Biochemistry

● Basic Chemistry - Atomic Structure

○ An atom consists of protons, neutrons and electrons
■ Protons have a charge of +1 and a mass of 1 amu (in nucleus)
■ Neutrons have no charge and a mass of 1 amu (in nucleus)
■ Electrons have a charge of -1 and no mass (outside nucleus)
● Ground state = electrons in the lowest available energy level
● Excited state = can be induced when energy is absorbed
○ Forces electron to move to a higher energy level
● The number of electrons in an atom’s valence (farthest from the
nucleus) shell dictates how it can bond
■ The charge of an atom is usually equal (same number of protons and
electrons)
■ Isotopes are atoms of the same element that have an alternate number of
neutrons
● Some are radioactive (radioisotopes)
○ These emit particles from their nuclei and decay
progressively (at the rate of their half-life)
■ Half-life allows for researchers to measure the ages
of fossils and other things
○ Radioisotopes can also be used in medicine (diagnosis,
treatment and research)
■ Radioactive iodine (I-131) is often used for disease
in the thyroid gland
○ Tracers
■ Radioactive carbon can be used as a tracer to track
metabolic pathways (by being incorporated into
CO2)
● Bonding
○ Bonds are formed when two nuclei attract the same electrons
■ When bonds are formed, energy is released
■ To break a bond, energy is needed
○ Atoms bond to be more stable (octet rule)
■ Ionic bonds form with the total transfer of an electron
● The atom that gains the electron becomes an anion (negative ion)
● The atom that loses the electron becomes a cation (positive ion)
■ Covalent bonds involve the sharing of electrons between atoms (result in
the formation of a molecule)
● Nonpolar covalent bond
○ Electrons shared equally (formed between atoms with
similar/the same electronegativities)
● Polar covalent bond
 ○ Electrons shared unequally (formed between atoms with
different electronegativities)
○ Intermolecular Attractions
■ Attractions between molecules also exist
● Polar-polar attraction
○ Polar molecules can bind to other polar molecules
■ By attaching to the opposite charge
● Hydrogen Bonding
○ Bonds between hydrogen and oxygen or hydrogen and
nitrogen between different molecules
■ Important in keeping the strands of DNA bonded
together (maintain the double-helix)
■ Helps water molecules stick together (make special
properties of water arise)
● Nonpolar molecules
○ Only van der Waal forces can exist between different
nonpolar molecules
● Hydrophobic and Hydrophilic
○ Hydrophobic = water hating/repelled by water
■ Hydrophilic = water loving/attracted to water
○ Polar molecules tend to be hydrophilic
■ Dissolve in water (like dissolves like)
○ Nonpolar molecules (like lipids) are hydrophobic
■ Do not dissolve in water
● Can go through the nonpolar (lipid bilayer) plasma membrane
○ Through hydrophilic protein channels
● Characteristics of Water
○ Because of the polarity and strong intermolecular attraction between water
molecules, special characteristics arise
■ High specific heat
● Specific heat = amount of heat that must be absorbed for 1 gram
of substance to change its temp by 1 degree celsius
○ Water can absorb or lose lots of heat while resisting
significant temperature changes
■ Provide stable environment for marine life
● Also make coastal areas maintain more mild
climates
■ High heat of vaporization
● A lot of heat is needed to evaporate water
○ Causes evaporative cooling (i.e. evaporating sweat cools
the body surface)
■ High adhesion
● Adhesion = the attachment of one substance to another
○ Important in capillary action (in plants)
 ■ The force of evaporating water helps pull up water
from the roots
■ Universal solvent
● Because of its high polarity, water is able to dissolve in all
polar/ionic substances
■ Strong Cohesion
● Cohesion = the ability of the same molecules to stick to each other
○ Water molecules tend to stick to each other
■ Water can move from the roots to the leaves in a
plant without using energy (transpirational-pull
cohesion tension)
○ Also gives water a high surface tension
■ Allows for some organisms to walk on water without
breaking its surface
■ Ice is less dense than liquid water
● Because ice floats, it can serve to insulate the water underneath it
(helps maintain marine life during winter)
○ When the ice melts, nutrients given off can be returned
back down to the bottom (spring overturn)
■ The process of spring overturn is vital in the health
of any body of water
● pH
○ pH is a measure of how acidic/basic a solution is
■ Measures hydrogen ion concentration
● If pH is less than 7, acidic
● If pH is greater than 7, basic
● If pH = 7, neutral
■ Each pH 1 lower is 10x as acidic as the one above it
● A pH of 2 is 10x more acidic than a pH of 3
○ pH is regulated with the use of buffers
■ Buffers absorb/donate hydrogen ions to balance pH
● I.e. In human blood, a bicarbonate ion is an important buffer
● Organic Compounds
○ Organic compounds are compounds containing carbon
■ Can be present as carbohydrates, lipids, proteins or nucleic acids
● Carbohydrates
○ Carbohydrates are made up of Carbon, Oxygen and Hydrogen
■ Are used to supply quick energy (4 calories per gram released when
burned)
● Monosaccharides
○ All have the formula C6H12O6 (i.e. glucose/galactose/fructose)
■ Isomers = same molecular formula, different molecular structure
