Table of Contents: SAT 2 Biology Turquoise Waffles ® 1

SAT
2 Biology Turquoise Waffles ® 1

Table of Contents

Biochemistry ............................................................................................................................................................. 2
Basic Chemistry – Atomic Structure ............................................................................................................................... 2
Intermolecular attractions ................................................................................................................................................ 2
Characteristics of water ..................................................................................................................................................... 2
Organic Compounds ............................................................................................................................................................ 3
The Cell ........................................................................................................................................................................ 5
Cell Theory .............................................................................................................................................................................. 5
Prokaryotes vs. Eukaryotes .............................................................................................................................................. 5
Different structures in plant and animal cells ............................................................................................................ 5
Transport across cells ......................................................................................................................................................... 7
Tools and Techniques to study cells .................................................................................................................. 8
Cellular Respiration ................................................................................................................................................ 9
Pyruvate Dehydrogenase Complex (PDC) .................................................................................................................... 9
The Krebs cycle ..................................................................................................................................................................... 9
Electron transport chain and Oxidative Phosphorylation ..................................................................................... 9
Anaerobic respiration ....................................................................................................................................................... 10
Transcription and Translation .......................................................................................................................... 10
DNA replication ................................................................................................................................................................... 10
Protein synthesis ................................................................................................................................................................ 10
Mitosis and Meiosis ............................................................................................................................................... 11
Genetics ..................................................................................................................................................................... 12
Microorganisms ...................................................................................................................................................... 13
Plants ......................................................................................................................................................................... 15
Photosynthesis .................................................................................................................................................................... 15
Transport in plants ............................................................................................................................................................ 16
Flowers and reproduction ............................................................................................................................................... 16
Control: Nervous and Endocrine Systems ..................................................................................................... 16
The Nervous System .......................................................................................................................................................... 16
The Endocrine System ...................................................................................................................................................... 17
The Circulatory System .................................................................................................................................................... 19
The Respiratory System ................................................................................................................................................... 20
The Digestive System ........................................................................................................................................................ 20
The Urinary System ........................................................................................................................................................... 21
The Skeletal System ........................................................................................................................................................... 22
The Muscular System ........................................................................................................................................................ 22
The Skin ................................................................................................................................................................................. 23
Male Reproductive System .............................................................................................................................................. 23
Female Reproductive System ......................................................................................................................................... 23
Fertilization, Embryology and Fetal development .................................................................................................. 24
Evolution and Diversity ....................................................................................................................................... 25
Phylogeny ................................................................................................................................................................. 26
Behavior .................................................................................................................................................................... 29
Ecology ....................................................................................................................................................................... 30

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SAT 2 Biology Turquoise Waffles ® 2
Biochemistry

Basic Chemistry – Atomic Structure
à Atoms in the elemental stage have a neutral charge
à Electrons in the lowest available energy level are said to be in the ground state
à When an atom absorbs energy, it enters the excited state where electrons move to a
higher energy level
à Radioactive Carbon can be used as a ‘tracer’ in CO2 to track metabolic pathways
à Radioactive Iodine can be used to diagnose and treat certain diseases of the thyroid
gland
à Energy is released when a bond is formed

Intermolecular attractions
à Polar-‐polar attraction
Negative end of one polar molecule attracts positive end of another polar molecule
à Hydrogen bonding
o Keeps two strands of DNA together
o Causes water molecules to stick together
à Non polar molecules
Weak Van der Waals forces
à Hydrophobic vs. Hydrophilic
o Hydrophobic are non polar and do not dissolve in water
o Hydrophilic are polar and dissolve in water; they need a protein channel to cross
plasma membranes

Characteristics of water

1. Water has a high specific heat
à Large water bodies absorb a lot of heat and resist changes in temperature
à This characteristic allows water bodies to provide a stable environment for marine life

2. Water has a high heat of vaporization
à Large amount of heat is required to evaporate water
à This is why evaporation of sweat significantly cools down the body

3. Water has high adhesion properties
à Contributes to capillary action in plants

4. Water is the universal solvent
à It is highly polar so it dissolves almost all polar and ionic substances

5. Exhibits strong cohesion tension
à No energy needed in transpiration because of this
à Allows some insects to walk on water due to surface tension

6. Solid form (ice) less dense than liquid form
à Insulates water bodies in winters (when layer of ice covers the surface)
à Stratification of lakes in winters and mixing in spring
à Oxygen and nutrients are circulated; “Spring overturn”

⊗ Power of Hydrogen
à The more the concentration of H+ ions, the less the pH
à pH is regulated through buffers, the most important one being the bicarbonate ion
HCO3-‐
à pH increases by a factor of 10 (conc. Of H+) each successive level

Organic Compounds

Hydrolysis is opposite
Carbohydrates of dehydration
• Supply quick energy synthesis and occurs
• 1 gram releases 4 calories when burned during digestion
a) Monosaccharides
i. C6H12O6
ii. Glucose, Galactose and Fructose
b) Disaccharides
i. C12H22O12
ii. Consists of 2 Monosaccharides joined together by dehydration synthesis

a) Glucose + Glucose à Maltose + Water
b) Glucose + Galactose à Lactose + Water
c) Glucose + Fructose à Sucrose + Water

c) Polysaccharides
i. Polymers of carbohydrates
ii. Formed when many Monosaccharides join together
• Cellulose – plant cell walls
• Starch – storage in plants
• Chitin – exoskeleton in arthropods and cell wall in fungi like
mushroom
• Glycogen – animal storage in liver and muscles

Lipids
• Fats, oils and waxes
• One glycerol and three long fatty acids
• Glycerol is an alcohol
• Fatty acid is hydrocarbon chain with carbonyl group at one end
o Saturated: mostly from animals, solid at rtp1, related to heart disease
o Unsaturated: extracted from plants, liquid at rtp, have at least one C=C (Carbon double
bond) hence fewer Hydrogen atoms
• Functions:
i. Energy storage – 1 gram releases 9 calories when burnt in a calorimeter
ii. Structural – Phospholipids are a major component of cell membranes
iii. Endocrine – Some hormones are made of lipids

1 Room temperature and pressure

Proteins
• Polypeptides are formed by amino acids joined by peptide bonds
• Amino acids consist of a carboxyl group, an amine group and a variable (R) group

H O
H
N—C— C —OH
H
R
Complex macromolecules responsible for growth and repair
•
1 gram releases 4 calories when burned
•
Consists of S, P, O, C, H and N elements
•
There are only 20 different types of amino acids
•
A dipeptide consists of 2 amino acids and 1 peptide bond
•

à Structure
1. Primary – sequence of amino acids making the chain
2. Secondary – Hydrogen bonding within the molecule
3. Tertiary – 3D shape that most directly determines its function and specificity. Affected
by high temperatures or adverse pH depending on the types of bonds present
4. Quaternary – more than one polypeptide chain

Enzymes
• Large proteins
• Lower activation energy in chemical reactions
• Induced fit model for working of enzymes replaced the lock and key hypothesis
• Reused after they participate in catalysis of a reaction
• May function with assistance from cofactors (minerals) or coenzymes (vitamins)
• Efficiency depends upon temperature and pH
• When denatured, they lose their shape and ability to function

Prions
• Group of infectious proteins that cause several brain diseases such as mad cow disease
• Version of a protein normally found in brains of mammals that isn’t folded properly

Nucleic acids
• Includes DNA and RNA which carry hereditary information
• Polymers of nucleotides
• A single nucleotide consists of a phosphate, a 5 Carbon sugar and a nitrogenous base
• DNA: Adenine, Guanine, Cytosine, Thymine
• RNA: Adenine, Guanine, Cytosine, Uracil
• Adenine and Guanine are purines
• Cytosine, Thymine and Uracil are pyrimidines


The Cell

Cell Theory à Most plant and animal cells have

I. All living things are composed of cells diameters between 10-‐100μm
II. Cells are basic units of all organisms à They are divided into prokaryotes and
III. All cells arise from preexisting cells eukaryotes

