Chapters 14-15

DNA and Molecular Genetics

Chapter 14
Questions:
1. Where is the hereditary material located?
2. What chemical is it?
3. What is its structure?
4. How does it function?

Where is the hereditary material?

 Hammerling (Danish biologist): 1930s (See Page 280) Cells Store Hereditary
Information in the Nucleus
 Acetabularia algae
- Unicellular, large (5 cm)
- Surgically altered
- Distinct foot (bottom), stalk (middle), and cap (top) regions
- Hypothesized that hereditary information within the foot and tested through his
experiment
- Experiment: - 2 species from the genus Acetabularia (different caps A.
mediterranea: disked shaped cap and A. crenulata: flowerlike, narrow
cap)
- took a section from the stalk of each plant and placed them in section
missing from the other plant  called grafting
- what was discovered was that the original cap developed thus came to
the conclusion that the nucleus-containing foot dictated which cap formed
rather than the stalk
 Briggs and King (American biologists) – 1952 (See Page 281) Each Cell Contains a
Full Set of Genetic Instructions
- Nuclei transplant-frogs
- Totipotency observed (each nucleus contains a full set of hereditary instructions and can
generate an entire adult individual)
- Experiment: - a nucleus was removed from a frog egg (sucking w/ micropipette or by
destroying it with UV light)
- Differentiated cell nucleus is inserted into enucleate egg
- Three results were obtained:
1. No growth occurred (perhaps from damage to the egg cell during
nuclear transplant operation)
2. Normal growth and development occurred up to early embryo
stage then development was not normal and the embryo did not
survive.
3. Normal growth and development occurred leading to
development of an adult frog
 *Point?!?!?*
- Nucleus holds hereditary material and contains a full set of genetic instructions
- But what was that material made of?
- Early idea: protein
-Gene: the units of hereditary information study by Mendel (arranged in the chromosomes)
-DNA: deoxyribonucleic acid
-RNA: ribonucleic acid
 Griffith (British microbiologist): 1928 (See Page 282) Hereditary Information Can
Pass Between Organisms
- Worked with ‘Streptococcus’ bacteria and mice
- Bacteria with virulent (pathogenic or “disease causing”) coat
- Experiment: - Virulent strain of S. pneumoniae  mice died of blood poisoning
- Mutant strain of S. pneumoniae that lacked the virulent strain’s
polysaccharide coat  showed no ill effects
- Therefore: coat = virulence
-Four Trials:
1. Mice were injected with a live pathogenic strain S. pneumoniae
mice die
2. Mice were injected with a live nonpathogenic strain of S.
pneumoniae  mice live
3. Mice were injected with heat-killed pathogenic strain of S.
pneumoniae mice live
4. Mice were injected with a mixture of heat-killed pathogenic and
live nonpathogenic strains of S. pneumoniae mice die; their
blood contains live pathogenic strain of S. pneumoniae
** Griffith concluded that the live cells had been “transformed”
(transformation: transfer of genetic material from one cell to another)
by the dead ones; that is, genetic information specifying the
polysaccharide coat had passed from the dead cells to the living
ones.**
 *Point?!?!?*
- Figured out “transformation”  happens in bacteria not in humans
- Gene transfer from cell to cell
- “Dead” DNA  Live bacteria

 Avery: 1940s  The Active Principle is DNA

- What chemical was transforming the bacteria?
- Avery repeated Griffith’s work but…
* 99.98% protein removed (solution that was injected)
- Infection of mice the same
*Conclusion: DNA!!!!
 Hershey and Chase: 1952 (See Page 283)  The Active Principle is DNA
- Avery not widely believed
- Hershey and Chase: bacteriophages (viruses that attack bacteria)
*Labeled phage DNA and protein differently with isotopes…
- Experiment: - In a series of experiments using two different mediums
- One virus was grown in a medium containing an isotope of phosphorus,
32
P, and the isotope incorporated into the phosphate groups of newly
synthesized DNA molecules
 - The other virus was grown in a medium containing an isotope of sulfur,
35
S, which is incorporated into the amino acids of newly synthesized
protein coats.