● Form fits function (different structure gives them different
physical/chemical properties)
● Disaccharides
○ Have the chemical formula C12H22O12
■ Consist of two monosaccharides joined together by a dehydration
synthesis reaction
● Two glucose = maltose
● Glucose + galactose = lactose
● Glucose + fructose = sucrose
○ All release water
■ Hydrolysis reactions break down compounds with the addition of water
● Occurs during digestion (reversal of dehydration synthesis)
● Polysaccharides
○ Polymer chains of carbohydrates
■ Formed by monosaccharides joining together with a succession of
dehydration synthesis reactions
● I.e…
○ Found in plants
■ Cellulose (important ingredient in plant cell walls)
■ Starch (how plants store carbohydrates)
○ Found in animals
■ Chitin (makes up the exoskeleton in arthropods and
the cell walls in mushrooms)
■ Glycogen (“animal starch”; used by animals to store
carbohydrates)
● Lipids
○ Made up of one glycerol (alcohol) and three fatty acids (hydrocarbon chain with a
carboxyl at one end)
● Saturated Fats
○ Bonded to the maximum number of hydrogens and containing single bonds
between carbon atoms (allows for it to be a solid at room temperature)
■ Usually know as “animal fats”
● Unsaturated Fats
○ Have carbon atoms with more than one covalent bond (results in less bonds with
hydrogens)
■ Kinks caused by double bonds don’t allow for these to become solid
(usually liquid at room temperature)
● Lipid Functions
○ Energy storage
■ When burned, 1 gram of lipid releases more than double the amount of
calories released by carbohydrates
○ Structural
■ The hydrophobic/hydrophilic qualities of phospholipids make them vital
components of the cell membrane
○ Endocrine
■ Some lipids can also serve as hormones
● Proteins
○ Proteins = polymers of amino acids (joined together by peptide bonds)
■ Amino acid = carboxyl group, amine group, and a variable R group (what
makes the different amino acids)
○ Proteins are important in growth and repair
■ Can give energy (4 calories per gram burned)
○ Consist of Sulfur, phosphorus, carbon, oxygen, hydrogen and/or nitrogen
○ Dipeptide = two amino acids connected with one peptide bond
● Protein Structure
○ Proteins can act as…
■ Enzymes
■ Membrane channels
■ Hormones
■ Etc.
● Function of a protein depends on its shape
○ A protein’s unique shape is a result of…
■ Primary structure
● Results from the specific sequence of amino acids (that make up
a polypeptide chain)
■ Secondary Structure
● The result of hydrogen bonding with different parts of the molecule
(creates a helical shape in many proteins)
○ Usually appear in the form of repeated coils or folds
■ Tertiary Structure
● The specific shape/conformation of a protein (most directly
determines how it functions)
○ When a protein is denatured, it cannot function because of
damage to its tertiary structure
● Found in the form of bumps/kinks that appear because of irregular
interactions between side chains on the different amino acids
■ Quaternary structure
● The structure when each of the polypeptide chains are brought
together
● Enzymes
○ Enzymes = proteins
■ Speed up (catalyze) reactions by lowering activation energy (amount of
energy needed to begin a reaction)
○ Enzymes work on a chemical (substrate)
■ Each enzyme has a specific shape (can only bind to a specific substrate
molecule)
● When the substrate enters the active site of the enzyme, the
enzyme alters its shape to better fit the substrate (induced fit)
○ Enzymes can be reused many times
■ Not degraded over the course of the reaction
 ○ End in “ase”
■ Usually named after their substrate
○ Function with assistance from cofactors (minerals) or coenzymes (vitamins)
○ Enzymes tend to function best at an optimal temperature and pH
■ As temperature and pH stray away from this, enzymes can denature and
lose their unique shape (and therefore their ability to function)
● Prions
○ Proteins that work like viruses and can cause disease
■ They are infectious (found to cause brain diseases like mad cow disease)
○ Prion = a misfolded version of a protein that is usually found in the brains of
mammals
■ When prions get into unaffected brains, it can cause the normal proteins
to fold in a similar way
● Nucleic Acids
○ Nucleic acids carry hereditary information
■ They are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
○ They are polymers of nucleotides
■ Nucleotide = phosphate, 5-carbon sugar (deoxyribose or ribose) and a
nitrogenous base
● DNA bases = adenine, thymine, guanine and cytosine
● RNA bases = adenine, guanine, uracil (instead of thymine) and
cytosine
○ Adenine and guanine = purines
○ Cytosine, thymine and uracil are pyrimidines
 The Cell
● Cell Theory
○ Cell theory states that…
■ All living things are made up of cells
■ Cells are the most basic unit of life in all organisms
■ Cells can only arise from preexisting cells
○ All cells are surrounded by a semipermeable membrane
■ Dictates what can come in and out of the cell
○ Cells all contain nucleic acid (in some form)
■ Controls inheritance and directs cell activity
○ Prokaryotes
■ Have no nucleus or internal membranes
● No membrane bound organelles
■ Smaller than eukaryotes
■ I.e. bacteria
○ Eukaryotes
■ Have a nucleus and membrane bound organelles (internal membranes)
● Much more complex than prokaryotes
○ Make up everything other than bacteria (i.e. human cells)
○
Prokaryotes Eukaryotes