Prokaryotes vs. Eukaryotes

• Unlike eukaryotes, prokaryotes do not have membrane bound organelles like nuclei
• Prokaryotes contain a single circular chromosome while eukaryotes contain chromosomes
composed of DNA coiled and condensed around histone proteins
• Prokaryotes have 70s ribosomes while eukaryotes have 80s ribosomes
• Prokaryotes do not have cytoskeletal elements such as microfilaments
• Eukaryotic organisms respires aerobically in almost all cases while prokaryotes may respire
aerobically or anaerobically
• Prokaryotes are mostly unicellular while eukaryotes are mostly multicellular
• Prokaryotes are generally smaller in size (1-‐10μm) vs eukaryotes (10-‐100μm)
• Most prokaryotes have cell walls while most eukaryotes don’t (except plants and protists)

à Theory of endosymbiosis: 2 billion years ago, smaller prokaryotic cells took residence in larger
areas, forming complex eukaryotic cells. The internal membranes made the cell efficient and led to
the evolution of multicellular organisms.
à Eukaryotic cells have different shapes specific to their functions

Different structures in plant and animal cells

1) Nucleus
• Contains chromosomes made of DNA which is wrapped around histone proteins in a
chromatin network
• Surrounded by double membrane that contains nuclear pores

2) Nucleolus
• Where components of ribosomes are synthesized
• Contains tangles of chromatin and unfinished bits of ribosomes

3) Ribosomes
• Site of protein synthesis
• Made of ribosomal RNA and protein

4) Endoplasmic Reticulum
• System of membrane bound channels
• Rough Endoplasmic Reticulum: site of protein synthesis and transport
• Smooth Endoplasmic Reticulum:
i. Synthesizes steroid hormones and lipids
ii. Connects Rough ER to the Golgi apparatus
iii. Detoxifies the cell
iv. Carbohydrate (glycogen) metabolism

5) Golgi Apparatus
• Flattened sacs of membranes
• Modifies, stores and packages substances produced in the rough endoplasmic
reticulum
• Secretes these substances to other parts of the cell and for export outside the cell

6) Lysosome
• Sac of hydrolytic (digestive) enzymes
• Principal site of intracellular digestion
• Responsible for programmed cell death (apoptosis)

7) Mitochondria
• Site of cellular respiration
• A very active cell could have up to 2500 of them
• Enclosed in a double membrane with cristae
• Contains DNA and can self replicate

8) Vacuole
• Single membrane bound storage organelles
• Contractile vacuoles in Protista pump excess water out of cell
• Plant and human fat cells have large central vacuoles for storage

9) Vesicle
• Tiny vacuole
• Releases neurotransmitters into synapses in axons of neurons

10) Plastids:
i. Chloroplasts (photosynthesis)
• Contain a double membrane and grana which lie in a colorless fluid called
stroma
• Contain DNA and can self replicate
ii. Leucoplasts
• Colorless plastids that store starch
• Found in roots like turnips or tubers like potatoes
iii. Chromoplasts
• Store carotenoid pigments
• Responsible for bright colored pigments in petals, which attract pollinating
insects

11) Cytoskeleton
• Complex network of protein filaments extending throughout the cell
• Gives shapes to cell and allows for movement
à Microtubules
• Thick hollow tubes that make up cilia, flagella and spindle fibers
à Microfilaments
• Made up of actin protein; help support the shape of the cell
• Help animal cells form a cleavage furrow during cell division
• Help amoeba to move by sending out pseudopods
• Help skeletal muscles to contract by sliding along myosin filaments

12) Centrioles and centrosomes
• Two centrioles perpendicular to one another form a centrosome
• Organize spindle fibers for cell division
• Contain 9 triplets of microtubules

13) Cilia and Flagella
• Similar structures but flagella are longer
• Contain 9 pairs of microtubules organized around 2 singlet microtubules

14) Cell wall
• Composed of chitin in fungi and cellulose in plants/algae
• Primary cell wall is immediately outside plasma membrane in plants
• Middle lamella between plant cells holds adjacent cells together and plays an
important role in cell division

15) Cytoplasm and cytosol
• Cytosol is semiliquid portion of cytoplasm which surrounds organelles and gets
carried around the cell i.e. cyclosis

16) Cell or plasma membrane
• Fluid mosaic model is used to describe the membrane as it contains phospholipid
bilayer with proteins along with cholesterol to give it stability
• Has carbohydrate chains on exterior to aid cell recognition
• Composed of 60 percent proteins which include enzymes and pumps

Transport across cells

Passive transport
à Down the concentration gradient
à No energy needed
à Two types:
i. Simple diffusion
ii. Facilitated diffusion (with specific proteins in membranes)

Osmosis
à Movement of water molecules from region of higher water potential to region of lower
water potential
à When cell loses too much water, it shrinks (called crenation in animals and plasmolysis
in plants)
à When cell gains too much water, it bursts in the case of animal cells and gets turgid if it
is a plant cell
Hypertonic: greater concentration of solute
Hypotonic: lower concentration o f solute
Isotonic: same concentration of solute


Active Transport
à Movement against the concentration gradient which requires energy
à Exocytosis: active release of molecules from a cell
à Pinocytosis: uptake of large, dissolved molecules
à Phagocytosis: engulfing of large particles by pseudopods
à Receptor mediated endocytosis: take up of large quantities of very specific substances,
which bind to specific receptors on the cell membrane such as the take up of cholesterol

Tools and Techniques to study cells

The Life functions
à Main tool is compound microscope 1. Ingestion
à High magnification and high resolution is needed 2. Digestion
à Magnification= (strength of ocular lens)*(strength of objective lens) 3. Respiration
à Image being viewed is upside down 4. Transport
5. Regulation
1. Phase contrast microscope 6. Synthesis
• Light microscope that enhances contrast 7. Excretion
• Useful to examine unstained cells 8. Egestion
9. Reproduction
2. Transmission electron microscope 10. Irritability
• Useful for studying the interior of cells 11. Locomotion
• Source of electrons is tungsten filament 12. Metabolism

3. Scanning electron microscope
• Useful for studying the surface of cells where images have a 3D appearance

à Drawbacks of electron microscopes
1. Tissue is dead
2. Elaborate preparation
3. Specialized engineers needed to maintain it
4. Specimen must be sliced very thin
5. Very expensive

à Ultra centrifuge: Isolates specific components of cells in large quantities by cell fractionation.
The layers are separated based on differences in density.
à Freeze fracture: used to study details of membrane structure under electron microscope.
à Tissue culture: studies properties of cells in-‐vitro in labs

Cellular Respiration

C6H12O6 + O2 à CO2 + H2O + ATP

⊗ Electron carriers:
NAD+ + H+ + 2e-‐ à NADH
FAD + 2H+ + 2e-‐ à FADH2

Glycolysis (sugar splitting)
• Occurs in cytoplasm of cells
• It is an anaerobic process
C6H12O6 + 2ATP + 2NAD+ à 2Pyruvate + 4ATP + 2NADH

Pyruvate Dehydrogenase Complex (PDC)

• It is a group of enzymes that prepares pyruvate so it can enter the Krebs cycle
• Krebs cycle can only accept molecules with 2 Carbons so PDC removes 1 Carbon and
attaches remaining structure to coenzyme A
• Another NADH is produced in the process

CO2

Pyruvate Acetyl co-‐A
(3 Carbon atoms) (2 Carbon atoms) X2

NAD+ NADH

The Krebs cycle
• Occurs in matrix of mitochondria
1. Acetyl co-‐A + oxyloacetic acid à citric acid
2. Citric acid is broken down one at a time to release energy and rearranged to form
oxyloacetic acid molecule
3. {3NADH, 1 FADH2 and 1 ATP released} x2

Electron transport chain and Oxidative Phosphorylation

• Until now, only 4 ATP molecules have been produced
• Two main goals of ETC:
i. To oxidize electron carriers
ii. To use energy from these electrons to make ATP

• Takes place along inner membrane of mitochondria

• Carrier molecules of ETC use energy of electrons to pump H ions out of the matrix
+
and into the inter-‐membrane space

• Now there is a high concentration of H+ ions between membranes and these ions cannot
enter back (they are charged)
• They go back by means of ATP synthase, an enzyme in the membrane, which uses their
energy to convert ADP to ATP

Altogether, roughly 36 ATP molecules are produced from 1 glucose molecule

Anaerobic respiration

⊗ When oxygen isn’t available
à At the end of glycolysis, there are 2 ATP, 2 NADH and 2 Pyruvate molecules
à NADH gives electron to pyruvate to form NAD+ and,
i. Ethanol+CO2 in yeast
ii. Lactic acid in humans

⊗ Problems with fermentation
• End products are toxic to the organisms. Yeast die when ethanol concentration exceeds
12%. Muscle cells stop contracting if lactic acid levels are too high.
• Only 2 ATP molecules are produced instead of the regular 36 from aerobic respiration.
These are not enough for multicellular organisms.

