iro e t
- fundamental niche: range of conditions that allows a species to survive and reproduce
o (e.g. test survivability of individuals at different temperatures)
- realized niche: range of conditions under which a species actually occurs in natural communities
o e.g. competing species and how they affect population

-
o a niche difference that allows them to coexist by living at different heights in the intertidal zone
- two species cannot coexist permanently in a community in their niches are identical
- ecologically similar species can coexist in a community if there are one or more significant differences in their niches
-
Evolution
- resource partitioning: niche differentiation that allows similar species to coexist in ecological communities
o each species uses only portion of all resources available
- some partitioning occurs due to current species interactions:
o e.g. Balanus: actively prevents Chthamalus from occupying space in lower intertidal zone
- many of partitioning are result of natural selection and have evolved slow over time:
o in past, Chthamalus evolved physiological and morphological traits that allowed it to survive many hours of
exposure to air  allows it to occupy high intertidal niche
o lizard species that perch on shrubs and fence posts evolved long legs that allow them to jump to ground to
capture prey, while those that live on twigs evolved elongated bodies and short legs to creep
CHARACTER DISPLACEMENT
Evolution
- ghost of the competition past: adaptations that allow species to partition resources may be a consequence of
competition in the past
- e.g. where two species of finch are present on the same island, one has evolved a smaller beak and the other a larger
beak  evolution of greater differences reduces interspecific competition for resources
- character displacement: evolution of differences in morphology and resource use as a result of competition

- e.g. threespine sticklebacks: some lakes have only one species = generalist feeder consuming benthic (lake bottom)
invertebrates and zoo plankton in limnetic (surface) zone
o two species in other lakes: small limnetic species and larger benthic species
o discovered that marine sticklebacks (limnetic zone feeders) first colonized lakes 10 000 to 12 000 years ago
▪ sea level fell  sticklebacks trapped in lakes  became generalists
▪ 2000 years later sea level rose  marine sticklebacks invaded lakes again  competition between
early and late colonizers  evolution of greater differences in morphology and resource use
o over time, early colonizers became benthic and later colonizers remained in limnetic
o in lakes without second invasion, sticklebacks remain generalists
PREDATION
- predation = +/-: eating and avoiding being eaten are prerequisite to reproductive success  adaptations of both
predators and prey tend to be refined through natural selection
- common behavioural defenses of prey: hiding, fleeing, forming herds, schools (active self defense is less common)
o alarm calls that summons prey and mob predator etc.
- cryptic colouration/ camouflage: makes prey difficult to see
-
- aposematic colouration: animals with effective chemical defenses often exhibit bright aposematic colouration
(warning colouration) e.g. poison dart frog  predators often avoid prey that have bright colour patterns
- Batesian mimicry: palatable or harmless species mimics unpalatable or harfum one
o e.g. larva of hawkmoth (Hemeroplanes ornatus) puffs up its head and thorax when disturbed  looks like
head of poisonous snake  mimicry even involves behaviour: larva weaves its head back and forth and hisses
like a snake
-
- Mullerian mimicry: two unpalatable species (e.g. suckoo bee and yellow jacket) resemble each other
o the more unpalatable prey there are, the more quickly predators learn to avoid prey with that particular
appearance  becomes a kind of aposematic colouration
- e.g. convergent evolution: unpalatable animals in several different taxa have similar patterns of colouration: black and
yellow or red stripes characterize unpalatable animals as diverse as yellow jackets and coral snakes
- predators can use mimicry: alligator snapping turtles have tongues that resemble wriggling worm  lurks small fish
o anglerfish: lure prey with their own bait (modified bone of dorsal fin that luminesces)
HERBIVORY
- herbivory: +/- in which organisms eats plants or alga
o most herbivores are actually invertebrates such as grasshoppers and beetles
- herbivores may have specialized adaptations: e.g. chemical sensors on feet that enable them to distinguish between
toxic and nontoxic plants as well as between more nutritious and less nutritious plants
o goats: use sense of smell to examine plants
o specialized teeth/ digestive systems adapted for processing vegetation
- plant may produce chemical toxins or structures such as spines and thorns
o e.g. poison strychnine by tropical vine Strychnos toxifera, nicotine, tannins

o locoweeds Astragalus accumulate selenium: cattle and sheep that eat them wander aimlessly in circles
SYMBIOSIS
- symbiosis: when individuals of two or more species live in direct and intimate contact with one another
PARASITISM
- +/- symbiotic interaction in which parasite derives its nourishment from host which is harmed in process
o endoparasites: parasites that live within body of their host e.g. tapeworms
o ectoparasites: parasites that feed on external surface of host e.g. ticks and lice
- e.g. parasitoid insects (e.g. wasps) lay eggs on or in living host  larvae feed on body of host
- complex life cycles involving multiple hosts:
o e.g. blood fluke: requires humans and freshwater snails
- some parasites change behaviour of their hosts in a way that increase the probability of parasite being transferred
from one host to another:
o e.g. presence of parasitic acanthocephalan (spiny headed worms)  crustacean hosts engage in variety of
atypical behaviours (e.g. moving into the open)  crustaceans have greater chance of being eaten by birds
that are se o d host i parasiti or ’s life le
- parasites can significant affect survival, reproduction, density of their host population
MUTUALISM
- +/+: e.g. photosynthesis by unicellular algae in corals
- obligate mutualism: at least one specie has lost ability to survive without its partner
o e.g. interaction between termites and microorganisms in their digestive system
- facultative mutualism: each species can survive alone
- sometimes involve coevolution of related adaptions in both species with changes in either species likely to affect
survival and reproduction of other
o e.g. most flowering plants have adaptations such as nectar that attract animals that function in pollination 
in turn many animals have adaptations that help them find and consume nectar
-
COMMENSALISM
- +/0: hard to document because any close association between species likely affects both species even if only slight
- e.g. hitchhiking species such as algae live on shells of aquatic turtles that attach to whales
o hitchhikers gain palce to grow while having seemingly little effect on ride
o ho e er, hit hhikers a i fa t de rease reprodu ti e su ess of their hosts redu i g hosts’ effi ie of
movement in searching for food/ escaping from predators
o or benefit in the form of camouflage
- e.g. cowbirds and cattle egrets feed on insets flushed out of grass by grazing bison, cattle, horses, other herbivores
o birds increase feeding rates when following herbivores  benefit form association
o much of time, herbivores may be unaffected by relationship
o sometimes derive benefits from birds being opportunistic feeders that remove ticks and parasites

FACILITATION
- facilitation: positive effects on survival and reproduction of other species without necessarily living in the direct and
intimidate contact of a symbiosis, common in plants
- black rush Juncus gerardi: makes soil more hospitable for other plant species in some zones of New England salt
marches  prevent salt build up by shading soil surface  reducing evaporation; also prevents salt marsh soils from
becoming oxygen depleted as it transports oxygen to its belowground tissues
-
Concept 54.2 Diversity and trophic structure characterize biological communities
- species composition: number of species present, relative abundances, feeding relationships  nature of interactions
SPECIES DIVERSITY
- species richness: number of species present in community/ ecosystem; one component of community diversity
- relative abundance: portion that each species represents of all individuals in community
-
o species richness is same for both communities: both contain four species of trees
o relative abundance is very different  community 1 is more diverse
- Shannon diversity (H): index of diversity based on species richness and relative abundance
o where A, B, C are species in community; p is relative
abundance of each species
o higher H = more diverse community
- most species in community are relatively rare, difficult to census highly mobile/ less visible members (e.g.
microorganisms)  sometimes must use molecular tools to help determine microbial diversity
DIVERSITY AND COMMUNITY STABILITY
- examine potential benefits of diversity: increased productivity and stability of biological communities
- higher diversity communities are generally more productive and better able to withstand and recover from
environmental stresses; also more stable year to year in their productivity
- higher diversity communities often more resistant to invasive species: organisms that become established outside
native range
o e.g. scientists found that exotic tunicate was 4x more likely to survive in lower diversity communities than in
higher diversity ones  relatively diverse communities captured more of resources available in system,
leaving fewer for invader and decreasing its survival
TROPHIC STRUCTURE
- trophic structure: feeding relationships between organisms
- transfer of food energy up the trophic levels from its source in plants and other autotrophic organisms (primary
producers) through herbivores (primary consumers) to carnivores (secondary, tertiary, quaternary consumers) and
eventually decomposers = food chain
FOOD WEBS