No internal membranes/internal Contain membrane bound organelles

membranes

Contain a single circular chromosome Contain linear chromosomes (kept in

(kept in a nucleoid region) the nucleus)

Can contain plasmids Never contain plasmids

Small ribosomes Larger ribosomes

Respiration can be carried out with or Respiration is usually carried out with
without oxygen oxygen

No cytoskeletal elements Cytoskeleton present

Most are single celled Most are multicellular (with some

exceptions)

1-10 microns 10-100 microns

Have tough external cell walls With the exception of protists and
plants, most only have a cell
membrane
○ It is believed that all living organisms have evolved from a common prokaryotic
ancestor
 ■ The endosymbiotic theory proposes that eukaryotes came about because
small prokaryotes (like mitochondria and chloroplasts) became
permanent residents of larger prokaryotes
● This led to the creation of a eukaryote with an organized system of
internal membranes
○ All eukaryotic cells have the same organelles
■ Different functions mean that they also take on different shapes
● Structures of Plant and Animal Cells
○ All cell types tend to have the same organelles
■ Plant cells have cell walls while animal cells have centrioles
● Nucleus
○ Control center of the cell
■ Surrounded by a selectively permeable double membrane (called the
nuclear envelope)
○ Inside the nucleus, chromosomes (made up of DNA wrapped in histones) form a
chromatin network
■ From which instructions for inheritance and protein synthesis can be
given
● Nucleolus
○ Region inside of the nucleus (nondividing)
■ Ribosomal subunits are constructed here
○ Nucleoli are not surrounded by a membrane
■ Tangles of chromatin and unfinished ribosomes
● Ribosome
○ Site of protein synthesis
■ Ribosomes = rRNA (ribosomal RNA) + proteins
○ Ribosomes can either be “free” (in the cytoplasm) or “bound” to the endoplasmic
reticulum
● Endoplasmic Reticulum
○ System of membrane channels in the cytoplasm
■ Rough ER (studded with ribosomes)
● Site of protein synthesis and transport throughout the cytoplasm
■ Smooth ER
● Synthesize steroid hormones/other lipids
● Connects the rough ER with the golic apparatus
● Detoxifies the cell (of alcohol/hydrogen peroxide)
● Helps in the metabolism of carbohydrates (glycogen)
● Golgi Apparatus
○ Lies near the nucleus
■ Made up of a stack of flat membranous sacs
● Surrounded by vesicles
○ Modify/store/ship/package products of the rough ER
■ Can secrete these substances to other parts of the cytoplasm or to the
cell surface (for secretion outside of the cell)
● Lysosome
○ Membranous sac of hydrolytic enzymes
■ Site of intracellular digestion
○ Allows the cell to break down/recycle cell parts
■ Apoptosis (programmed cell death) is also important in the development
of embryos
● Can only be carried out by a cell’s own hydrolytic enzymes
○ Usually not found in plants
● Mitochondrian
○ Site of cellular respiration
■ Found in all cells
○ Consist of a double membrane on the outside
■ With a highly folded inner membrane (cristae)
● In the cristae are embedded enzymes that are vital in cellular
respiration
○ Have their own DNA
■ Can replicate themselves (proof that they were formerly free-living
prokaryotes)
● Vacuole
○ Vacuoles are membrane-bound structures that store substances in the cell
■ Contractile vacuoles pump excess water out of the cell
■ Plant cells and fat (adipose cells) have large central vacuoles
● Vesicle
○ Tiny vacuoles
■ Found all over the cell (carry out different jobs)
● Plastids
○ Organelles in plants containing pigment or food (surrounded by a double
membrane)
■ Only found in plants and algae
○ Three types
■ Chloroplasts
● Sites of photosynthesis
○ Green color because of chlorophyll
● Have an inner system of thylakoid membranes
○ Sacs of membranes stacked into grane (separate thylakoid
space with the stroma)
● Contain their own DNA and can replicate independently (like
mitochondria)
■ Leucoplasts
● Colorless
○ Store starch (found in the roots)
■ Chromoplasts
● Store carotenoid pigments
 ○ Responsible for red-yellow coloring of carrots and
tomatoes
● Help attract pollinating insects with the bright pigment
● Cytoskeleton
○ The cytoskeleton is made up of a vast network of protein filaments extending
through the cytoplasm (giving structural support and shape to a cell)
○ Two main types of structures
■ Microtubules
● Thick hollow tubes (i.e. cilia, flagella and spindle fibers)
○ Formed with tubulin
■ Microfilaments
● Made up of actin
○ Vital in supporting the shape of the cell
● They help…
○ Form a cleavage furrow during division (in animal cells)
○ Amoeba move by sending out pseudopods
○ Muscles to contract (by sliding along myosin filaments)
● Centrioles and Centrosomes
○ Lie outside of the nucleus
■ Organize the spindle fibers (necessary in cell division)
○ Animals have both centrioles and centrosomes
■ Plants only have microtubule organizing centers
○ Two centrioles make up a centrosome
■ Centrioles consist of 9 microtubule triplets
● Cilia and Flagella
○ Both are made of microtubules
■ Cilia are short, flagella are long
○ Both consist of a 9-2 microtubule arrangement (9 microtubule triplets around 2
single microtubules)
● Cell Wall
○ Found only in plant cells
■ Fungi cell wall = chitin
■ Plant and algae cell wall = cellulose
○ In plants, the primarily cell wall exists right outside the plasma membrane
■ There can be another wall underneath (secondary cell wall)
○ During division, the middle lamella keeps the daughter cells attached
● Cytoplasm and Cytosol
○ The entire region between the plasma membrane and the nucleus is the
cytoplasm
■ The gelatinous, semi-liquid substance in which the organelles are
suspended is called the cytosol
● Organelles are moved during cyclosis (when the cytoplasm cycles
around the cell)
● Cell or Plasma Membrane
 ○ The plasma membrane is selectively permeable (controls what can go in and out
of the cell)
■ Described as a fluid mosaic (made up of many different parts that can
move and change)
● The plasma membrane consists of a phospholipid bilayer (with
different proteins dispersed throughout)
○ Carbohydrate chains on the outside of the membrane are vital in cell-to-cell
recognition
■ Cholesterol is embedded into the membrane to make it less fluid (and
therefore more stable)
○ About 60% of the membrane is made up of proteins
■ Proteins in the membrane can serve many different functions
●
Animal Cells Plant Cells

Centrioles and centrosomes No centrioles or centrosomes

Have no chloroplasts/plastids Have chloroplasts and plastids

Usually have small vacuoles (exception of Have a large central vacuole

adipose cells)