Transcription and Translation

Complementary bases:
Adenine and Thymine
DNA replication Cytosine and Guanine
1. Double helix unwinds and strands separate
2. DNA polymerase lines up nucleotides to form new strands with complementary bases
3. Hydrogen bonds form between bases, bonds form between sugar-‐phosphate components of
newly aligned nucleotides
4. Double helices form by twisting
• Each DNA strand acts as a template for the formation of a new complementary strand
• Chromosomes exist in homologous pairs
• DNA’s job is to carry the instructions for making proteins

Protein synthesis DNA à RNA à Proteins

1. Transcription (transcription) (translation)
• DNA molecule unwinds and one strand serves as a template for transcription by RNA
polymerase
• The RNA is then released and DNA strands join together again
• Only some genes needed for a specific protein are transcribed
• Types and functions of RNA:
i. mRNA – Messenger: Carries information for protein synthesis from DNA in nucleus to
ribosomes in cytoplasm
ii. rRNA – Ribosomal: interacts with ribosomes to make them functional

iii. tRNA – transfer: Carries amino acids from cytoplasm to ribosomes during protein
synthesis
2. Translation
• Sequence of 3 nucleotides is called a codon and order of codons on mRNA specifies order of
amino acids in protein
There are 64
• Start codon AUG for methionine
possible codons
• Stop codons UAA, UGA, UAG which do not specify any amino acid

PART 1
à tRNA carries amino acids from cytoplasm to the ribosomes
à The anti-‐codon is a region on the tRNA which base pairs with codons on the mRNA
à On the other end of tRNA, there are amino acids that correspond to the codon on the mRNA
PART 2
à The mRNA binds to ribosomes and tRNAs carry amino acids to them
à There are two binding sites in ribosomes, A site and P site
à Then ribosomes form a peptide bond between every two successive amino acids
à The mRNA keeps sliding onwards till it reaches a stop codon
à P site: Peptide/ A site: Amino acid When a gene creates a
protein, it is said to be
‘expressed’
Mitosis and Meiosis

⊗ Interphase
à Cell carries out all of its normal activities Mitosis only occurs
à In S phase (synthesis), chromosomes replicate into two in meristems
(growth regions) in
⊗ Mitosis plants
1. Prophase
• Chromosomes condense and coil and nuclear envelope disappears
• Centrioles move away from each other
2. Metaphase
• Chromosomes line up at the equator (metaphase plate)
• Spindle fibers attach to centrosomes
3. Anaphase
• Chromatids are split apart and are pulled towards the poles of the cell
• Cell pinches inwards at the equator (cleavage furrow)
4. Telophase
• Nuclear membrane reappears and cytoplasm divides by cytokinesis
• Two daughter cells are formed which then enter interphase

⊗ Meiosis
To form gametes, where PMAT occurs twice
à Meiosis 1
1. Prophase 1
• All chromosomes find their homologous partners and pair up forming 23 pairs of
replicated chromosomes (also called a tetrad). This is called synapsis.
• After synapsis occurs, ‘crossing over’ takes place where like segments on homologous
chromosome are exchanged
2. Metaphase 1
• Chromosomes line up on equator of cell as 23 pairs

• ‘Independent Assortment of Chromosomes’ occurs where outcome of genetic
information depends on how the chromosomes line up
• Genes on same chromosome are called ‘linked genes’ and are inherited together,
crossing over may separate them
3. Anaphase 1
• Centromeres remain intact; homologous chromosomes separate and move to opposite
poles of the cell (no longer tetrads)
4. Telophase 1
• Cytokinesis occurs but the cells do not have homologous pairs of chromosomes, they
have 23 replicated chromosomes (both chromatids are identical) hence the cells are
considered haploid at this stage
à Meiosis 2
• Both cells formed undergo same stages as mitosis but there is no pairing of homologous
chromosomes in Prophase 2
• Telophase 2 gives us 4 haploid cells

à During Meiosis 1, division in a sperm cell is equally divided while in females; most of the cytoplasm
is concentrated in one of the two cells, which divides again. The other cell degenerates.

⊗ Spermatogenesis: Starts with a diploid cell called spermatogonium located in testes in the
seminiferous tubules
⊗ Oogenesis:
• Initial cell is a primary oocyte found in ovaries
• 2 cells are polar bodies which disintegrate as they receive no cytoplasm or organelles
• Occurs on a monthly basis from puberty to menopause

à Three causes of variation in genes of offspring:
1. Independent assortment of chromosomes during metaphase 1
2. Crossing over during synapsis in Prophase 1
3. Random fertilization

Genetics
• Phenotype refers to the actual traits that an organism possesses
• Genotype refers to the genes responsible for those traits
• Dominant: allele which expresses itself
• Recessive: allele which can not express itself in the presence of a dominant allele
• Alleles: different versions of a gene for the same characteristic

⊗ Homozygous and Heterozygous
à Homozygous is where the alleles are in agreement on a certain trait; the same
à Heterozygous is where the alleles are different b b
⊗ Co-‐dominance: Where a heterozygote expresses a mixture of traits of both B Bb Bb
alleles such as blood group AB
b bb bb
⊗ Punnett Square: Easy way to predict possible genotypes and phenotypes in a
given genetic cross
⊗ Sex chromosomes:
à They are the 23rd pair of chromosomes in humans that determine sex
à All other chromosomes are called autosomes

à Have many genes that determine sexual attributes as well as some genes that determine
nonsexual attributes
à Sex depends on whether offspring inherits X or Y chromosome from father
⊗ Mendelian Genetics
• Gregor Medel is known as the father of genetics
• He studied cross breeding on pea plants that were genetically pure and came up with 3 laws:
1. Law of Dominance
à Crossed tall plants with short plants
à Plants produced were all tall which shows that one trait masked the effect of the other
2. Law of Segregation
à When offspring from the first cross between tall and short plants are self pollinated, a
short plant may appear
3. Law of Independent Assortment
à When considering more than one genes, the alleles combine to give us more than 2
different gametes
à The two traits segregate randomly A test cross is used to
determine the
⊗ Dihybrid Cross genotype of a plant
• Uses 4 gametes instead of 2
• Produces 16 results in the Punnett square

⊗ Sex-‐linked traits
à A trait whose allele is carried on one of the sex chromosomes
à The X chromosome is larger and carries more genes
1) Hemophilia
2) Color blindness
3) Male pattern baldness
à All three are X linked recessive traits which only express themselves in homozygous females
while being expressed in all males as there is only one X-‐linked allele present
à X-‐linked recessive traits can not be passed down from father to son as only the Y chromosome is
involved in this case

⊗ Pedigree Analysis: It is a chart that shows the presence of a particular phenotype in a given
family over generations

Microorganisms

Fungi
à Mostly Multicellular eukaryotes which means they have nuclei and other organelles
à Some fungi don’t have cell walls separating cells and appear as one big cell with many nuclei
à Lack chloroplasts so they are heterotrophs and are absorptive feeders as they secrete hydrolytic
enzymes, which digest food outside their bodies. The digested food is then absorbed
à Reproduction:
i. Asexual spores: like seeds
ii. Sexual spores: combine to form new organism
iii. Vegetative growth: portion breaks off and forms new fungus
iv. Budding: new fungus grows on side of old fungus

Bacteria
à Reproduce asexually by binary fission
à The only prokaryotes; don’t have nuclei or membrane bound organelles
à Circular DNA; double strands joined at the ends
à Cell wall made of peptidoglycogen
à Binary fission does not allow genetic variation but the following do:
i. Transformation: bacteria pick up new DNA from extracellular environment
ii. Conjugation: replicates DNA and donates some of it to another bacterium through pilus
iii. Transduction: virus carry DNA from one bacterium to another during infection
à Types of Bacteria: àObligate aerobes n eed O2
• Saprobes: decomposers àObligate anaerobes poisoned by
• Parasites: nutrition from other organisms O2
• Symbionts: like parasites but not harmful for organisms àFacultative anaerobes can
survive either way
à Auxotrophs:
• Most bacteria are not auxotrophs and produce all they need from Carbon compounds such as
glucose
• Auxotrophs need additional substances, like amino acids, that they can’t make on their own
• If a substance they can’t synthesize isn’t added to their diet, they can’t grow
à Bacteria and Nitrogen:
• Ammonifying bacteria convert nitrogen released from breakdown of dead organic matter to
ammonium
• Nitrogen fixing bacteria convert nitrogen from atmosphere to ammonia in soil
• Nitrifying bacteria convert ammonium in soil to nitrates
• Some nitrogen fixing bacteria form a symbiotic relationship with plants where they live in
roots and supply nitrates in exchange for nutrients. They are called legumes.