- liked together in food webs: linking species according to who eats whom
- e.g. Antarctic pelagic community: primary producers are phytoplankton  zooplankton (euphausids, copepods) 
eaten by various carnivores (penguins, seals, other plankton)
o squids, which are carnivores that feed on fish and zooplankton are another important link in these food webs
as they are in turn eaten by seals and toothed whales
-
- some species can have more trophic links than do other species
o e.g. lemmings: consumed by all vertebrate predators while caribou are eaten only by grizzlies
▪ also eat most of plant types  lemmings are important in community
- some species may be omnivores: feed more than one trophic level
-
LIMITS OF FOOD CHAIN LENGTH
- why food chains are relatively short:
1. energetic hypothesis: length of food chain is limited by inefficiency of energy transfer along the chain
a. prodder level consisting of 100 kg plant material can support about 10 kg of herbivore biomass (total
mass of all individuals in population) and 1 kg of carnivore biomass
b. predicts that food chains should be relatively longer in habitats of higher photosynthetic production,
since starting amount of energy is greater than in habitats with lower photosynthetic production
2. dynamic stability hypothesis: proposes long food chains are less stable than short chains

a. population fluctuations at lower trophic levels are magnified at higher levels potentially causing local
extinction of top predators
b. variable environment: top predators must be able to recover from environmental shocks that can
reduce food supply all the way up to food chain
c. longer food chain  more slowly top predators can recover from environmental setbacks
- e.g. tree-hole communities in tropical forests as experimental models to test energetic hypothesis: many trees have
small branch scars that rot forming holes in tree trunk
o holes hold water and provide habitat for tiny communities consisting of microorganisms and insects that feed
on leaf litter as well as predatory insects
o manipulated productivity by varying amount of leaf litter in tree holes  energetic hypothesis  holes
with most leaf litter supported longest food chains
- carnivores in food chain tend to be larger at successive trophic levels  put some upper limit on size of food it can
take into its mouth: large carnivores cannot live on very small food items because they cannot procure enough food
in given time to meet their metabolic needs (exceptions: baleen whales consuming lots of krill)
SPECIES WITH A LARGE IMPACT
DOMINANT SPECIES
- dominant species: species that are most abundant or collectively have highest biomass
- dominance of sugar maples: impact of shading, soil nutrient availability  affect which other species live there
- one hypothesis: dominant species are competitively superior in exploiting limited resources such as water or nutrients
 species becomes dominant
- another hypothesis: dominant species are most successful at avoiding predation or impact of disease  could explain
high biomass attained in some environments by invasive species
- remove dominant species from community: e.g. American chestnut died due to fungal disease chestnut blight  oaks,
hickories, beeches, red maples increased in abundance and replaced chestnuts  no mammals or birds seemed to
have been harmed by loss of chestnut but seven species of moths and butterflies became extinct
KEYSTONE SPECIES AND ECOSYSTEM ENGINEERS
- keystone species: not usually abundant but exert strong control on community structure not by numerical might but
by their pivotal ecological roles/ niches
- sea otter: keystone predator feed on sea urchins, and sea urchins feed mainly on kelp
o sea urchins can eliminate kelp forests, destroying habitat used by many fish and invertebrates
o sea otters keep sea urchin populations in check  overhunting had driven most otter populations extinct 
urchin populations expanded and kelp forests nearly disappeared
- ecosystem engineers (foundation species): species that dramatically alter their environment (changes physical
environment)  effects can be positive or negative depending on the needs of other species
BOTTOM-UP AND TOP-DOWN CONTROLS
-

POPULATION ECOLOGY
LIFE HISTORY EVOLUTION
- how organisms obtain fitness, organize their life  life history evolution: growth, maturation, reproduction, death
- spectrum of r selected species vs. K selected species:
o gene homologies shaped in different ways

o differences in size
o parental care: albatross: sit on eggs before egg hatches and care for their offspring (parental care)  can only
afford to raise very small number of offspring (1 chick)
▪ fruit flies: eggs are laid to hatch on their own
o reproductive output: drosophila can produce a shit ton of eggs, rapidly
▪ albatross: slow process (not ready to breed until 15 years old), long lifespan
o drosophila = r selected species
- r selected species: r = population growth parameter: explosive reproductive output species, opportunists (colonizes
patchy resources)
o opportunists for colonizing patchy resources but often fail  can lay thousand eggs but only a few wind up
successfully replacing themselves (on average 2)
o if population is stable, not growing, organism is replacing itself = only 2 survive to reproduce
o in favourable patch: explosive growth
- k selected species: k = strategy = much slower growth, higher parental investment, higher probability of surviving
o in stable population: relatively high success rate of offspring
- life histories are constrained by tradeoffs: occur at two different levels
o individual level: invest on reproduction, then your survival suffers  over generations shape qualities of
species
o species level: over generations, qualities of species change: fruit flies is invested in early reproduction because
of selection where survival to later ages is improbably (early reproduction is better)
▪ virgin female flies live longer (not immortal but life extended)
-

- individual level:
o comman eider: high probability of avian cholera
o
o individuals that try to rear large clutches when there is disease, parasite  paid a big price
▪ tradeoff on an ecological scale for an individual within its life
- Y model of energetic investment:
o acquisition: energy coming into the system/ how much energy is feeding into resource fork
o energy is split  invested into somatic maintenance and reproduction
- evolution at loci can affect acquisition
- e pe i e tall : epli ati g a o ga is ’s natural habitat better than for another organism, it may do everything
better (gain energy better)
o looking for negative association between characters
o must look under the circumstances from which they evolved
- semelparous: ultimate example of trade off between investment and reproduction and investment and survival e.g.
salmon
SEMELPAROUS SPECIES
- Antechinus: semelparous mammals
o marsupials found in Australia and New Guinea
o most populations, males and females have one year life span (some have more)
o males only make 1 reproductive bout
o synchronized breeding cycles of females (not clear for males): females become receptive and begin to breed
at the same time  tremendous competition on males to fertilize those females
o extended and repeated copulation, invest enormously into testes tissue because there is strong
postcopulatory sexual selection (sperm competition)
▪ males burn themselves out  hyperinvestment in reproduction  die afterwards