Plasma membrane only Cell wall/s around the plasma membrane

Lysosomes No lysosomes
● Transport Into and Out of the Cell
○ Selectively permeable
■ Depending on what the cell needs, different substances are allowed in
and out of the plasma membrane
● Characteristic of cell membranes
○ Solvent
■ The substance that does the dissolving
○ Solute
■ The substance that dissolves
○ Hypertonic
■ Having a greater concentration of solute
○ Hypotonic
■ Having a lesser concentration of solute
○ Isotonic
■ Two solutions containing equal concentrations of solute
● Passive Transport
○ Passive transport is the movement of molecules in accordance with (down) their
concentration gradients (from higher concentration to lower concentration
■ Doesn’t require energy
● Simple Diffusion
 ○ Passive transport
■ The movement of particles down their gradient
● Steeper the gradient = faster the rate of diffusion
● Facilitated Diffusion
○ Passive transport, but requires the help of protein membrane channels
■ Help transport substances across a membrane
● Osmosis
○ The diffusion of water across a membrane
■ Down its gradient (towards a region with higher solute concentration)
○ If a cell is put into a hypertonic solution, water will leave the cell
■ The cell with shrivel and shrink (called plasmolysis)
○ If a cell is put into a hypotonic solution, water will flow into the cell
■ Can cause an animal cell to burst (in plant cells, the cell walls prevents it
from bursting)
● Plant cells can only swell up and become turgid
○ When water is lost, turgor pressure goes down (and a plant
can wilt)
○ If a cell is put into an isotonic solution, water can diffuse in and out
■ No net change
● Active Transport
○ Active transport is the movement of molecules against a gradient (needs energy)
● Exocytosis
○ The active release of molecules from a cell
● Endocytosis
○ Endocytosis is a process where a cell takes in different molecules by forming
new vesicles from the plasma membrane
■ Pinocytosis
● Pinocytosis = cell drinking
○ Uptake of large, dissolved molecules
● The plasma membrane encloses these particles within a vesicle
■ Phagocytosis
● Phagocytosis = engulfing large particles with pseudopods
○ Again, the cell membrane wraps around the particle and
engulfs it to form a vacuole
■ Receptor-mediated endocytosis
● Receptor mediated endocytosis helps cells take up large
quantities of specific substances
○ Substance bind to unique receptors on the cell membrane
(and can be taken in with vesicles)
● The Life Processes
○ Ingestion
■ Intake of nutrients from outside the cell
○ Digestion
■ Breaking doing food with enzymes (so that it can be used by the body)
 ○ Respiration
■ A series of metabolic processes that can create energy (usually in the
form of ATP)
○ Transport
■ Distributing molecules to different parts of the cell (or to another cell)
○ Regulation
■ The ability to maintain balance/stability (homeostasis)
○ Synthesis
■ The ability to combine small molecules into more complex products
○ Excretion
■ The ability to remove metabolic waste
○ Egestion
■ The ability to remove undigested waste
○ Reproduction
■ The ability to copy and generate offspring
○ Irritability
■ The ability to respond to sudden fluctuations or stimuli in the environment
or in the cell
○ Locomotion
■ The ability to move around (only in animal cells)
○ Metabolism
■ The total of all of the chemical processes taking place in the cell
● Tools and Techniques to Study Cells
○ Compound microscopes are usually used to study cell structure (cytology)
■ The first microscopes were developed by Anton van Leeuwenhoek
○ Total magnification = ocular lens (eyepiece) x objective lens
■ Image in microscope appears upside down and backwards
○ Phase-contrast microscope
■ Light microscope
● Used to enhance contrast
○ Electron microscopes (use a beam of electrons to magnify)
■ Transmission electron microscope can be be used to study the interior of
cells
● Can’t by used by living cells
● Need elaborate preparation of the samples
● Expensive and fragile
■ The scanning electron microscope is used to study the surface of cells
● Other Tools for Studying Cells
○ The ultracentrifuge can be used to study tissue
■ Allows scientists to isolate specific components of cells in large quantities
(through a process called cell fractionation)
○ Freeze fracture (freeze-etching) can be used to study details of membrane
structure (with an electron microscope)
○ Tissue culture
■ Can be used to study the properties of cells
● Can be examined with a light microscope
 Cell Division -- Mitosis and Meiosis