Virus
à Consist of a protein coat called capsid and a nucleic acid called the genome (DNA or RNA)
à Can only reproduce with the help of another organism
à Viral life cycle begins with:
1. Attachment: to a host cell
2. Infection: injects genome to a host cell
à Once it has entered, it follows one of two cycles:
1. Lytic cycle
§ Viral genome is transcribed and translated using host’s RNA polymerases and
ribosomes to make viral proteins
§ Host DNA polymerases replicate viral genome which are injected into the capsids
§ Finally, host cell is lysed (broken down) by a special viral enzyme
2. Lysogenic cycle
§ Viral genome is integrated into host’s genome and is dormant
§ Viral genome is replicated every time host replicates
§ Viral genome can sty dormant for ages until host cell experiences stress (like illness)
of some sort where virus removes itself and enters the lytic cycle
à Virus in animal cells do not have to lyse it as there is no cell wall, they can simply escape through
the membrane, forming an envelope around the capsid as they leave
à Virus with RNA genome cannot use DNA polymerase or RNA polymerase of hosts as they both
depend on DNA, not RNA. It has to:
I. Carry an RNA dependent RNA polymerase with it to inject into host genome
II. Synthesize the protein during translation of the viral genome
à Retroviruses
• RNA viruses that undergo lysogenic life cycles
• A DNA copy of genome must first be made before integration

• RNA dependent DNA polymerase enzyme (reverse transcriptase) must be carried with
virus during translation
• AIDS and cancer causing viruses belong to this group

⊗ Restriction enzymes
§ Enzymes that recognize a particular short DNA sequence and cut the DNA strand within it
§ First discovered in bacteria that used it to cut and destroy foreign viral DNA
§ Own DNA of that specific sequence is protected by CH3 group
§ They read sequences that are palindromes
§ They may cut in a staggered way where short tails called sticky ends are left (Eco RI in E.coli/
Pst I in Providencia Stuartii) or cut in a blunt way where both strands are cut evenly (Hpa I in
Haemophilus parainfluenzae)
§ Blunt cut strands can be ligated with any other strands but staggered cut DNA can only be
ligated with a complementary strand
⊗ Plasmids
§ Circular piece of DNA found in bacteria and sometimes in yeast
§ Not a part of their genome and can reproduce independently
§ Its sequence contains restriction sites as it is DNA
⊗ Recombinant DNA technology
§ Creation of new DNA molecules by cutting and splicing the DNA with restriction enzymes
§ Instead of harvesting lots of DNA, specific gene is taken out and inserted into plasmid using
DNA ligase
§ Plasmid is inserted in bacteria and grown and same restriction enzymes are used to remove
the genes from the plasmids later on

Plants

⊗ Leaf structure
• Outer layers are epidermis covered with waxy layer (cuticle) to protect the leaf from
microorganisms and excessive water loss
• Guard cells in lower epidermis
• Mesophyll layer with palisade and spongy cells

Photosynthesis
à Occurs in chloroplast whose structure includes:
o Inner fluid called stroma
o Thylakoids found in stacks called grana
o Membranes of thylakoids containing chlorophyll
à Basic reactions:
1. Light Dependent reaction
§ Requires solar energy to excite electrons and produce ATP (like in respiration)
§ Chlorophyll causes light to be absorbed and electrons to become excited
§ These elctrons now have more energy and pass down an electron transport chain after
which they are handed off to NADP+ to form NADPH
§ Water is split into H+ and O2 (waste product) where H+ are used to make ATP through
ATP synthase when they exit the thylakoids
2. Light Independent reaction
§ Occurs in stroma and is called the Calvin cycle

§ Starts with ribulose biphosphate which is made of 5 Carbons and a molecule of CO2 is
added to make it a 6 Carbon chain
§ This chain is then made into 2 glyceraldehyde-‐3-‐phosphate chains
§ One of the G3Ps is used to make glucose and other carbohydrates while the other is
used to regenerate ribulose biphosphate
§ This process requires energy from ATP and NADPH and is also called ‘carbon fixation’

Transport in plants

à Xylem transports water and minerals; the specific cells transporting water are tracheids and
vessel elements
à Food from photosynthesis is transported by phloem which contains sieve cells and companion
cells

Flowers and reproduction

à Flowering plants are called angiosperms
1) The Stamen
§ Male component consisting of anther and filaments
§ Microspores make pollen in anthers
2) The Pistil
§ Female part containing stigma, style, ovules and ovaries
§ Ovules form megaspores which divide to make eggs and polar bodies
à One pollen grain contains two sperm cells, one fertilizes the egg to make the embryo while the
other fertilizes the polar bodies to make the endosperm

Control: Nervous and Endocrine Systems

The Nervous System

§ Nerve cells are also called neurons
§ Neurons have a cell body (soma) and processes sticking out called dendrites and one axon
§ They carry impulses by receiving them at the dendrites and passing them down the axon
§ When not carrying an impulse, a neuron is polarized
§ Resting Membrane Potential
o The inside of a cell is more negative (-‐70mV) due to two membrane proteins ‘Na+/K+
ATPase’ and ‘K+ leak channel’
o Na+/K+ ATPase pumps 3 Na+ outside and 2 K+ inside resulting in higher concentration of K+
inside the cell which leak out through the K+ leak channel
o This results in many positive ions leaving and negatively charged substances like DNA, DNA
and proteins being left behind
§ Voltage gated channels
o Neurons have these channels in their membranes which are closed at normal resting
potential but open at threshold potential (-‐50mV)
o Two types: Sodium and potassium voltage-‐gated channels
§ Action potentials
o When potential reaches -‐50mV, Na+ ions flood in till +35mV at which point the Na voltage
gated channel closes
o Now K voltage gated channel opens and K+ ions flood out of cell till -‐90mV when it closes
o The Na+/K+ ATPase and K+ leak channels restore balance of ions at -‐70mV

o An “impulse” is a traveling action potential where Na released from one voltage gate
+
creates a chain reaction all the way down the axon

o In some neurons, axons are wrapped in special
àPolarized: state of membrane at rest
cells called Schwann cells (Myelin sheath) with àDepolarization: membrane potential
spaces in between called nodes of Ranvier increases
o These nodes fire action potentials called àRepolarization: returns to resting value
salutatory conduction at instantaneous speeds
o Refractory period: the time period during which a portion of membrane can’t fire a second
action potential till the channels reset
§ Synapses (when impulse reaches end of axon)
o A neuron-‐neuron or neuron-‐organ junction
o Neurotransmitters are released, when action potential reaches the end of an axon, by
exocytosis and they diffuse across the synaptic cleft where they bind with receptors on
dendrites
o Binding of neurotransmitters opens ion channels causing Na+ to enter and depolarization
top start another action potential
o Some neurotransmitters cause stimulation while some cause inhibition
o Neurons add all inputs and then take action (Summation)
§ Types of Neurons: Difference in frequency of
o Sensory neurons – send information from sensory organs action potentials results in
strong or weak sensation
o Motor neurons – send information from muscles and glands
o Interneurons – within brain and spinal cord; often connect sensory and motor neurons