- The protein was radioactive in 35S and the DNA was radioactive in 32P.
- After both viruses infected bacteria, the 35S and 32P the agitated the
surface of the bacteria and was removed from the surface.
- The 35S was nearly all removed and thus the viral protein, which was not
located within the virus’s DNA, was removed.
- The 32P was removed as well however the viral DNA were transferred in
the interior of the bacteria.
-Viruses subsequently released from the infected bacteria contained the
viral DNA thus spreading the more.
- Conclusion
* Hereditary information injected into bacteria was DNA and not protein…
What was the structure of DNA?
 1869: Miescher (German chemist) “discovered” DNA
- Extracted from nuclei of cells
*Called it “nuclein”…
 Levene, 1920s
- Figured out basic structure of DNA
- Had 3 components:
1. Nitrogenous bases
2. 5 carbon sugar (deoxyribose)
3. Phosphate group
(These three things make up a single nucleotide)
- Purines: 2 rings
* Adenine (A)
* Guanine (G)
- Pyrimidines: 1 ring
* Thymine (T)
* Cytosine (C)
- DNA polymers
- Linked through phosphodiester bonds
- Note 5’ vs 3’ direction
- Problem:
- Levene thought the nucleotides repeated AGTC….AGTC…etc
- Puzzling – How could it be the genetic material?
 Another DNA discovery
 Chargaff – 1940s
- His data…
- Chargaff’s rule
* Amount of G always = amount of C
* Amount of A always = amount of T
 Putting the pieces together
 Rosalind Franklin: late 1940s
- Studied DNA’s 3-D structure
 - Franklin worked in the lab of Maurice Wilkins
- Technique used  X-ray diffraction
- Wilkins good at preparing DNA for this process
- Franklin being a woman in a man job, people did not take her seriously
- Franklin was very conservative in jumping to conclusions that she did not want to be
wrong in her conclusions  she would test and test her conclusion before presenting
information as fact…and she knew that DNA was a double helix but she waited too long
 Finally…
 James Watson and Francis Crick: 1953
- Built models of DNA to figure out its structure
- Importance: figured out the shape was a double helix
- Their model
* 2 strands: complementarity (fit together perfectly)
* N- bases paired by H bonds
A with T
C with G
* “Backbone” of P and sugar
* Strands run antiparallel (runs backwards from each other 3’ to 5’ and on the
other side 5’ to 3’)
- Importance of structure
1. Suggested how DNA could be duplicated
2. Suggested how DNA could allow for all the diversity of life
- Only 4 bases, but could be in any order
- Not simple repetition of bases
 DNA Replication
- When does this occur?
- During the S phase of the cell cycle
- Chromosomes are duplicated (DNA replicated)
- Method of replication is semiconservative (Each strand of the old DNA becomes half of
the new strand
- before replication: one DNA molecule
5’-ATTGCAT-3’
3’-TAACGTA-5’
-after replication: two DNA molecule
5’-ATTGCAT-3’
3’-TAACGTA-5’

5’-ATTGCAT-3’
3’-TAACGTA-5’
 History
-f
- Labeled DNA of bacteria with isotopes of N
- Then followed DNA replication…
See page 289
 Replication process
- Speed: 1000 nuc per second
 - Enzyme: DNA polymerase III (aka. pol III)
- Adds new nucleotides
- Can only begin if a temporary primer of RNA added first
- Added by primase
- DNA pol III then recognizes the primer
 Other enzymes
- Helicases: Open up the old strand (unwinding)
- Gyrases: Relieve the twisting force on the old strand
- Strands held in place by single-strand binding proteins
 Strand assembly
- DNA polymerase can only add to the 3’ end of DNA
- Replication goes 5’  3’
- So…2 strands assembled differently
- Why? b/c they are antiparallel
 Process (See 292)
- Leading strand: new DNA added toward the replication fork
- Lagging strand: new DNA added away from the fork in short segments
- Called Okazaki fragements (100-200 nucs long)
- Joined by DNA ligase
 So now we’ve answered everything but…
- How does DNA actually function?