● Introduction
○ Cells gave divide through mitosis or meiosis
■ Mitosis = divides to help in the growth/repair of body (somatic) cells
● Produces identical diploid daughter cells
■ Meiosis = division that occurs only in gametic cells (sperm and egg)
● Each daughter cell is a haploid (with half the chromosome count
of their parents)
○ Two of these haploids come together to form a gamete
○ Chromosomes are vital parts of cell division
■ Chromosome = highly condensed/coiled DNA
● Replicated chromosomes have two identical sister chromatids
(joined together by the centromere)
○ The centromere is connected to the centrosome with
spindle fibers
● The Cell Cycle
○ When dividing, cells pass through the cell cycle (sequence of growth and
development)
■ The rate/phases of cell division in an organism help maintain normal
growth and development
● Different cells divide at different rates
○ Nerve cells never divide
○ Skin cells and cells that line the digestive tract divide
constantly
○ Stem cells (from human embryos) can divide
○ The cell cycle is regulated by proteins
■ I.e. cyclins
■ Some proteins are internal regulators (makes sure to inhibit division
between certain conditions are met)
○ Interphase phases
■ G1
●Newly created cell enters immediately after undergoing division
○ The cell increases in size
■ Prepares to replicate its DNA
● G1 Checkpoint
○ First point to check if a cell can undergo division
■ If it is healthy and has undamaged DNA/adequate
resources, then growth factors are secreted (and
continuation of the cell cycle is promoted)
● If it is not deemed healthy enough, the cell
can die or go into a resting (G0) phase
■ S Phase
 ○ DNA is replicated (s = synthesis)
● S-Checkpoint
○ DNA synthesis is closely monitored for errors
■ If it is correct, the production of growth signals
allows the cell to proceed
■ G2
○ The cell has to produce the organelles/cellular components
for the daughter cells
● G2 Checkpoint
○ All chromosomes/organelles/cellular components must be
fully replicated
○ Interphase
■ Makes up more than 90% of a cell’s life
● Includes the G1, S and G2 phases
■ During this period, the cells prepare for division
● Chromosomes replicate
● Nucleoli become visible in the nucleus
● Nuclear membrane still intact
○ Mitosis
■ Consists of the actual division of the cell
● Prophase
○ Chromosomes start to condense (become visible)
○ Nucleoli disappear
○ Spindle fibers begin to form on opposite sides of cytoplasm
(extend from one centrosome to the other)
○ Centrioles move to opposite poles
○ Nuclear membrane begins to break apart
● Metaphase
○ Chromosomes line up (one by one) on the metaphase
plate
■ Centrosomes placed at either end (with spindle
fibers running through all of the centromeres of the
chromosomes)
● Anaphase
○ Centromeres separate (spindle fibers begin to pull sister
chromatids apart)
● Telophase
○ Chromosomes move to opposite poles
■ The nuclear membrane begins to reform
○ Chromosomes start to unravel (resemble their pre-division
state)
○ Cytokinesis
■ Cytokinesis = division of the cytoplasm (and its contents)
 ● In animal cells, the formation of a cleavage furrow allows for the
split of the cytoplasm
● In plant cells, the formation of a cell plate allows for the split of the
cytoplasm
○ Unlike in animals, the two daughter cells stick together
(because of the sticky middle lamella)
○ Meiosis
■ The form of cellular division undergone by sex cells