- what determines that life history strategy:

o probability of surviving to subsequent reproductive bout and your fitness if subsequent reproductive bout
- salmon: anadromous behaviour (migrating from salt water to spawn in fresh water)
o for them to breed and exit the freshwater and change their gills to adapt to salt water, survive again to breed
 small probability  pays to invest everything in one reproductive bout because of that migratory
behaviour
AGING/ SENESCENCE
- life span, organism usually deteriorates in performance (especially reproductive performance) before its death
o does ’t ha e to happe ; e olutio a puzzle of agi g
- as juveniles: capable of healing  ability declines with age (not all)
- separation between somatic tissues and germline tissues:
o soma is a vehicle: body is vehicle for transmission of germline (Dawkins popularized the idea that genes are
hat’s d i i g e olutio a ha ge, od is disposa le deli e s ste
- extrinsic factors: high risk of extrinsic mortality (e.g. fruitfly)  selection for early reproduction
o selection can favour characteristics of early reproduction even if they cause lower success later in life =
antagonistic pleiotropy (antagonism, multiple gene effect)
- antagonistic pleiotropy: selection for something beneficial (early reproduction) has negative consequence later in life
o one gene controls for more than one trait where at least one of these traits is beneficial to the organism's
fitness and at least one is detrimental to the organism's fitness
o if a gene caused both increased reproduction in early life and aging in later life, then senescence would be
adaptive in evolution
-
- senescence/ decline can be adaptive because early reproduction is more favourable than later reproduction
- another reason for senescence: heat sexual maturity, start to have offspring  value in eyes of natural selection
declines
o for kid to die before maturity  fitness goes to zero (never had opportunity to transmit genes)
o after sexual maturity and reproduce: value of individual goes down for natural selection because it already
contributed to the gene pool
o kid dying vs. individual with genetic predisposition for cancer later in life: genes will be passed down to
offspring that has the same predisposition  those genes are weakly selected against (already transmitted
offspring) because they express themselves postreproductively
- individual is more valuable early in life than late in life because there is low probability of making it there to late in life
o selection for genes that help make it late in life are not strongly selected for
o survival genes for early development is more favoured
HYDRAS: DIVIDING BY FISSION
- can bud itself off and produce new daughters: no germline, soma distinction

- in hydra: organism is highly capable of repairing itself/ regeneration

o maintain genes that we lost millions of years ago
o
o hydra undergoes undetectable gaining process: survivorship is constant is constant
▪ because they divide by fission: no increase in mortality in age
▪ get better as they get bigger
o vertebrates: selection for survival is more relaxed after maturity
▪ soma is also disposable for us (occurs at different rates for different organisms)
POPULATION DYNAMICS
-
- if organism has explosive growth  large population then contracting due to a crash
- must consider birth rates vs. death rates: birth rate = death rate = no growth in simple system
- carrying capacity of environment: if death rate is density independent and birth rate is density dependent (less energy
per individual)

o predicts that if population extends density beyond equilibrium point (birth = death), population should
contract back towards equilibrium point
- equilibrium point: fluctuations can occur over time
- big horn sheep survival as a function of density: resources are limiting, when densities of lambs are high  low survival
rates compared to when densities are low
ANOTHER ARMS RACE: FLUCTUATION IN EQUILIBRIUM
- red queen phenomenon: cycling of lynx and hare
- column: hare abundance, line: lynx abundance
- hare increases  with a lag time, lynx population booms  prey population declines  lynx population crashes
-
- another population regulation: female hares have unsuccessful pregnancies in the presence of predators
o hormonally stressed out by predators and their environment
CLICKER QUESTION
- conservation of function of gene MYH16 over last several million years is supported by which evidence?: low dn/ds in
relatives of homo (e.g. great apes)
- dN/dS: changes in codon that causes amino acid change  nonsynonymous changes (dN)
o codon: there are changes in codon that causes an amino acid change
▪ change in first two positions in codon  change in amino acid (dn nonsynonymous)
▪ change in third site/ silent site  no amino acid site, redundancy etc. (ds synonymous)
▪ look at ratio between dn and ds
o rapid evolutionary change = change in phenotype  nonsynonymous dominates (dN/dS is larger than 1)
o gene conserved by evolution (e.g. jaw muscles in apes) = low dN/dS: new mutations are deleterious and
removed by selection (nonsynonymous is selected out)
- in humans: inactivation of MYH16  e o es pseudoge e: o e fu tio al ut does ’t ork a ore
o same ratio of nonsynonumous to synonymous: everything is neutral; gene has been knocked out  can
neutrally drift
WORLD POPULATION GROWTH: THOMAS MALTHUS
- exponential human growth  struggle for existence: turns out to be true
- USA: 13 births/ 1000, Kenya: 34 births/ 1000
- world fertility rate is declining (since 1950s): humans are doing something different (stopped growing at same rate)

o population dynamics: overpopulation may no result, rather population may just taper off at steady state (9 –
11 billion people)  predicted to level off within 100 years
-
- development in country  improve quality  lower infant mortality AND FERTILITY
- e.g. Sweden: kept records of population size, birth, death, marriage etc.: improved in terms of health conditions 
lower infant mortality  lower fertility rate (fewer kids made)
o stabilization: birth rates = death rates
HUMAN POPULATION DYNAMICS
- provide rich conditions, improved quality of life  birth rate declines, less offspring
o no other species that do this
- Tho pso ’s de ographic stages:
- less offspring when more energy is given (only animal

that does this is humans)
- in Sweden: steady decline in death rates, birth rates follow with a lag
- death rates fall  birth rates fall

- total population grows as long as birth rate

exceeds death rates  post industrial stable stage when birth rate = death rate
o as death rate declines and birth rate stays high  population grows exponentially
o post industrial stable stage: no population growth or even decline in population
ENGLAND
-
AGE DISTRIBUTION

o stage 4: reached balance point where birth and deaths met each other (becoming top heavy)
- exam: mostly lecture notes, few textbook notes
- 20-minute quiz: 12 questions
OVERPOPULATION (POPULATION ECOLOGY)
THE PARADOX OF MODERN INFERTILITY
- good living conditions for humans  fewer children, reduced fertility, less offspring when resources are abundant
o middle class immediately curves its reproduction
o if humanity was able to distribute wealth equally  overpopulation may be lessened
- if income and wealth is shared  population growth will slow down
o growth has to stop and equilibrium has to be established  requires population control, sharing wealth with
underdeveloped communities  develop middle class
-
IDEAS ABOUT THE TRANSITION: WHY DOES MIDDLE CLASS MAKE LESS OFFSPRING
- less of need for child labour for agriculture: moving away from harvesting lives to more urban environments 
reduces necessities for child labour
- decline in child labour through outlawing:
- anti child labour acts; children are no longer contributing to income, they need higher levels of education, laws that
assure education for children (public education)  increases cost of having a child
o increase cost of education
o decrease contribution from children
o investing more on children education  wants fewer kids
- literacy: career ambitions for women (new role for women in society), traditional roles less accepted
- contraception: controlling pregnancy  more power in women to control when they want to have children
o women generally have more offspring than they want  give contraception  reduce children
o limits males to increase fitness with multiple partners etc.  enforces anagomous relationships and eliminate
sexual conflict