1. Central Nervous System
à Spinal cord: involved in primitive, reflex actions
à Cerebrum: voluntary actions and conscious awareness of sensations
à Cerebellum: coordinates muscle movement and balance
à Medulla: involuntary acts; primitive region
à Hypothalamus: maintains homeostasis, hormone levels, electrolyte balance, temperature and
controls pituitary gland
2. Peripheral Nervous System
à Somatic nervous system is a voluntary system mainly related to skeletal muscles and uses
acetylcholine
à Autonomic nervous system is an involuntary system including:
i. Sympathetic division: ‘fight or flight’ system which prepares the body for stress
situations by increasing heart rate, blood pressure, breathing rate etc. The
primary neurotransmitter in this division is norepinephrine
ii. Parasympathetic division: ‘resting and digesting’ system that works in the
opposite way of sympathetic division. Primary neurotransmitter over here is
acetylcholine
à When norepinephrine is released, epinephrine (adrenaline) is released by endocrine system
à Nervous systems of arthropods and annelids are made up of a ventral nerve cord and a brain
with a series of ganglia (clusters of nerve cell bodies)

The Endocrine System

§ Hormones are chemicals secreted by endocrine glands that affect organs with specific receptors
§ Hormones are of two types:
o Peptide hormones – amino acid based hormones which bind to receptors outside the cell
and activate enzymes (insulin, glucagon, prolactin etc.)

o Steroid hormones – cholesterol based hormones which can cross membranes (lipids)
and bind to receptors incised the cell. They bind to DNA and change which genes are
transcribed which is why response is slower (estrogen, testosterone, aldosterone etc.)
§ Endocrine system controls ejection of breast milk
§ The Endocrine Glands:
1) Pituitary Gland (Master endocrine gland)
a. Anterior Pituitary Gland
i. Growth hormone – targets all tissues and organs, causing them to grow
ii. Thyroid stimulating hormone TSH – stimulates thyroid to secrete hormones
iii. Adrenocorticotropic hormone ACTH – stimulates the adrenal cortex
iv. Follicle stimulating hormone FSH – targets the gonads to stimulate maturation of
ova/sperm making, and release of estrogen in females
v. Luteinizing hormone LH – also targets the gonads to stimulate development of
corpus luteum in females and testosterone in males
vi. Prolactin – released after child birth to stimulate mammary glands
b. Posterior Pituitary Gland
i. Oxytocin – causes uterus to contract during child birth and mammary glands to
release milk during breast feeding
ii. Antidiuretic Hormone ADH – causes kidneys to retain water; vasopressin
2) Thyroid Gland
a. Thyroxin
à Increases metabolic rate of body cells
à Lack of thyroxin due to less iodine intake cause hypothyroidism where the person
tends to gain weight and become sluggish
à Excess thyroxin (hyperthyroidism) results in high metabolic rate and weight loss
b. Calcitonin
à Activates special cells in bones that remove calcium from blood and use it to build
new bone
3) Parathyroid Glands
à Four glands found in the back of the thyroid gland
à Secrete parathyroid hormone (parathormone) which has the opposite effect of
calcitonin to maintain calcium levels
4) Adrenal Glands
a. Adrenal medulla (inner part)
i. Secretes epinephrine and norepinephrine
b. Adrenal Cortex (outer part)
i. Glucocorticoids – cause gluconeogenesis in liver resulting in production of glucose
from fats and proteins. They also target body organs to use fat for fuel. ‘Cortisol’ is
an example of a hormone that promotes glucose synthesis.
ii. Mineralocorticoids – target the kidneys. Mainly ‘aldosterone’ which causes kidneys
to retain Sodium
iii. Sex steroids – These are of little importance as primary producers for sex steroids
are the gonads
5) Pancreas
a. Insulin
i. Produced in islets of Langerhans and secreted when blood glucose levels are high,
allowing cells to take out glucose from blood to use it in glycolysis, Krebs cycle etc.
b. Glucagon
i. Targets liver to break down glycogen (glycogenolysis)
6) Gonads (primary sex organs which produce gametes)
a. Testes

i. Produce male sex steroids called androgens, the primary one being testosterone,
which is responsible for developing male secondary sex characteristics
b. Ovaries
i. Produce steroids, estrogen and progesterone, responsible for developing female
secondary sex characteristics
ii. Regulate the menstrual cycle where estrogen stimulates growth of uterine lining
and progesterone maintains it in the second half of the cycle
iii. Most common estrogen is estradiol

Blood composition
The Circulatory System Plasma – 50%
§ ‘Hemolymph’ is blood that is not in the circulatory system RBCs – 45%
§ Blood consists of fluid and cells in the fluid Others – 5%
§ Plasma:
o Mostly water with dissolved substances such as glucose, hormones, ions and gases
o Also contains proteins such as albumin made by liver
§ Red Blood Cells RBCs:
o Contain hemoglobin which binds with oxygen
o Lack of iron results in less production of RBCs which causes anemia
§ White Blood Cells WBCs:
o Phagocytes eat harmful substances by endocytosis (phagocytosis)
o B cells make antibodies
o Helper T cells help other B and T cells divide
o Killer T cells attack infected cells
o AIDS virus lives in Helper T cells, destroying them in the process which prevents B and killer
T cells from dividing and fighting against various infections
§ Platelets:
o Very small structures that aid blood clotting by converting fibrinogen in blood to fibrin, a
process that requires other substances as well such as calcium, Vitamin K etc.
§ Blood typing:
o Genes determine the type of protein on RBC membranes
o The gene for ABO blood typing is called ‘I’
o Three types: IA for A proteins, IB for B proteins and i.IA for no proteins
o IA and IB are co-‐dominant while i.IA is recessive
o Blood transfusion:
§ If proteins on new RBCs aren’t recognized, the cells are clumped (agglutination) and
destroyed
§ Type AB is universal recipient but cannot be given to any blood type other than AB
§ Type O is universal donor but can only receive type O
§ Blood Vessels
o Blood leaves heart in arteries, which have thick muscular walls, at great speeds and divides
into arterioles and capillaries
o Capillaries merge to form venules and then veins which return blood back to the heart aided
by the movement of skeletal muscles and valves
o On the arterial side, fluid is forced out of capillaries and into tissues (intercellular fluid) and
then it returns back to the system through the side of the veins
§ Lymphatic System
o Begins at tissues and ends at veins before heart where the tissue fluid is returned
o Fluid is filtered through lymph nodes or glands where it is exposed to WBCs
o Lymphatic vessels are structurally similar to veins
o Edema is swelling of body parts due to trapped fluid in the lymphatic system


§ The Heart
o Pulmonary Circuit
§ Blood from anterior and posterior vena cava passes from right atrium to right
ventricle to pulmonary artery to lungs
§ Oxygenated blood returns through pulmonary veins into the left atrium then left
ventricle then aorta
o Systemic Circuit
§ It is the flow of blood from aorta to the body and back through the vena cava
§ There are atrioventricular valves between atria and ventricles and semilunar valves
between ventricles and arteries
§ Heartbeat begins in sinoatrial node in right atrium (pacemaker) and travels towards
atrioventricular node and then the Purkyne tissue
§ Systole and Diastole are the contraction and relaxation of ventricles
§ Fish have a two chambered heart and one circulation circuit
§ Amphibians have three chambered hearts
§ Arthropods have open circulatory systems

The Respiratory System

§ Responsible for ventilation and gas exchange
§ Two zones:
o The Conduction Zone
§ Designed for ventilation only
§ Begins at nose where ait is warmed, filtered and humidified
§ Travels down the pharynx, larynx and into the trachea, branching into right and left
primary bronchi
§ These branch into bronchioles which along with trachea are lined with cilia and
mucus glands
o The Respiratory Zone
§ Gas exchange occurs in alveoli which have thin walls, large surface area and are
surrounded by capillaries
o Hydrophobic O2 and CO2 move through passive diffusion
o CO2 and H2O come out as waste products of Krebs cycle and Electron Transport Chain
§ pH regulation
o CO2 doesn’t dissolve well in plasma so it is converted to carbonic acid and then bicarbonate
o CO2 + H2O ßà H2CO3 ßà H+ + HCO3-‐
o When our body becomes too acidic, breathing rate increases to release more CO2 and vice
versa (this is controlled by medulla oblongata)
§ Lungs mechanism
o Lungs don’t have muscles but are aided by muscles in chest wall and diaphragm
o When diaphragm contracts, it flattens out and increases chest volume causing inspiration
o When it relaxes, it curves upwards under the lungs causing expiration
o Contraction of abdominal muscles results in forceful expiration