○ Meiosis I
■ Synapsis (chromosomes pair up) occurs
● This allows for crossing-over (random process in which
homologous chromosomes can exchange genetic material)
■ Homologous chromosomes separate (if not = disjunction)
● After, these separated chromosomes align on the metaphase
plate and separate
○ Makes a gamete
○ Meiosis II
■ Sister chromatids separate (maintains haploid nature of gametes)
● Now makes four unique haploid daughter cells
 Cellular Respiration

● Intro
○ Cell respiration is a series of reactions that leads to the generation of ATP from
food/glucose
■ Glucose and oxygen combine to form carbon dioxide, water, and energy
(in the form of ATP)
● ATP
○ ATP = adenosine triphosphate (adenosine = adenine + ribose)
■ Stores energy that can be hydrolyzed and used by the cell
○ The three phosphate groups have charges that repel each other
■ Removing one phosphate group makes a more stable ADP (and releases
energy)
● To reform ATP, energy must be added
● Structure of the Mitochondrion
○ Enclosed by a double membrane with a highly folded inner membrane (cristae)
■ The cristae divides the inside into the outer space (electron transport
chain) and the mitochondrial matrix (Krebs cycle)
○ In cell respiration, energy can be created with or without oxygen
■ Anaerobic (only glycolysis and fermentation can occur)
■ Aerobic (glycolysis along with the Krebs cycle and the electron transport
chain)
● Anaerobic Respiration (When Oxygen is not Present)
○ Fermentation (anaerobic respiration) consists of glycolysis with either alcohol
fermentation or lactic acid fermentation (to restore NAD+)
■ Ancient process that arose when there was no oxygen in the atmosphere
● Glycolysis
○ Occurs in aerobic and anaerobic respiration
■ Breaks one molecule of glucose into two molecules of pyruvate
○ Occurs in the cytoplasm
■ Releases four molecules of ATP (net gain of two) and two NADH
● Alcohol Fermentation
○ When pyruvate is reduced to ethyl alcohol (to restore NAD+)
● Lactic Acid Fermentation
○ Pyruvate is reduced to lactic acid (restore NAD+)
● Aerobic Respiration (When Oxygen is Present)
○ The Krebs Cycle (citric acid cycle)
■ After glycolysis, first stage of aerobic respiration
● Pyruvate is converted to acetyl coA (carboxyl group removed;
binds to coenzyme A)
■ Occurs in the mitochondrial matrix
● Produces 1 ATP, 1 FADH2 and 3 NADH (for each pyruvate)
 ■ NADH and FADH2 can take electrons and protons (products of the krebs
cycle and glycolysis) to the electron transport chain
○ The Electron Transport Chain and Chemiosmosis
■ The electron transport chain is embedded in the cristae (inner membrane)
● Has a system of carrier proteins with progressively higher
electronegativities (able to release energy in manageable spurts)
■ The energy created powers the creation of a proton gradient (proton
motive force)
● This potential energy is used to make ATP through
(chemiosmosis/oxidative phosphorylation)
■ When NADH and FADH2 bring electrons to the electron transport chain,
the energy they release is used to pump protons across the membrane
(creating a proton gradient)
● This stored energy is used to convert ADP into ATP
○ Depends upon the presence of an ATP synthase
(functions as a proton channel that can also attached
phosphates to ADP)
■ Oxygen (with a high electronegativity) is the last electron and proton
acceptor in the ETC
● When combined, water is formed as a waste product
 Photosynthesis