MEMES: LONNIE AARSSEN QUEEN’S

- suggests that part of our fitness drive to replicate out genes is replaced by cultural phenomenon: memes
o ideas can be passed on from generations to generations
o horizontal transmission: can spread from individual to individual
o argues that communication and modernization of society has led to a fitness drive for memes: deposition of
ideas and fame into society (legacy)
- cultural fitness that is not biological
-
- desire to be remembered
REBOUND: WHEN CONDITIONS BECOME REALLY RICH
- pattern may reverse at certain point
- Human Development Index: income/ family + gross domestic product/ capita + life expectancy, education level, quality
of living shit, housing
- initially strong negative relationship: as HDI improves, people have less offspring
- HDI over 0.90, fertility increases  rebound
o when conditions get really good, people start having kids again
▪ would not rise back to extremely high levels but will go up
▪ equilibrium will someday be reached
-
- reaching replacement level (not necessarily overgrowth)
- because of cultural transmission of knowledge  in a single generation  will move into higher economic class then
their behaviours will change (virtually instantaneously)
COMMUNITY ECOLOGY: SPECIES INTERACTIONS
- niches: parts of environment and resources that they can exploit
o in different species + large overlaps  competition
- Georgy F. Gause: experiment with paramecium (protozoa)
o different species of paramecium could live on the same diet of green algae (kept separately)  high
population level
o in competition  caudatum outcompetes first, Aurelia is better than caudatum in existing in high densities

- Aurelia drives caudatum populations down  extinction; they do not coexist

- o lusio : o petitors a ot oe ist if the ’re o plete o petitors o up i g the sa e niche = COMPETITIVE
EXCLUSION PRINCIPLE/ GAUSE’S LAW
-
- togethe the do ’t oe ist happil  Aurelia increases as caudatum goes extinct  law: two species are occupying
same niche  one will exclude the other because it is a little bit better
-
- where does this happen in real life:
- e.g. phytoplankton: grows in simple, wide ocean: plankton is really diverse despite them seemingly competing for
same resource (sunlight, minerals)  should be non diverse (not true)  does ot see to o e Gause’s la so e
syste s do ot follo Gause’s la
o lots of environments can look simple but their interactions can be really complicated  also can be sustained
as diverse systems
o negative frequency dependent of each other  diversity persists
NICHES AND PARTITIONING OF HABITATS
- one species can do better/ specialize in a special environment
- competition in intertidal between two barnacle species: stratification of different kinds of organisms
o remove balanus, cthalamus can live happily in lower intertital (balanus was a little bit better at exploiting that
habitat)
o fundamental niche of cthalamus: broad, can live under broad habitats
o in competition, cthalamus realized niche: more restricted set of habitats
o niches are defined by competition  resource partitioning (e.g. some living higher up in trees)  finding a
way to coexist
- typical ecosystem: CHARACTER DISPLACEMENT: species specialize in special part of environment
o competition gets tough  eed tradeoff a ’t e good at e er thi g

-
STICKLEBACK: GASTEROSTEUS ACULEATUS
- little, hardy fishes, easy to maintain, spread worldwide in northern hemisphere, live in marine habitats  come into
fresh water to spawn (anadromous)
o often, marine sticklebacks have colonized freshwater repeatedly and stayed there
o cool system of sexual selection
- males have bright colours, courtship display, territorial: entices female to lay eggs in the nest he built  he will patrol
and chase away competitors, display for female, tend to eggs, parental care giver
- ales do ’t displa Bate a ’s pri iple: hy?
o paternity certainty: eggs in controlled space so he can fertilize them (external fertilization)  worth tending
them
o male can attract a lot of females if he is successful: can simultaneously protect thousands of eggs  has
higher reproductive success potential
o male potential reproductive output > female potential reproductive output
▪ he competes harder, paternity assurance
- at the end of breeding season, males will not survive: tradeoff (do not live as long as females)
o male competition is fierce and stakes are big; males have more to shoot for annual reproductive success
STICKLEBACKS
- colonize freshwater over and over again  all around northern hemisphere
o one of the most evolutionary amazing systems
- marine sticklebacks along coast water + freshwater sticklebacks in lake
o PARALLEL EVOLUTION: starting from marine ancestor that is widespread, heavily armoured, sharp spines,
pelvic armour along length of body  well protected 
o in freshwater: they always lose their pelvic armour within human life time (fast) (less predators)
o Pitx1 gene from chapter 25.5: key component of this developmental progress (knocked out)
- rapid change can come about through suppression of few simple switches in genes (heterochrony)
- degree of parallelism and convergence is high in sticklebacks
- Dolph Schluter: Strait of Georgia, Vancovuer Island

CHARACTER DISPLACEMENT IN STICKLEBACKS

1. they can be generalists: small lakes in particular with one occupant = generalists; gill raker length is reduced (from
marine to freshwater)
2. two different species: do not interbreed (could but breed at different locations + reject each other)  morph that is
benthic/ limnetic
a. body size and shape: benthic (deep water) = deep bodies; limnetic (surface level) = smaller bodies
b. character displacement (characteristic becomes separated in presence of other competing species)  via
sympatric speciation of the original colonist or repeated invasion?
- recent research:
o wave of colonization  freshwater sitcklebacks established as generalists
o sea wave rose again  new population of marine sticklebacks enter (limnetic, freeswimmers)  drove
displacement  se o d olo ize ’s li eti spe ializatio as ette tha the ge e alists fo ed to diffe e t
role  benthic; second colonizers cannot do benthic)
- some lakes had one species and a lot of variation in traits: can feed at surface and deep
- other lakes had 2 species, each specialized for high water/ fast swimming or bottom dwellers  do not breed with
each other even though they can breed with each other
- in some lakes, original population diverges into two specialists
- or recent research: differentiation occurs because of drop in sea level at some point  traps original population,
years later, second invasion  forced original population to take benthic habitat
-
PREDATOR AVOIDANCE
- species – species interactions: benefits one and harms other (+/- association)
- how to escape predation:
1. be cryptic: take on less noticeable both so nobody can see you
o Amphibia is really diverse
2. aposematic colouration: warning colouration: individual may be distasteful or toxic
a. e.g. dart poison frogs (for darts)
- Batseian mimicry: copies other organisms that are noxious  frequency dependent game
o model (poisonous), mimic (not poisonous)  if mimic is common, predator does not learn avoidance
- Mullerian mimicry: mimic is distasteful and copies a model  doubles effect of mimicry
MIMICS
- hover fly: tries to look like wasp (but not edible)  benefits from copying wasps
o cannot be frequency  predators will not learn to avoid them  must be at lower frequency than the model

- Mullerian mimicry = positive frequency dependent: the nastier things there are that gives predators a warning in
the same language  the more successful it will be because predators learn not to mess with it
- other species may copy aposematic colouration: mimicry strategy:
-
MONARCH BUTTERFLY AND VICEROY
- Batesian mimicry: monarch feeding on milkweed becomes nasty/ toxic  viceroy copies it (not toxic)
o more recent work suggests that viceroy is actually nasty (Mullerian)
o e.g. take wings off and present them as food to birds  see reaction  viceroy may taste nasty
- Mullerian association: strengthens their capacity to deter predators

o top row: same species (Dendrobates imitator): imitates poison dart frogs  takes on similar morphology to
other species of Dendrobates that live in those areas
▪ imitators are sympatric with species with dart poison frogs in areas of overlap + Mullerian
▪ highly polymorphic species: different parts of range  mimics other common Dendrobates
- coral snake: extremely dangerous; scarlet kingsnakes are pets  clear case of mimicry
-
MIMIC (1997): THE MOVIE
- tries to curb disease in US  virus by cockroaches, killing babies  Sorvino invents judice bug  combines termites
(social insects) and cockroaches so judice bugs can be trained to attack a coordinated army of attack on cockroaches
o mixes in mantis DNA
- judice bug lives on over one generation  in 3 years  size of human  becomes human mimic and preys of humans