- How are Mendel’s units of heredity related to DNA?
- History: early research – Garrod and Bateson – 1902
- Recessive diseases caused by lack of one enzyme (Ex. Alkaptonuria )
[ http://www.alkaptonuria.info]
 How does DNa work?
- Beadle and Tatum -1940s – guessed that genes specify particular enzymes
- “One gene/One enzymes”
- Fungi mutations
- See Figure 14.21
- 1953 – Sanger – AA sequence of insulin
- 1956 – Ingram – sickle cell
- Led to revelation:
- DNA “works” by coding for AA seq
- “one gene/one polypeptide”
- GENE: a sequence of DNA that determines a sequence of amino acids
(genes are instructions for proteins)
Chapter 15
 The ‘Central Dogma of Biology’
= Gene Expression
- 2 step process
- Transcription: in nucleus
- DNA  RNA
- Translation: in cytoplasm (at ribosomes)
- RNA  protein
 Transcription
 - DNA into RNA
- RNA polymerase
- builds new RNA based on DNA sequence
- Template strand – DNA strand that is transcribed
- Coding strand – not transcribed
 RNA
- Structure:
- 1 strand
- P group
- Ribose sugar
- N base
- Uracil, not Thymine
 3 Types of RNA
- Ribosomal RNA (rRNA)
- Makes up ribosomes
- Transfer RNA (tRNA)
- Carries AA to ribosome
- Messenger RNA (mRNA)
- Codes for proteins
 What happens to the mRNA?
- Leaves nucleus
- Attaches to ribosome
- Undergoes translation
- A sequence of AA built from RNA
 How is mRNA read?
- Every 3 nucleotides (A codon) codes for ONE amino acid
-EX: GUA codes for valine
-See p. 305
 Translation: actual process
- First step: Initiation complex formed
- mRNA
- Small ribosome subunit
- tRNA (Carries 1st amino acid)
- tRNA has “anti-codon”
- matches mRNA
- Then: large ribosome subunit creates three binding sites on the ribosome
- E, P, A
E = “exit” – tRNA exits
P = “peptidyl” – where tRNA binds and new amino acids link up
A = “acceptor” or “aminocyl” – where the next tRNA binds
 Genetics Recap:
-How does DNA “work”?
-Coding system for making proteins
-Technological applications?
-Stem Cell Research, Cloning, Gene Therapy, Saving Endangered Species,
BioChemistry using genes (Homework 5)
 Animal Biology
-First Question: What is an animal?
Kingdom Animalia
- Heterotrophic: you have to eat other organisms in order to survive
- Multicellular
- Eukaryotic without cell walls
- Motility
- Sexual reproduction
- Common evolutionary history
-phylogeny: hypothetical evolutionary history
- Our Focus: Phylum Chordata
-Notochord: flexible rod
-Dorsal nerve cord
-Pharyngeal gill slits
-Post-anal tail
 Chapter 42
- What is the vertebrate body plan?
-Coelom: body cavity
- Divided by diaphragm
1) Peritoneal cavity: lower cavity  holds your guts
2) Thoracic cavity: heart and lung region
-Pericardial cavity: holds heart
-Pleural Cavities: holds lunges
- How is the body organized?
Macromolecules  Organelles  Cells  Tissues  Organ  Organ System 
Organism
- Seven Systems of our body
1. Digestive
2. Respiration
3. Circulatory
4. Excretory: get rid of nitrogenous waste
5. Endocrine: Hormones
6. Immune/Lymphatic
7. Muscular
8. Skeleton
9. Nervous
10. Integumentary
11. Reproduction
- Be sure you can
- Name them
- Give Their function
- Know components as listed on page 857
First Topic: Muscles and Movement
- 3 types of muscle:
- Cardiac, smooth, skeletal
- Question: How does a skeletal muscle contraction cause the body to move?