● Intro
○ Photosynthesis uses a series of reactions to turn light energy into glucose
■ Carried out by plants and algae
○ Uses carbon dioxide and water (along with light energy) to make sugar (in the
form of glucose), water and oxygen
■ Reduction reaction
● Structure of the Chloroplast
○ Enclosed by a double membrane
■ Consists of grana (stacks of thylakoid membrane sacs)
● Where the light reactions take place
■ And the stroma (where the Calvin cycle occurs)
● Light and Photosynthetic Pigments
○ Light can either be reflected, transmitted or absorbed by an object
■ The color that appears is the color being reflected (i.e. green in green
plants)
○ Pigments = substances that can absorb light
■ Different pigments absorb light at different wavelengths
○ Chlorophyll a is the only pigment that can participate directly in photosynthesis
■ Other (accessory) pigments form an antenna complex and help widen the
wavelengths of light that can be absorbed (i.e. carotenoids, chlorophyll b
and phycobilins)
● These accessory pigments then pass the photons absorbed to the
chlorophyll a at the reaction center
● Light-Dependent and Light-Independent Reactions
○ Photosynthesis is made up of light reactions and light-independent reactions
■ The light reactions make ATP and generate protons and electrons (in the
form of NADPH)
● The light-independent reactions use these things to make sugar
● Light-Dependent Reactions
○ The light reactions take place within the thylakoid membrane sacs called grana
■ In the thylakoid membranes, there are a vast number of photosystems
(light-absorbing complexes)
● Photosystems consist of pigments (chlorophyll a along with other
accessory pigments)
○ Produces ATP through chemiosmosis
■ The absorption of light excites electrons, which are quickly fed into
electron transport chains
● Used to create a proton gradient (that allows for protons to flow
through ATP synthase channels)
■ To fill the hole left by the excited electrons, water is broken down (oxygen
is released)
● Light-Independent Reactions -- Where Sugar is Made
○ The light-independent reactions occur in the stroma
■ These reactions combine Co2 with protons and electrons to make sugar
○ Incorporating carbon dioxide into the sugar is called carbon fixation
■ Occurs during the Calvin cycle (with the help of the ATP that had
previously been produced)
○ Uses rubisco (ribulose biphosphate)
●
Cellular Respiration Photosynthesis

● Occurs continuously ● Can only occur with a steady

● Oxidation reactions supply of light
○ Catabolic ● Reduction reactions (anabolic)
● Uses the mitochondria ● Uses the chloroplasts
● Uses the ETC to make a proton ● Uses the ETC to make a proton
gradient gradient
● Requires Ox and releases Co2 ● Requires Co2, releases O2
● NAD is used to transfer protons ● NADP is used to transfer protons
● Protons flow through ATP ● Protons flow through ATP
synthase channels synthase channels
● Cyclical process = Krebs Cycle ● Cyclical process = Calvin cycle
● Structure of the Leaf
○ The palisade layer is where photosynthesis mainly occurs (have lots of cells with
chloroplasts)
■ In the mesophyll, cells also can contain chlorophyll and carry out
photosynthesis
● The cells in the mesophyll can better accommodate for
photosynthesis (less tightly packed -- air space for release and
consumption)
○ The clear epidermis serves to protect the cells underneath it/allow light to pass
through
■ Guard cells control the opening and closing of the stomata (pores in the
leaf)
 Classical Genetics