PIRANHA 2 THE SPAWNING: MOVIE BY JAMES CAMERON (first movie)

- piranha + grunion + flying fish  military secret weapon
-
- flies into hotel rooms and devour people
HERBIVORE AVOIDANCE
- plants = sessile organisms: physical defences, can involve spikes, distasteful compounds and chemical compounds
o e.g. cinnamon, capsaicin etc.
- deterrents to herbivory  basis of spices and flavours for humans
o originally there as distasteful flavours
- fruits are different: one thing that wants to be eaten  many plants use fruits to entice herbivory and to get seeds
into GI tract  defecates and spreads them as fertilizers: fruits are sweet because they want to be dispersed
-
CHILES: PEPPER PLANTS
- peppers: originated in south America; very young cuisine
- capsaicin, peppers in Bolivia, capsaicin content is variable: really intensive, mild etc. variety of spiciness
- study: why peppers are spicy and vary in their levels:
o in Bolivia: looked at rate of infection with Fusarium fungus
o seed death: infection by Fusarium fungus transmitted by insects that move from fruit to fruit that causes lesion
o scored level of attacks by insects: positive relationship between number of insect bites vs. rate of infection
o capsaicin is a microbial inhibitor (antimicrobial properties may allow it to spread as a food preservative)
o apsai i also good dete e t to i se t he i o ; i ds do ’t ha e the e epto s  bird dispersal
- spice evolving as a mean of regulating of means of dispersal  discourages infection by fusarium and encourages
seed dispersal by birds
- capsaicin is a costly compound to make: drop in pungency of fruits  highly polymorphic
o trade off: pepper a ake healthier, seed ri h fruit if it does ’t ha e to ake apsai i
o protection against insects vs. making bigger healthier fruits

CHILLIES NOT CHEAP

- capsaicin has variety of purposes in fruit:
o deter insect herbivory by peppery taste
o limits spread of fusarium (fungus) and bacterial infection
▪ if herbivory threats are strong  worth investing in expensive capsaicin
▪ deters mammals and insects but not so much birds  selective dispersal system (favour avian
dispersal)
-
SYMBIOSIS
- e.g. mitochondrial endosymbiosis, commensalism of ungulates and birds,
PARASITISM
- parasitism: e.g. malaria (plasmodium) that negatively impacts insect host
o mosquito female is affected by taking up plasmodium
- Marrelli et al.:
o in the absence of gametocytes produced by plasmodium in the blood of host: females are capable of laying
70 eggs
o females (secondary host mosquitos) infected by gametocytes of plasmodium: fertility is impaired (fed on host
that has plasmodium gametocytes)
▪ directly interfere with metabolic, digestive process and induces immune response that takes energy
away from investment of eggs  costly  reproductive output decreases
- t a sge i os uitoes: a ies utatio / t a sge e that i te fe es ith the pa asite’s a ilit to passage th ough the
midgut of the insect:
o fertility in absence of plasmodium = wild type mosquito
o fitness of female in presence of gametocytes is relatively higher than those without transgene
▪ better at coping with uptaking plasmodium

BENEFITS OF TRANSGENE: MARRELLI ET AL.

- multigeneration experiment, alternate hosts (mouse system that carries plasmodium parasites)
- frequency of transgene rises and plateaus at frequency of 0.7
- does not go to fixation: transgene gets passed back and forth between males and females
o male gain no benefit from transgene since they are not blood feeders  impede rate of increase of transgene
o but still, resistance against transgene helped stop the spread of plasmodium to humans (possible solution)
- mathematical model of experiment fits nicely with observation; transgenics outcompeted wildtype mosquitos
-
- use of modern biotechnology in biocontrol context
- CRISPR Cas 9: system first discovered in bacteria: use to target viruses via their sequence  cut and disable virus
o can target specific gene sequences and cut that DNA
o supply cell with another copy of gene: will mend gene with uncut copy of gene
o can do replacements throughout entire organism of undesirable genes with desirable genes
o mice yes, human no: ethical issue for future (e.g. unborn infant and predisposition of certain diseases)
MUTUALISM
- mitochondrion (endosymbiont): mitochondria in all of the eukaryotes, in all of eukaryotes (diverse)  parasitism and
a hostile relationship turning something is later mutualism
o now, mitochondrion – cell = codependency: neither can survive without the other
- coral: use bacteria to fix photosynthetic energy
o may of them capture algae out of water column
o algae are kept hostages within coral
o mutualism?: slaves, would they do better when they were free living
ANTS: APPARENT MUTUALISM
- ants that farm aphids: sucks sap out of trees  makes honey dew (nectar)  in presence of ants release these
o aphid gains protection, ants gain easy to digest food source that ants cannot easily get to
- leafcutter ants and fungi: travels far and wide to bring material back to nest
o feed plant material to often several different fungi that grow based upon energetic input underground
o ants are farmers that farm fungi which provide rich food source for ants
o Quee ’s takes spo es of fu gi to sta t e fa s i e olo ies
o many different species of fungi are found in association with ants and propagated by ants (e.g. cultivated corn
by humans)
▪ ho’s the aste a d ho’s the sla e: e.g. o s a e usi g hu a s to p opagate
- acacia plant mutualism with ants: ants tend to acacia trees in tropics

o acacia trees have some protection against herbivores with spines

o spines also provide hollow cavities for ants to nest in  ants are loyal to acacia: chase away other insects, eat
other herbivores, tend lawn around acacia: removes competitors, snipping out seedlings growing around
acacia, protects against being burned up in forest fire by creating ring
o acacia tree provides ants with rich sap that ants can use/ digest (sugar)
- turns out (from Martin Heil) that ants lack ability to digest sugars produced by acacia:
o acacia trees give them necessary enzymes
o invertase is perfectly active in growing ant larvae, adults lack it
▪ acacia tree disables genes that allows invertase expression via its own antagonistic enzymes
▪ adult ant that is perfectly capable of digesting sugars with invertase  first sip of nectar from acacia
neutralizes that ability  makes ants dependent on acacia
o acacia holds ants hostage: making them dependent
o ants allow certain herbivores that provide them with other sources of sugars to persist on acacia, feeding
on acacia plant matter  a ts’ o tri k to pla o a a ia
DIVERSITY AND STABILITY
- measuring diversity:
- Shannon diversity index (H): (frequency of species in community) x (ln frequency of species in community)
o high H: maximize species numbers with equal frequencies in communities (e.g. 10 different trees all found
in 10 percent)  evenness representation is favoured
- complex communities can deter invasion
o losing diversity  accelerating process because it becomes more vulnerable to invasions
-
- complex communities: deter invasion: because fewer available niches and digitation of niches within more complex
communities  biodiversity is important; losing it can be accelerating process by having communities becoming
more vulnerable to generalist invaders with large number of food sources
-
FOOD WEB
- describe multispecies interactions within communities, how energy flows within communities
- largest number of steps usually: 3
o relatively low number of steps: food chains defined in food webs are limited in length
- e.g. lemmings: keystone species: grizzly bears depend on lemmings as a key food source
o they do not throw themselves off the cliff when population levels are high