- Answer: Moves bone
- Attachment:
o Insertion- attached to bone that moves
o Origin- stationary
- Movement
- Flexion- bones towards each other
- Extension- bones move apart
- Action
- Synergists- muscles cause same action
- Antagonists- produces opposing action
- Question: What is the structure of a skeletal muscle?
- See page 874
- Tendon- bone to muscle
- Ligaments- bone to bone
- Muscle fascicle- a bundle of muscle cells
- Muscle fiber- a single muscle cell
- Myofibril- a bundle of muscle proteins
- Myofilament- individual actin or myosin protein
- “Myo”= muscle
- Question: How are myofilaments arranged in a cell?
- Actin and myosin- distinct bands
- Gives striated appearance
- Question: How does a muscle contract (shorten)?
- How? Proteins slide past each other
-The proteins don’t shorten
- Called “Sliding Filament Mechanism”
- How does it work?
- Forming cross bridges
- Myosin: heads
- Binds to actin
- Does contraction use Energy?
- Yes: ATP!
- Binds to myosin
- “Activates” heads
- When ATP leaves > head released
- (Adenosine Tri Phosphate: ADP + P)
- Rigor mortis? Cause by lack of ATP in the body
- The Cross- Bridge Cycle is where the the ATP comes in and attaches to the Myosine
head and then the ATP is cleaved (ADP +P) and it moves back when the ADP + P leaves
the head. It then attaches to the actin moving it
- How is muscle contraction regulated?
- Ca+2
- If low: no sliding
- If high: sliding
- Why?
- Ca binds to troponin
 - causes tropomyosin to shift
- Exposes binding site on actin
- Cross bridge forms
- Pg. 878
- Ca stored in SR (Sarcoplasmic Reticulum)
-Released when muscle stimulated
-“Signal” travels down T tubule
- When finished
-Ca: active transport back to SR
- How are muscles stimulated to contract?
- By somatic (body) motor (cause some kind of reaction) neurons (nerve cell)
- At synapse – synaptic cleft
- Release of Acetylcholine (ACh)
- Neurotransmitter
- Stimulates muscle contraction
- Acetylcholinesterase  enzyme (ACh is broken down by
(Acetyl)cholinesterase) Pg. 948
- Degrades ACh in synapse
- Motor Unit: muscle fibers plus neuron
- Which would have smaller units?
- (smaller = fewer fibers per neuron)
- Eye or leg muscle?
- Eye: Finer degree of control
- Types of muscle fibers
- Type 1 (slow twitch or red fibers)
- Contract slowly
- Slow to fatigue
- Lots of myoglobin
-“dark meat”
- Types 2: fast twitch or white fibers
- Contract fastly
- Fast to fatigue
True or False: bodybuilders have more muscle cells than most people?
False:
 Strength training increases muscle fiber size by adding protein
 Metabolism: a higher % of ATP from fat metabolism
 Better blood flow to muscles
Chapter 43: Digestion
Definitions:
 Digestion: Breaking it down
 Absorption: bringing it into the circulation
 Mastication: Chewing
Types of digestive systems…
 Gastrovascular Cavity: one pouch that food goes into/ one opening for food to go in and
out
 Nematode: Mouth, Pharynx, Intestine, Anus (See 43.3)
  Earthworm: Mouth, Pharynx, Crop, Gizzard, Intestine, Anus (See 43.3)
 Salamander: Mouth, Esophagus, Stomach, Liver, Pancreas, Intestine, Cloaca, Anus (See
43.3)
Human digestive tract
 Can you trace the path of food through the digestive tract, naming the correct sequence of
organs/ structures?