Peristalsis (muscular
The Digestive System contraction) helps
movement along the
§ Divided into two main groups, the alimentary canal and accessory organs alimentary canal
§ The alimentary canal is the long muscular tube from the mouth to the anus
§ Accessory organs are all other components; many of which are involved in exocrine secretions
§ The Mouth
o Ingestion happens here and food is turned into a bolus with help of saliva
o Saliva also contains amylase which digests some starch

§ The Stomach
o Has a pH between 1-‐2 due to HCl secreted by gastric glands which helps kill germs and
break up food even further
o Secretes pepsinogen which is activated to pepsin by HCl
o Mucus secreted by stomach protects the stomach lining from the acid
o Food leaving stomach is called chime
§ The Small Intestine
o Chyme is subjected to bile which is stored in gall bladder and produced in liver
o Bile emulsifies fat, allowing it to mix with chime better and letting lipase act on it
o Pancreas secrete amylase, lipase and proteases along with bicarbonate which is a base and
increases the pH to make it close to neutral
o The small intestine is 23 feet long and has many folds and villi to maximize surface area
o Absorbed nutrients are transported through portal veins (hepatic portal vein) to the liver
for further processing
§ The Large Intestine
o Chyme moves to the colon where water is reabsorbed, making chime solid (feces) which is
egested though rectum and anus
o Contains large population of non pathogenic E. Coli bacteria which keep pathogenic
bacteria from growing and supply us with vitamin K
§ Some animals additional have a crop to store food and a gizzard for grinding it in their complete
digestive tract

Vitamins and Minerals
Type Use Deficiency
Vitamin A To make retinal (sight) Night blindness
Vitamin B Cellular respiration and DNA replication Skin disorders, mental confusion, anemia
Vitamin C Collagen Scurvy
Vitamin D Calcium absorption Rickets
Vitamin E Protect cell membranes Anemia
Vitamin K Blood clotting Bruise easily and bleed excessively
Iron Hemoglobin Anemia
Calcium Strong bones and muscles Rickets (children) Osteomalacia (adults)
Iodine Thyroxin Decreased metabolic rate

The Urinary System

§ Waste products are filtered by kidneys and removed as urine
§ These waste products include:
o Urea from breakdown of amino acids
o Uric acid from breakdown of nucleic acids
o Creatinine from muscle metabolism
§ Blood enters through renal arteries branching into capillaries
§ Plasma in blood is forced into Bowman’s capsule from capillaries at glomerulus and is called
filtrate which travels in nephron
§ Urine formation
1) Filtration – at Bowman’s capsule
2) Reabsorption
• Useful substances like glucose and amino acids absorbed
• Reabsorption of water an mineral ions is regulated depending on the need of the body
3) Secretion – substances like creatinine taken out of blood and added to filtrate
§ The Nephron

o After Bowman’s capsule comes the proximal convoluted tubule where most reabsorption
and secretion takes place
o Then comes the loop of Henle where a large quantity of water is absorbed and salt is
transported from filtrate to kidney which helps establish a concentration gradient for water
absorption
o This is followed by distal convoluted tubule where reabsorption and secretion tend to be
more specialized and regulated
o Aldosterone also acts here by increasing the amount of Sodium being absorbed
o Final part is the collecting duct where water absorption is regulated under the effect of
ADH which causes its walls to become permeable to water allowing water to leave by
osmosis as duct passes through salty regions
§ Blood pressure regulation
o Primarily regulates blood pressure by releasing enzyme rennin
o This causes production of angiotensin II that constricts blood vessels and increases
secretion of aldosterone by cortex, which increases absorption of Sodium. This results in a
greater uptake of water
o Increased blood volume causes increase in blood pressure
§ Fish excrete nitrogen wastes in form of ammonia, land mammals in form of urea and
birds/reptiles in form of uric acid
§ Worms have metanephridia and insects use malphigian tubes instead of kidneys

The Skeletal System

§ All vertebrates have endoskeletons made of bones
§ Some animals have exoskeletons made of hard crusty shells containing chitin like arthropods
§ There are two types of skeletal tissues:
o Bones – rigid substance made of cells embedded in a solid calcium-‐phosphate matrix
o Cartilage – more flexible than bone and found at ends of joints or bones or in ears, nose and
anterior portion of ribs
§ Ligaments join bone with bone, tendons attach bone to muscle

The Muscular System

§ Postural muscles such as those in the back help keep the body upright
§ There are three types of muscles:
o Cardiac muscle in the heart (self excitatory)
o Smooth muscle in walls of hollow organs
o Skeletal muscle
§ Voluntary tissue which helps movement
§ Have many nuclei (multi nucleate)
§ Structure of a muscle
o Actin (long thin chains) + myosin (thick fibers) proteins arranged in a structure called
sarcomere
o Sarcomeres line up end to end to form myofibril
o Myofibrils bundle with cytoplasm, organelles, nuclei and a cell membrane to form a muscle
cell
o Muscle cells are organized in groups called fascicles
o Fascicles are grouped together to form whole muscle
§ In contraction, myosin binds to actin, pulling it inwards which in turn pulls the Z lines inwards
making the sarcomere shorter. This is called sliding filament theory
§ Skeletal muscles are described as striated/striped due to regular arrangement of protein filaments
into sarcomeres

§ Muscular contraction requires calcium

The Skin
§ Largest organ of the body, made of three layers: Epidermis, Dermis and Hypodermis
§ Main functions include protection from friction, heat loss, water loss, infection and UV radiation
§ Other functions are vitamin D production and sensation
§ Cold blooded/ ectothermic/ poikilothermic organisms cannot regulate body temperature
§ Warm blooded or endothermic organisms retain body heat
§ When temperature rises, blood vessels in dermis dilate and sweat glands become active
§ When temperature falls, blood vessels constrict, sweat glands are inactivated and shivering starts
(shivering is rapid involuntary muscle contraction to raise heat)

Male Reproductive System

§ Testes are found outside the body in a sac called scrotum
§ Sperm is produced in the seminiferous tubules in response to FSH
§ These tubules merge to form the Vas deferens which connects with urethra to lead sperm out of
the body with glands in between that release semen to provide nutrients

Female Reproductive System

§ Has to produce gametes and prepare for pregnancy
§ The Menstrual Cycle
o Ovaries are controlled by FSH and LH from pituitary gland and uterus is controlled by
hormones from ovaries (estrogen and progesterone)
o Average cycle lasts 28 days and consists of uterine and ovarian cycles
o Uterine cycle:
i. Menstruation – shedding of old uterine linings, the endometrium (Day 1 à 5)
ii. Proliferative phase – new uterine lining is built where new endometrium grows in
uterus under the effect of estrogen (Day 5 à 14)
iii. Secretory phase – uterine lining is maintained and enhanced with new blood vessels
and secretion of glucose and glycogen for richness/nourishment. This is under the
control of progesterone (Day 14 à 28)
o Ovarian cycle:
i. Follicular phase – FSH from anterior pituitary causes development of a follicle in the
ovary which is a maturing oocyte and its surrounding cells which secrete estrogen as
they grow (Day 1 à 14)
ii. Ovulation – release of oocyte from follicle into Fallopian tubes caused by surge of LH
while some of it stays behind and, under LH, matures into corpus luteum (Day 14)
iii. Luteul phase – corpus luteum secretes progesterone till it degenerates two weeks
later (Day 14 à Day 28)
§ If ovum gets fertilized then the embryo releases human chorionic gonadotropin hCG to prolong life
of corpus luteum to continue the release of progesterone so uterine lining doesn’t fall off
§ hCG levels stay high for four months till placenta takes over