FOOD CHAINS ARE SHORT

- hypothesis 1: energy is transferred relatively inefficiently between trophic levels in biotic systems
o 10 000 J primary producers  1000 J primary consumers  100 J secondary consumers  10 J tertiary
consumer  argument for vegetarianism
o vegetarianism: primary consumer: amount of energy required is reduced by not being predators of higher
trophic levels
o caterpillar: ½ lost as feces, much for cellular respiration, less than 20% for growth in the end  caterpillar has
to eat a lot for pupal case etc. into adult
- food chains are longer where primary production is high
- hypothesis 2: dynamic stability, long chains are innately unstable
o fluctuations in lower levels: make energy availability unreliable to higher trophic levels
▪ theoretical but less evidence for it
-
DOMINANT VS. KEYSTONE: SPECIES INTERACTIONS AT COMMUNITY LEVEL
- some species are common: their impact may be minor when removed
o e.g. American Chestnut: dominant in forest, disappeared by logging, replaced by other species that seem to
form same role in community
o community is not affected by diversity by losing that species
o Shannon index would have increased with reduction of that dominant species (American Chestnut)
-
- keystone species: species which are often not very common but have large impact
o sea otters exert strong control over sea urchins (stronglus centratus populatus)
o eat sea urchins at high frequencies: sea urchins in turn in absence of sea otters due to furtrade and trapping
 sea urchin populations exploded  mowed down kelp forests
o kelp forests important for diversity for fish, baby fishes, adult fishes, invertebrates in kelp forest
▪ big part of determining diversity of ecosystem
- top down control as predacious species on otters by humans  sea otters made a compact after conservation
efforts  kelp forest increased due to increase in sea otters
- orcas that eat sea otters  boom in sea urchins and reduced kelp forests

BOTTOM UP VS. TOP DOWN CONTROL

- top down control: trophic cascade occurs
o  all the way to primary producer
-
- bottom up control: put more photosynthesizing material
o  more plant material  support more lemmings  support more species above
o greater numbers and higher diversity
o input of energy into bottom of food chains
-
ENERGY FLOW IN ECOSYSTEMS
- lots of solar radiation input to planet, much lost (cloud cover, rays hitting obliquely)
- solar energy into primary producers  consumed by herbivores etc. etc.
- net productivity = gross productivity of primary producers – respiratory needs of primary producers (autotrophs)
o what primary producers put into the system energetically  amount of energy declines as it goes up
o whole system produces a lot of detritus: dead organic matter (minerals trapped in dead organic matter)
- to complete circuit: detritivores break up dead organic matter  freeing inorganic compounds and returning them
to primary producers and generating new productivity into system
o detritivores: mainly bacteria and fungi
-
NET ECOSYSTEM PRODUCTIVITY
- consider gross primary productivity and respiratory needs of all members of ecosystem
- across all trophic levels: net ecosystem productivity = gross primary productivity – respiratory needs of all consumers
within it: using energy to run themselves
- carbon sinks: reduces carbon emission into atmosphere: hopefully more primary producers fixing carbon dioxide
o measure CO2 flux (easier than measuring O2): flux more than 0 = more CO2 going into system than coming
out  carbon sink: area fixes carbon from system and turning it into biomass

o kg of carbon/ m^2/ year: 3kg/m^2 is high net ecosystem productivity

▪ found in few systems in world: e.g. Amazon jungle with lots of solar radiation, stable climate, lots of
moisture in system
- heat and moisture combined with intense solar radiation = productivity
- much of Earth is oceans: important for carbon cycle
o but lots of it have very low productivity:
▪ limits of productivity: common nutrients that are in low supply in open ocean (N, P)
• phytoplankton take these up from seawaters, if they die  sink to bottom as detritus if
the ’ e ot o su ed pla kti o es hi h ulti atel e ome detritus)
▪ iron Fe: limiter of productivity in open oceans: iron fertilizer into open ocean brings alive ocean with
phytoplankton  increases productivity and number of other species in ocean
o supplementation: possible solution to increase ocean productivity to trap more carbon from atmosphere,
release that via phytoplankton as oxygen (reversing process on planet)
-
LIMITATIONS OF PRODUCTIVITY IN TERRESTRIAL ECOSYSTEMS
- moisture and warmth (big factors)
- in soil: nitrogen and phosphorus (fertilizers): increase productivity of agricultural crops
o run off into freshwater systems: produce algal blooms
o run off eutrophies the water: make it too rich causing algal blooms  negative impact
▪ e.g. riff lake cichlids: fertilizers creating turbid waters with lower visibility  reduce capacity of species
flo ks of i hlids to e og ize othe spe ies that the do ’t o all eed ith
- plants: increase ability to capture nitrogen in their roots using nitrogen fixing bacteria (kept in nodules, symbioses,
mutualism)
- mycorrhizae: fungi that are associated with roots  help take up phosphorus and others
o mushrooms: fruiting bodies (spores) of organism that is much more extensive living under soil surface
▪ not main show, just gonad of organism

CONCLUSION
- Henri Rousseau
- happy future: mutualistic relationship with nature and manage populations in a way that sustains biodiversity
Bio Week 24 Textbook Notes
- ecosystem: sum of all organisms living in a given area and abiotic factors with which they interact
o involves energy flow and chemical cycling
o both energy and matter are transformed in ecosystems through photosynthesis and feeding relationships
- unlike matter, energy cannot be recycled: ecosystem must be powered by continuous influx of energy from external
source (e.g. sun): energy flows through ecosystems, whereas matter cycles within and through them
Concept 55.1 Physical laws govern energy flow and chemical cycling in ecosystems
CONSERVATION OF ENERGY
- first law of thermodynamics: energy cannot be created or destroyed but transformed
o amount of energy stored in organic molecules = solar energy intercepted – amount dissipated as heat
- second law of thermodynamics: every exchange of energy increases entropy of universe
o energy conversions are inefficient  lost as heat
o energy flowing through ecosystems ultimately dissipate as heat  sun must continuously provide energy
CONSERVATION OF MASS
- law of conservation of mass: how much of a chemical element cycles within ecosystem or is gained/ lost by ecosystem
- unlike energy, chemical elements are continually recycled within ecosystems
- in forest ecosystem: most mineral nutrients enter as dust or as solutes dissolved in rainwater or leached from rocks
in the ground; nitrogen is also supplied through biological process of nitrogen fixation
- losses: some elements return to atmosphere as gases, others carried out by moving water
- ecosystems are open systems
- in nature, most gains and losses to ecosystems are small compared to amounts recycled within them
o still, balance between inputs and outputs determines whether an ecosystem is source or sink for given
element  if i e al ut ie t’s output e eed its i puts, it ill e e tuall li it p odu tio i that s ste
o human activities often change balance of inputs and outputs considerably
ENERGY, MASS, AND TROPHIC LEVELS
- primary producers: trophic level that ultimately supports all others, autotrophs
o most autotrophs are photosynthetic organisms that use light energy to synthesize sugars and other organic
compounds which they then use as fuel for cellular respiration and for growth
o plants, algae, photosynthetic prokaryotes are main autotrophs; chemosynthetic prokaryotes in deep sea
hydrothermal vents and places deep under ground or ice
- heterotrophs: depend directly or indirectly on outputs of primary producers for their source energy
- herbivores: eat plants and other primary producers = primary consumers
- carnivores: eat herbivores = secondary consumers
- tertiary consumers: carnivores that eat other carnivores
- detritivores/ decomposers: heterotrophs, consumers that get their energy from detritus
o detritus: nonliving organic material e.g. remains of dead organisms, feces, fallen leaves, wood
o many detritivores are eaten by secondary and tertiary consumers
o prokaryotes + fungi: secrete enzymes that digest organic material, absorb breakdown products and recycle
them  making them once again available to producers
- e.g. birds eat earthworms that were feeding on leaf litter and its associated prokaryotes and fungi
- detritivores convert organic matter from all trophic levels to inorganic compounds usable by primary producers 
loses loop of e os ste ’s he i al li g
o producers then recycle these elements into organic compounds