1. Mouth
(salivary glands)
2. Esophagus
3. Stomach
(Pancreas, Liver, Gallbladder)
4. Small Intestine
5. Large Intestine
6. Rectum
Layers of the GI (gastrointestinal) tract
See 43.5
 GI layers (inside  out)
- Lumen (space)
1. Mucosa (epithelial tissue)
2. Submucosa (connective)
3. Muscularis  Circular layer
 Longitudinal layer
4. Serosa (connective/ supportive layer)
(Surrounding the GI Layers are nerve plexus & glands)
Swallowing reflex
See 43.9
- Pharynx: Back of the throat
- Larynx: “voice box”
- Epiglottis: Flap of tissue covering resp. system
- Glottis: opening to resp. system
How do we not chock when eating?
- The back of the throat closes up and the larynx moves upward and the Epiglottis closes
off your trachea allowing the food to proceed down the esophagus
See 43.10
- Peristalsis: movement of food through GI via smooth muscle / “waves” of contraction
- We don’t have a true contracted muscles which allows us the have heart burn and
enables us to throw up
Stomach Structure
See 43.11
- Esophagus
- Stomach
- Mucosa
- Epithelium
- Pyloric sphincter
- Villi
- Duodenum
Stomach
 Functions
- Mixing
- Holding
- Secretions…
- Partietal cells
- HCl (ph of 2)
- Intrinsic Factor (for B12)
- Chief cells
- Pepsinogen
- Mucous cells – mucus
- Secretions + food = “Chyme”…
- Why a low pH?
- Denature food protein
- Activates pepsin
- Kills some bacteria
- What is digested?
- Proteins mostly
- What is absorbed?
-
Small Intestine
- Length: ~10 feet (alive)
- Why “small”?
- Overall function of sm. Intestine?
- Digestion and absorption
- Shape?
- Very folded
(See 43.12)
- Villus- projection of mucosa
- Cell membrane- folded “brush border”
Digestive accessory organs
Pancreas
- Acini cells secrete:
- Zymogens (inactive enzymes)
- Activated in s.i.
- Trypsin, chymotrypsin
- Amylase
- Lipase
- Bicarbonate
- Hormones
- From “Pancreatic islets”
- Insulin – Beta cells
- Regulate glucose untake into cells
- Glucagon – Alpha cells
- Breakdown of glycogen in liver
Diabetes mellitus
 - Characteristic of diease?
- Type 1: not enough insulin
o Why injected?
- Type 2: cells not sensitive to insulin
Liver and pancreas
- Liver – produces bile
o Emulisifies fats
- Also filters bloobd after digestion
- Gallbladder
- Stores bile
Nutrient Absorption
(See 43.14)
Large Intestine
- Why “large”?
- Main Function?
- Waste concentration
Who has a longer digestive system?
- Herbivore or carnivore? Why?
- Herbivore has a longer digestive system and has to eat more.
Chapter 44 ~ Circulation and Respiration

Circulatory system types:

- Open: blood flows over organs freely
- “Hemolymph” = blood plus extra fluid
- Example: insects
- Closed: blood is contained within vessels
- Example? US and Earthworms
Functions?
- Transport
o Respiration, nutritive, excretory
- Regulation
o Hormonal, temperature
- Protection
o Clotting, immune defense
Vasodilation: vessel + open up / when blood comes close to surface and capillaries open up and
heat is given off
Vasconstricion: keeps blood away from capillaries which are close to the skin so heat is
conserved
Countercurrent Heat Exchange: keeps the core of the animal warmer so that the warm blood is
pumped out to the extremities keeping the animal warm/ cold blood out and warm blood pumped
in
Blood
- 2 main parts:
o 55% plasma, 45% cells
- How much?
o 4-6 liters in adults
 - Plasma
o Contents: metabolites, wastes, hormones, ions, proteins
 Albumin – osmotic pressure
 Globulins – carry lipids
 Fibrinogen – for clotting
 Serum = plasma w/o fibrinogen
Blood Cell:
 Erthrocytes - red blood cells
o 99% of blood cells
o For what?
 Transports oxygen
- How many?
o 5 million in 1 mL
- Form where?
o Stem cells in bone marrow
o Stimulated by erythropoietin
- Leukocytes – white blood cells
- Defense
- Platelets: clotting
- From megakaryocytes in marrow
Blood vessels
 Blood flow
o Can you trace the flow from heart and back?
o Heart > arteries > arterioles > capillaries > venules > veins > heart
Vessel structure
- See 44.7 – difference?