Fertilization, Embryology and Fetal development
1. Gametes are formed
2. The egg is fertilized
a. Sperm released during copulation swims up the Fallopian tube and acrosome digests a path
for fertilization to occur
3. A zygote is formed
4. Cleavage
a. Rapid mitosis with no accompanying growth as zygote travels down the tube and towards
uterus
b. Ultimately becomes a solid ball of cells called morula
5. Implantation in the uterus
a. Bumps around and starts hollowing out into a blastocyst
b. The inner mass of cells forms embryo and embryonic structures while outer ring forms part
of the placenta
6. The embryonic stage
a. Gastrulation – The inner cell mass divides into three layers:
i. Endoderm: gives rise to inner linings of respiratory, digestive, reproductive and
urinary systems along with glandular organs
ii. Mesoderm: gives rise to middle structures such as bones, blood vessels, muscles,
heart and non-‐glandular organs
iii. Ectoderm: forms external structures, linings of mouth and anus and nervous sytem
structures (brain, cords, eyes etc.)
b. Neurulation
i. Organs of nervous system are formed
ii. Every other organ is also formed (organogenesis)
7. The fetal stage
a. Lasts from embryonic stage (8 weeks) till birth

à Fish and amphibians have external fertilization and embryo develops in non waterproof egg with
rare parental care
à Turtles, snakes and lizards have internal fertilization and lay eggs with waterproof shells with
little parental care
à Crocodiles and birds have internal fertilization and lay eggs with waterproof shells with some
degree of parental care
à Extra embryonic membranes
o Yolk sac
§ Surrounds the yolk which is food for embryo
§ Bird and reptile eggs have more yolk due to absence of placenta
o Amnion
§ Clear membrane that surrounds developing embryo with clear, watery amniotic
fluid which acts as a shock absorber
o Allantois
§ Becomes umbilical cord in humans and forms disposal site for solid waste in birds
and reptiles
o Chorion
§ Outermost membrane which forms embryo’s part of placenta in humans and lines
the inside of the shell in other cases

Evolution and Diversity

§ According to heterotroph hypothesis, life began due to spontaneous production of RNA etc
§ Early organisms were initially heterotrophs and then evolved into autotrophs
§ They were anaerobic which is why oxygen, which wasn’t initially present, entered the atmosphere
§ Evolution
o All the genes of organisms in a population are collectively called the gene pool
o Difference between these genes is called genetic variability
o Gene variability is a product of random mutation of DNA during replication and the new
gene type is expressed in that organism
o If the mutation occurs in the gametes, the new trait is passed on
§ Natural selection
o It is the driving force of evolution and occurs at the individual level
o Nature ‘chooses’ fittest organisms which compete for resources, with the weaker ones
eventually dying off
§ Genetic variability and evolution
o Changes in gene pool can occur due to random mutation which can take a long time or by
competition which results is swifter change
o Geographic isolation is where species are separated
o Features favorable in the given environment are passed on and become more dominant
o Fitness describes an organism’s ability to contribute to the next generation’s gene pool by
producing offspring that survive to adulthood
§ Evolution and Species
o Individuals of different species can’t produce viable offspring together
o Speciation or divergent evolution is the formation of a new species by evolution. Divergent
evolution is at a small scale where individuals can still mate
o Similarities in structure among species give evidence of their evolutionary history
o Homologous structures are common in species that share a common ancestor
o Analogous structures are similar adaptations that result from convergent evolution
§ Homologous vs Analogous structures
o Functionality: Same in analogous but different in homologous
o Fundamentals: Different in analogous but same in homologous
o Ancestry: Different in analogous (convergent evolution) but same in homologous
(divergent evolution)
o Example: Wings in birds/insects are analogous while human arm and whale flippers are
homologous
§ As populations evolve due to environmental pressures, some structures that were important once
become unimportant and become smaller and are eventually only seen as remnants of their
former selves like the appendix in humans

Phylogeny
Domain à Kingdom à Phylum à Class à Order à Family à Genus à Species
(Less in common) ààà (More in common)
Acronym to remember: Dumb King Philip Came Over From Germany – So?

à Phylogeny is the classification or organisms based on evolutionary relationships
à Taxonomy is the science of classification and naming
à Carolus Linnaeus came up with the binomial system of classification based on a two part name, the
genus and species. Both are italicized and Genus starts with a capital letter

Kingdom and Species
1. Domain Bacteria
a. Made up of prokaryotes which lack a nucleus and any membrane bound organelles and
have circular DNA
b. It has one kingdom called Eubacteria which includes cyanobacteria (blue-‐green algae)
which can photosynthesize
2. Domain Archaea
a. Also made up of prokaryotes in the kingdom Archaeabacteria
b. Also lack nucleus and organelles and have circular DNA but have features in common
with eukaryotes
c. Often live in very harsh/extreme conditions that most others can’t tolerate
d. Called ‘extremophiles’:
i. Extreme halophiles – salty conditions
ii. Extreme thermophiles – hot conditions
iii. Methanogens – anaerobes that release methane
3. Domain Eukarya
a. All eukaryotes contain nuclei, membrane bound organelles and have linear DNA
b. Four main kingdoms: Protista, Plantae, Fungi and Animalia

v Kingdom Protista
o Most are unicellular while some are multicellular (algae)
o Divided into three main phyla (groups) including protozoa, algae and protists
i. Phylum Rhizopoda (Amoebas)
a. Unicellular and move using pseudopodia
b. Found in soils and water and some are parasitic
ii. Phylum Apicomplexa (Sporozoans)
a. All animal parasites such as plasmodium
b. Most have life cycles with both sexual and asexual stages that often require
two or more host species
iii. Phylum Ciliophora (Ciliates)
a. Use cilia for movement and feeding (like paramecium)
iv. Phyla Myxomycota and Acrasiomycota
a. Resemble overgrown amoeba and have many nuclei
v. Phylum Euglenophyta (Euglena)
a. Unicellular; photosynthetic algae that move with a flagellum
vi. Phylum Bacillariophta (Diatoms)
a. Have unique glasslike walls and live in freshwater/marine environments
b. The walls remain behind when organism dies and form sediments called
diatomaceous earths, which are filtering mediums. They are the most
important producers of phytoplankton
vii. Phylum Phaeophyta (Brown algae)

a. Commonly knows as seaweeds and are the largest and most complex of
plant-‐like protists
v Kingdom Plantae
o All plants are multicellular, eukaryotic and photosynthetic
o Plants are either vascular and nonvascular based on how they transport water
o Vascular plants are further divided into seedless and seed plants which are wither
flowering or nonflowering
§ Division Bryophyta (Non vascular)
• Lack xylem and phloem and must live in damp areas while also requiring
water for fertilization
• Mosses, liverworts and hornworts
§ Division Pterophyta (Ferns)
• Earliest vascular plants containing stems, leaves and roots
• They do not have seeds but have spores instead
§ Division Coniferophyta (Conifers)
• ‘Conifers’ refers to the cones that carry the seeds of this plant
• Most are large, evergreen trees
• These are ‘naked-‐seed’ plants or gymnosperms
§ Division Anthophyta (flowering plants)
• Produce flowers and pollen with seeds protected by fruits and nuts
• Class monocots:
o Have single seed leaves called cotyledons
o Have parallel veins in their leaves, flower parts in multiples of three,
random arrangements of vascular bundles and fibrous root system
• Class dicots:
o Have two seed leaves (two cotyledons)
o Have netlike veins in leaves, flower parts in multiples of fours and
fives, vascular tissues arranged in a ring and a taproot system
v Kingdom Fungi
o All are eukaryotic, almost all are multicellular and have a cell wall made of chitin
o One exception is yeast which is a unicellular fungus
o Lack chlorophyll and are therefore heterotrophic
o Lack a digestive system and are absorptive feeders
o Often live on delaying matter (decomposers)
§ Division Zygomycota
• Reproduce sexually and include common molds as well as mycorrhizae
(mutualistic associations between plant roots and fungi)
§ Division Basidiomycota (Club fungi)
• Consists of about 25000 members including mushrooms, some of which are
edible
v Kingdom Animalia
o Eukaryotic, multicellular and heterotrophic
o Most diverse of the six kingdoms
§ Phylum Porifera (Sponges)
• Sessile (non moving) animals with a perforated body wall made of two layers
of cells
• Mostly live in marine environments
§ Phylum Cnidaria (Coelenterates)
• Body walls made of two layers of cells with a central, sac-‐like digestive
system
• Hydra and jellyfish