o decomposition stops  life would cease as detritus piled up and supply of ingredients needed to synthesize
new organic matter was exhausted
-
Concept 55.2 Energy and other limiting factors control primary production in ecosystems
- primary production: amount of light energy converted to chemical energy (in form of organic compounds) by
autotrophs during a given time period  starting point for most studies of ecosystem metabolism and energy flow
- ecosystems where primary producers and chemoautotrophs: initial energy input is chemical and initial products are
organic compounds synthesized by microorganisms
ECOSYSTEM ENERGY BUDGETS
- total a ou t of photos theti p odu tio sets spe di g li it fo e ti e e os ste ’s e e g udget
- intensity of sun striking Earth varies with latitude, with tropics receiving greatest input
o most solar radiation is absorbed, scattered, reflected by clouds and dust in atmosphere
o a ou t of sola adiatio that ulti atel ea hes Ea th’s su fa e sets uppe li it to possi le photos theti
output of ecosystems
- of the radiation that reaches photosynthetic organisms, only certain wavelengths are absorbed by pigments  rest is
lost as heat, reflected etc.
- only about 1% of visible light that strikes organisms is converted to chemical energy
- primary producers create about 105 billion metric tonnes of organic material each year
GROSS AND NET PRODUCTION
- gross primary production GPP: total primary production in ecosystem; amount of energy from light (or chemicals)
converted to chemical energy of organic molecules per unit time  some of it used for their own cellular respiration
- net primary production NPP: gross primary production minus energy used by primary producers for their autotrophic
respiration (Ra)
o on average, NPP is half of GPP
o key measurement, represents storage of chemical energy that will available to consumers in ecosystem
o expressed as energy per unit area per unit time (J/m^2yr) (biomass in dry mass of organic material)
o should not be confused with total biomass of photosynthetic autotrophs present (standing crop)
o amount of new biomass added in given period of time

- grasslands do not accumulate as much biomass as forests because animals consume plants rapidly and because
grasses and herbs usually have shorter lifespans than trees  but can have greater net primary production
- t opi al ai fo ests a e a o g the ost p odu ti e te est ial e os ste s a d o t i ute a la ge po tio of pla t’s
net primary production
o estuaries and coral reefs also have very high net primary production but their contribution to global total is
small because it covers only about 1/10 the area covered by tropical rain forests
- oceans are relatively unproductive but their vast size means that they contribute as much to total global net primary
production as terrestrial systems do
-
- net ecosystem production NEP: net primary production as amount of new biomass added in a given period time;
measure of total biomass accumulation during that time
o gross primary production – total respiration of all organisms in system (Rt), not just primary producers but
decomposers and other heterotrophs as well
o ; its value determines whether an ecosystem is gaining or losing carbon over time
o forest may have positive NPP but still lose carbon if heterotrophs release it as CO2 more quickly than primary
producers incorporate it into oganic compounds
- measure net flux (flow) of CO2 or O2 entering/ leaving ecosystem  if more CO2 enters than leaves, system is storing
carbon
o O2 flux is directly coupled to photosynthesis and respiration, system that is giving off O2 is also storing carbon
o in land: measure CO2, in oceans: use CO2 and O2
PRIMARY PRODUCTION IN AQUATIC ECOSYSTEMS
- both light and nutrients are important in controlling primary production in aquatic ecosystems
LIGHT LIMITATION
- depth of light penetration affects primary production though photic zone of ocean or lake
- about half of solar radiation is absorbed in first 15 m of water
- we would expect production to increase along gradient from poles toward equator which receives greatest intensity
of light  however another factor must strongly influence primary production in ocean
NUTRIENT LIMITATION
- limiting nutrient: element that must be added for production to increase
o nutrient limiting marine production most often is either nitrogen or phosphorus  typically low
concentrations in photic zone because they are rapidly taken up by phytoplankton and because detritus sink
- e.g. nitrogen was limiting phytoplankton growth off south shore of Long Island, New York  identify nutrient that had
to be reduced to prevent algal blooms in coastal waters
- Sargasso Sea: has low concentration of nitrogen and phosphorus  prevents phytoplankton density
o primary producers are also limited by micronutrient iron
o windblown dust from land supplies iron to oceans
- some large areas of ocean have low phytoplankton densities despite relatively high nitrogen concentrations
o iron limits production in some oceanic ecosystems encouraged marine scientists to carry out large scale ocean
fertilization experiments in Pacific and Antarctic Oceans

- researchers spread low concentrations of dissolved iron over 72km^2 of ocean dn then measured change in
phytoplankton density over a seven-day period: massive phytoplankton blood occurred
o addition iron had stimulated growth of cyanobacteria that fix additional atmospheric nitrogen and extra
nitrogen stimulated proliferation of phytoplankton
- extra primary production must sink into deep ocean water and sediments  does not appear to occur
o tends to be recycled by secondary consumers and decomposers in shallow waters, returning eventually to
atmosphere
- areas of upwelling where deep nutrient rich waters circulate to ocean surface have exceptionally high primary
production  nutrient availability determines marine primary production
o upwelling stimulates growth of phytoplankton that form base of marine food webs, upwelling areas typically
host highly production, diverse ecosystems and are prime fishing locations
- economically important fisheries depend on nutrients brought to surface by upwelling in Juan de Fuca Strait south of
Vancouver Island and over the Grand Banks of Newfoundland
- excessive algal growth also occurs in freshwater lakes when large amounts of nutrients are added
o  eutrophication  loss of many fish species from lakes
-
PRIMARY PRODUCTION IN TERRESTRIAL ECOSYSTEMS
- temperature, moisture  main factors controlling primary production in terrestrial ecosystems
o tropical rain forests promote plant growth, most productive of all terrestrial ecosystems
o temperate forest, grasslands: moderate climates, intermediate productivity
- predicting NPP through climate variables of moisture, temperature
o primary production is greater in wetter ecosystems
- actual evapotranspiration: total amount of water transpired by plants and evaporated from landscape
o increases with temperature and amount of solar energy available to drive evaporation and transpiration
NUTRIENT LIMITATIONS AND ADAPTATIONS THAT REDUCE THEM: EVOLUTION
- mineral nutrients in soil limit primary production in terrestrial ecosystems
o nitrogen and phosphorus (like aquatic systems)
- nitrogen limits plant growth, phosphorus limitations common in older soils where phosphate molecules have been
leached away by water (e.g. tropical)
o phosphorus availability: often low in soils of deserts and other ecosystems with basic ph where some
phosphorus precipitates and becomes unavailable to plants
- adding more of limiting nutrient will increase production until some other nutrient becomes limiting
- adaptations in plants that can increase uptake of limiting nutrients
o mutualism: symbiosis between plant roots and nitrogen fixing bacteria
o mutualism: mycorrhizal association between plant roots and fungi that supply phosphorus and other elements
o plants have root hairs and other features that increase area of soil that roots contact
Concept 55.3 Energy transfer between trophic levels is typically only 10% efficient
- secondary production: a ou t of he i al e e g i o su e s’ food that is o e ted to thei o e io ass i
a given period
- e.g. herbivores eat only a small fraction of plant material produced; globally 1.6 consumed of total plant production