- Diameter: Biggest vein > artery > capillary
- Artery has a thicker smooth muscle than vein
- Capillary exchange gases because it really has no layers and the layers if any are thin
Comparative anatomy
- Fish vs Amphibian vs Mammal
- Differences/similarities
- Fish Circulation (Pg. 915/ See 44.12)
o Goes from heart: Deoxygenated blood that goes to the gills then to the body and
back to the heart
o 4 chambers – linear sequence
o Heart > deoxy. gills > oxygen > body > deoxy> and back to the heart
- Amphibian and Reptile Circulation (Pg. 916/ See 44.13)
o Only 3 chambers that make up the heart
 Rt Atrium
 Lt Atrium
 1 ventricle (we have two): pumps out “mixed” (oxy. + deoxy) blood
- Mammalian and Bird Circulation (See 44.14)
o Heart: can you trace the flow of blood through the heart?
 (Deoxy) Ant. Vena cava & Post. Vena cava > Rt Atrium > Rt Ventricle > lungs >
(Oxy) Lt Atrium > Lt Ventricle > (aorta) to body > capillaries(back to deoxy.)
o Atrioventriclar: Tricuspid valve and Bicuspid mitral valve
o Semilunar: Aortic semilunar valve and Pulmonary semilunar valve
Cardiac cycle
- Systole - contraction
- Diastole – rest
- Blood pressure reading
- systolic over diastolic pressure
- Ex: 120/80
Respiration
- Respiration vs Cellular Respiration
- Basis: Diffusion
- Fick’s Law
o Diffusion rate determined by:
 Surface area
 Partial pressure (gas concentration)
 Difference in pp
- distance
Pg. 923/ See 44.19
Atmosphere
- Made of what gases?
 78% N2, 21% O2, traces of others
- Air pressure at sea level
o 760 mm Hg
- Each gas has a partial pressure
o For O2 = 159.2 mmHg (=760*0.21)
- Why can’t humans breathe at high altitudes? (See 44.20)
o The pressure of oxygen is different but the amount of oxygen is the same
Fish: Breathing in Water
- Need gills: increase surface area
- Countercurrent flow
o Blood flow opposite of water
o Maximizes oxygenation of blood
o Most efficient in nature
o 44.21
Breathing in Air
- Why can’t fish breath in air?
o Air contains 200x O2
 Buoyancy
 Evaporation
- Terrestrial respiration: 2 main types
o Tracheae – insects
o Lungs – terrestrial vertebrates
 Air becomes water saturated
Amphibians
- Create “positive” pressure
o Higher atm pressure outside body
- All other verts
o Use negative pressure
o Create lower aatm pressure in lungs
See 44.25/ Human Respiratory System
Hemoglobin – 4 subunits
- Each subunit = has heme group  Fe (iron) binds to O2
- Oxyhemoglobin = O2 + Hb (Hemoglobin)
Oxygen transport
- Po2 of air in alveoli = 105 mmHg
- Po2 = partial pressure of O2
- 105 mmHg
- Po2 of blood in lung? 40 mm Hg
- So, O2 diffuses into blood
- About 20 % of oxyen unloaded to tissues
o 80% remains in blood as reserve
Co2 and NO transport
- Co2 also carried in blood
o 8% dissolved
o 20% bound to Hb
o 72% in form of H2CO3 in RBC
- NO also carried by Hb
o Role: vasodilation
o Viagra?
System Circulation See 44.7
Breathing measurements
Tidal volume:
- Amt of sir exchanged in a breath
o (~500 ml)
Vital capacity:
- Max amt of air expired
o 4.6 L in men, 3.1 in women
Emphysema – reduction of vital capacity
Hypoventilation:
- Insufficient breathing (more Co2)
Hyperventilation:
- Excessive breathing (less Co2)