§ Phylum Platyhelminthes (Flatworms)
• Exhibit bilateral symmetry and a head (cephalization)
• Include planaria, flukes and tapeworms
§ Phylum Mollusca (Mollusks)
• Soft bodied organisms with hard external shells except octopi and squids
• Three major regions: ‘foot’ for movements, ‘visceral mass’ which has organs
and ‘mantle’ which may secrete a shell
§ Phylum Annelida (Segmented worms)
• Close circulation, a mouth and an anus, excrete waste through metanephridia
• Earthworms and leeches
§ Phylum Arthropoda (Arthropods)
• Most diverse phylum containing 1 million species and 1018 members
• Jointed appendages, hard exoskeleton containing chitin and a segmented
body with a head, thorax and abdomen
• Open circulatory system and malpighian tubules for waste excretion
• Crustaceans, insects and arachnids
§ Phylum Echinodermata (Echinoderms)
• Sessile organisms exhibiting radial symmetry and spiny exoskeletons
• They have a water vascular system ending in tube feet that function in
feeding, gas exchange and movement
• Sea urchins, sea stars and sand dollars
§ Phylum Chordata (Chordates)
• Almost all are vertebrates with hollow notochord, dorsal nerve cord and tail
o Class Chondrichthyes (Cartilaginous fish)
§ Flexible skeletons made of cartilage
§ Breathe through gills, lay eggs or give birth
§ Sharks and sting rays
o Class Osteichthyes (Bony fish)
§ Skeletons made of bones
§ Lay lots of shell-‐less eggs
§ Bass, tuna and trout
o Class Amphibia (Amphibians)
§ Land and water adapted
§ Shell-‐less eggs laid in water
§ Aquatic larval stage à metamorphosis into a terrestrial adult
§ Breather through lungs and/or skin
§ Frogs and salamanders
o Class Reptilia (Reptiles)
§ Terrestrial animals with thick, scaly skin
§ Eggs with shells to resist dehydration or live birth
§ Breathe through lungs
o Class Aves (Birds)
§ Tetrapods with forelimbs modified into wings
§ Endothermic
o Class Mammalia (Mammals)

Fish à Amphibians à Reptiles à Birds à Mammals
(ààà Evolution ààà)

Behavior
⊗ Instinctive Behavior
o Behavior that is inherited, not learnt
o Fixed-‐action patterns are stereotypical behaviors triggered by specific stimuli that just
happen on their own
o Imprinting is the recognition of some object as “mother” when seen during a critical time
period shortly after birth
o Both of these occur even if the stimulus is not the ‘real’ stimulus
⊗ Learned Behaviors
o Require interaction with the environment or with other organisms in order to occur
o Habituation occurs when a non-‐harmful stimulus occurs again and again till the organism
learns to ignore it. Basic response may be recovered after a while
o Conditioning (Associative learning) is a type of learning in which a stimulus is associated
with particular behavior
o Classical conditioning is where a neutral signal leads to a reflex
o Operant conditioning is learning that occurs because of a reward or punishment
o Insight learning (reasoning) is the highest form of learning which is the ability to approach
new situations and figure out how to deal with them
à Konrad Lorenz – carried out the mother of ducklings experiment
à Ivan Pavlov – classical conditioning of dogs to expect food on hearing a bell ring
⊗ Turning behavior in plants: The Tropisms
o In response to a particular stimuli
§ Phototropism – plant turns towards light
§ Positive gravitropism – growth of roots downwards
§ Negative gravitropism – growth of shoot upwards
§ Thigmotropism – growth along a surface
o Gravitropism is also called geotropism
o These behaviors are induced by plant hormones, auxins
⊗ Living things have instinctive biological clocks and when an organism does something on a daily
basis based on time, it is called ‘circadian rhythm’
⊗ Pheromones:
o Many animals communicate with other members of their species through pheromones
which include any chemical that:
§ Is released by the member of a species
§ Affects the behavior of other members of that species in a predictable way
⊗ Symbiosis
o Mutualism – both benefit from the relationship such as the relationship between humans
and their intestinal bacteria
o Parasitism – where one organism benefits and the other is harmed
o Commensalism – where one organism is benefited and the other isn’t affected

Ecology
Cell à Tissue à Organ à Organism à Population à Community à Ecosystem à Biome à Biosphere

⊗ Population
à A group of individuals in a particular area that interbreed and therefore share the same gene
pool
à Evolution acts on populations through changes in genotype/phenotype of individuals and
their offspring
à Exponential growth is rapid growth while limited growth is when environmental factors limit
the growth of a population
à Maximum population size is called ‘carrying capacity’
⊗ Community
à Group of populations that live in a particular environment
à Every organism has its ‘niche’ which is the role it plays
à When two organisms occupy the same niche, there is competition between them and the
losing population must evolve to survive
à Predation is when one organism eats another
à Predation may cause the prey to evolve to better escape which in turn causes the predator to
evolve to hunt better
à Alternate evolution of two species based on their interactions with one another is called
coevolution
à Predators affect the carrying capacity of an environment
⊗ Ecological Succession
à It is the process of gradual change in an ecological community
à Lichens are pioneer organisms (present at the very start of the development of a community)
à Climax community comes at the very end and is a stable community
⊗ Ecosystem
à The community along with the environment it lives in is called ecosystem
à This environment contains both biotic and abiotic substance
o The Water cycle
§ Water is taken up into the clouds by evaporation and transpiration
§ It returns to the land through precipitation
§ It enters the soil and returns to the ocean through runoff
o The Nitrogen cycle
§ When organisms die, nitrogen from their bodies returns to the soil
§ Bacteria convert it to usable form for plants
§ Plants use it to make protein while animals ingest it to do the same
⊗ Biomes
à Large area classified mostly by the ecosystems they contain
à Conditions such as light and temperature remain constant
1. Tundra
a. Permafrost, permanently frozen top soil
b. Deep root growth is difficult, most plants are short shrubs
2. Taiga
a. Found a bit south of tundra and contains many conifers
3. Deciduous forests
a. Lots of rain and wide variety of plants and animals
b. Distinct hot and cold seasons
c. Drop leaves in winter and regrow them in the spring
4. The Grasslands (Savanna)
a. Low growing plants and scattered trees

5. Tropical Rainforests
a. Highest rainfall and greatest diversity
b. Trees form a canopy
6. Desert
a. Driest biome with less than 30cm of rainfall annually
b. Deserts can be both, hot or cold
⊗ Aquatic Biomes
1. Intertidal zone (Marine)
a. Where land and water meet
b. Alternate periods of dryness and total submersion
2. Neritic zone (Marine)
a. From intertidal zone to edge of continental shelf
b. Coral reeves in warm waters
3. Ocean zone (Marine)
a. Open ocean
b. Very little nutrient concentration except phytoplankton
c. Further divided into pelagic (open water) and benthic (ocean bottom) zones with a
further subdivision, the abyssal zone, being the deepest
4. Littoral zone (Fresh water)
a. Near the shore of a lake
5. Limnetic zone (Fresh water)
a. Farther from shore and extends downwards as far as light will penetrate
6. Profundal zone (Fresh water)
a. Aphotic (dark) region of the lake
b. Nutrients from limnetic zone float down

⊗ Human impact on environment:
o Greenhouse effect
o Ozone depletion
o Acid rain
o Desertification
o Deforestation
o Pollution
o Reduction in biodiversity (by leading species to extinction)

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Characteristics of water

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Cell Theory à Most plant and animal cells have

Prokaryotes vs. Eukaryotes

Different structures in plant and animal cells

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Tools and Techniques to study cells

Pyruvate Dehydrogenase Complex (PDC)

Electron transport chain and Oxidative Phosphorylation

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and into the inter-­‐membrane space

Transcription and Translation

Protein synthesis DNA à RNA à Proteins

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Mitosis and Meiosis

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Transport in plants

Flowers and reproduction

Control: Nervous and Endocrine Systems

The Nervous System

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creates a chain reaction all the way down the axon

The Endocrine System

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The Respiratory System

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The Urinary System

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The Skeletal System

The Muscular System

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Male Reproductive System

Female Reproductive System

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and into the inter-‐membrane space