o cannot digest all plant material that they do eat

- ast ajorit of e os ste ’s produ tio is e e tuall o su ed detriti ores
PRODUCTION EFFICIENCY
- energy contained in feces remains in ecosystem temporarily but most of it is lost as heat after feces are consumed by
detritivores; energy used for respiration is also released as heat  energy flows through (not cycle within) ecosystems
-
o net secondary production = energy stored in biomass represented by growth and reproduction
o assimilation: total energy taken in, not including losses in feces, used for growth, reproduction, respiration
o production efficieny = percentage of energy stored in assimilated food that is not used for respiration
- birds and mammals typically have low production efficiencies because they use so much energy in maintaining
constant, high body temperature (1 – 3%)
- fishes (ectotherms) have production efficiencies around 10%
- insects and microorganisms have production efficiencies of 40% or more
TROPHIC EFFICIENCY AND ECOLOGICAL PYRAMIDS
- trophic efficiency = percentage of production transferred from one trophic level to next
o must always be less than production efficiencies: take into account energy lost through respiration, feces,
and also energy in organic material in lower trophic level that is not consumed by next trophic level
o generally, only 10%: 90% of energy available at one trophic level typically is not transferred to next
- progressive loss of energy along food chain severely limits abundance of top level carnivores
o only about 0.1% of chemical energy fixed by photosynthesis flows all the way to tertiary consumer (snake,
shark etc.  most food webs include only about 4 to 5 trophic levels
- pyramid of net production: trophic levels are arranged in tiers
o width of tier is proportional to net production in joules
- small population size typical of top predator species is one reason they tend to be vulnerable to extinction
- pyramid of net production

- biomass pyramid: each tier represents standing crop (total dry mass of all organisms) in one trophic level
o most biomass pyramids narrow sharply from primary producers at base to top level carnivores at apex: energy
transfers between trophic levels are inefficient

o certain aquatic systems however have inverted biomass pyramids where primary consumers outweight
producers  because producers (phytoplankton) grow, reproduce, and are consumed so quickly by zooplaton
that they never develop large population size/ standing crop
o phytoplankton have short turnover time  small standing crop compared to their production
-
o phytoplankton continually replace their biomass at rapid rate  can support biomass of zooplankton bigger
than their own biomass  pyramid of production is still bottom heavy because phytoplankton have much
higher production that zooplankton
-
- if humans fed more efficiently as primary consumers eating plant material, worldwide agriculture could successfully
feed many more people and require less cultivated land
Concept 55.4 Biological and geochemical processes cycle nutrients and water in ecosystems
- biogeochemical cycles: nutrient cycles involve both biotic and abiotic componenets
BIOGEOCHEMICAL CYCLES
- two general categories: global and local
o cycles of gases are essentially global
- main reservoirs of elements

- A: nutrients in living organisms and in detritus are available to other organisms
- B: nutrients in these deposits cannot be assimilated directly
- C: inorganic materials that are dissolved in water or present in soil or air are available for use
- D: nutrients may slowly become available through weathering and erosion
- two methods of finding out: isotopes: follow movement of naturally occurring nonradioactive isotopes through biotic
and abiotic components of ecosystem; other method involves adding tiny amounts of radioactive isotopes of specific
elements and tracing their progress

o or able to make use of radioactive carbon released into atmosphere during atom bomb testing: use spike of
14C to tract where and how quickly carbon flows into ecosystem components
DECOMPOSITION AND NUTRIENT CYCLING RATES
- decomposition controlled by same factors that limit primary production in aquatic ad terrestrial ecosystems
o temperature, moister, nutrient availability
- decomposers usually grow faster and decompose material more quickly in warmer ecosystems
o e.g. tropical rain forest: most organic material decomposes in few months to few years  relatively little
organic material accumulates as leaf litter on forest floor  relative low concentrations of some nutrients in
soil resulting from short cycling time not from lack of these elements in ecosystem
o e.g. temperate forests: decomposition takes 4 to 6 years on average  soil may contain as 50% of all organic
material in ecosystem  nutrients may remain for fairly long periods before plants assimilate them
- decomposition on land is lower when conditions are too dry for decomposers to thrive or too wet to supply them
with enough oxygen
o e.g. peatlands: ecosystems that are both cold and wet: store large amounts of organic matter but
decomposers grow poorly there and net primary production exceeds decomposition
- CO2 released during decomposition: faster decomposition will release more CO2 and may accelerate warming trend
o temperature strongly influences decomposition rates in Canadian soils
o northern soils contain much organic matter  increases in decomposition rates  add quantities of CO2(g)
- decomposition in aquatic ecosystems: detritus usually sinks and decomposes in bottom sediments of lakes and oceans
o can be slow due to low temperatures or if dissolved oxygen becomes depleted
o nutrients are released at bottom of lake or ocean, far from photosynthesizing organisms in surface  aquatic
ecosystems are very productive only when deep nutrient rich water is brought to surface in regions of
upwelling in ocean or during fall turnover in temperate lakes
-
FIELD STUDY: NUTRIENT CYCLING IN THE HUBBARD BROOK EXPERIMENTAL FOREST
- nutrient cycling at Hubbard Brook Experimental Forest: deciduous forest that grows in six small valleys each drained
by single creek, impenetrable bedrock underlies soil
o determined mineral budget: measured input and outflow of key nutrients; collected rainfall through
constructing small concrete dam
o found that 60% of water added to ecosystem as rainfall and snow exits through stream and remaining 40%
is lost by evapotranspiration
- internal cycling conserved most of mineral nutrients in system
o small net loss of calcium leaving valley via creek, rain water is replaced by chemical decomposition of bedrock
- deforested one of watersheds  over 3 years, water runoff from deforested watershed was 30 – 40% greater than in
control watershed  no plants to absorb and transpire water from soil
o concentration of Ca2+ increased 4 fold and concentration of K+ increased by factor of 15
o loss nitrate, concentration in creek increased 60 fold
- showed than amount of nutrients leaving intact forest ecosystem in controlled mainly by plants

- retaining nutrients in ecosystems helps to maintain productivity of systems and to avoid problems in enighbouring
ecosystems caused by excess nutrient runoff

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Queen's

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o do not need to look this up

FOOD VACUOLES IN PARAMECIUM (SLIPPER-FOOTED)

EQUINE DIGESTIVE TRACT

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Week 13.3 Lecture Notes

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o components of gastric juice are produced by cells in gastric glands of stomach

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o bicarbonate neutralizes acidity of chyme

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Week 14.1 Excretion Lecture Notes

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SALTWATER FISH (BONY FISH)

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- nitrogenous waste ammonia  urea when water is not available

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Week 14.2 Excretion Lecture Notes

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▪ sodium goes downhill  drags glucose uphill

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o ATP dependent bile salt transporter in liver: produces bile

- gout: have to cut down of meat intake

MOVEMENT AND MUSCLE CONTROL

ANIMAL CELLS MOVE USING CONTRACTILE PROTEINS IN MICROFILAMENTS

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- adds actin to the pseudopodia of the amoeba

PHAGOCYTOSIS AND MOVEMENT

- cell moves because of filaments

VERTEBRATES MOVE USING SKELETAL MUSCLES THAT ACT ON SKELETON

- two major proteins: actin and myosin

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SKELETAL MUSCLE STRUCTURE

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Week 14 Osmoregulation and Excretion Textbook Notes

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THE INFLUENCE OF EVOLUTION AND ENVIRONMENT OF NITROGENOUS WASTES

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SURVEY OF EXCRETORY SYSTEMS

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