● Law of Dominance
○ Mendel’s first law
■ States that when a homozygous recessive individual and a homozygous
dominant individual are crossed, all of the offspring will be heterozygous
(two different alleles)
● The Law of Dominance dictates that in this second generation,
only the dominant allele will be expressed (only for the recessive
trait to be expressed in the next generation)
● Law of Segregation
○ During the formation of gametes, the alleles from both parents separate
randomly
■ And randomly come back together during fertilization
● Monohybrid Cross
○ A monohybrid cross is a cross between two heterozygous individuals
■ Result in a 3:1 phenotypic ratio (1:2:1 genotypic ratio)
○ In the first generation after the cross, the recessive allele (not seen in parents)
can be expressed
● Backcross or Testcross
○ Testcrosses can be used to see whether or not an individual is heterozygous or
homozygous dominant
■ The unknown individual is crossed with a homozygous recessive
individual
● If the tested individual is homozygous dominant, all offspring will
be heterozygotes
● If the tested individual is heterozygous, at least one of the
offspring will express the recessive allele
● Law of Independent Assortment
○ This law is used when two heterozygous (for two different traits) individuals are
crossed
■ The genes from the one gene are not inherited with the genes of another
trait
● Depends on the random alignment of chromosomes during
meiosis
○ This cross produces a 9:3:3:1 phenotypic ratio
● Incomplete Dominance
○ Blending of sorts (white and black animals crossed, heterozygous individuals are
gray)
■ Neither trait is dominant (so a mix of both is seen)
● In the next generation, both the dominant and recessive
phenotypes can be seen
● Codominance
○ In codominance, both traits are expressed
■ I.e. MN blood groups
● This depends on the presence of two molecules on red blood cells
○ If both are present, then both traits are expressed in the
heterozygote
● Multiple Alleles
○ If there are more than two possible alleles for a particular gene (called multiple
alleles)
■ I.e. Blood types
● A, B, AB and O are decided by three alleles
○ A and B are codominant
○ O is the recessive trait
● Polygenic Inheritance
○ Some traits are developed and expressed as a result of the blending of several
different genes (making the trait vary along a continuum)
■ These traits are polygenic
● Sex-Linked Genes
○ Sex linked traits are carried/inherited on the x chromosome
■ Females inherit two copies of these genes (XX)
● Making them less likely to express recessive alleles (as they need
two)
■ Males suffer from sex linked diseases more often (XY)
○ I.e. Color blindness and hemophilia
■ All daughters with fathers who have the recessive trait will be carriers of
that trait
■ Sons inherit only the Y chromosome from the father (can not get his sex
linked recessive trait)
● Genes and the Environment
○ The expression of different genes can be altered by the environment
■ I.e. The development of intelligence
● Sex-Influenced Inheritance
○ The nature of the traits that one inherits can be influenced by their
■ I.e. The trait for baldness is expressed differently by both males and
females
● Karyotype
○ A karyotype is a diagram assembled in a lab to analyze the size, shape and
number of chromosomes in a specific organism
● The Pedigree
○ A family tree of sorts that can be used to show how one trait is passed down
through several generations
■ If a trait is expressed, the circle/square is fully shaded in
● Mutations
 ○ Mutations are random abnormalities found in the genome
■ Gene mutations (caused by changes in the DNA sequence)
■ Chromosome mutation (abnormalities in the chromosome/number of
chromosomes)
● Nondisjunction
○ Nondisjunction can occur when homologous chromosomes do not separate
correctly (during meiosis)
■ One gamete receives double the amount of homologous chromosomes,
while another receives none
● If either of these gametes binds to a normal gamete, the resulting
chromosome will be an aneuploid (trisomy = chromosomes
present in a triplet)
● Human Inherited Disorders
○ Mutations can cause genetic defects (which can lead to the inheritance of
disorders)
○ Different abnormalities in the chromosomes include…
■ Deletion (a fragment of the chromosome is lost during division)
■ Inversion (a fragment of the chromosome breaks off and reattaches in
reverse)
■ Translocation (a fragment of a chromosome breaks off and attaches to a
nonhomologous chromosome)
■ Nondisjunction (homologous chromosomes do not successfully separate
during division)
○
Genetic Disorder Pattern of Inheritance Description

PKU (Phenylketonuria) Autosomal Recessive Inability to break down

phenylalanine (can
cause mental retardation
if not eliminated)

Cystic Fibrosis Autosomal Recessive Causes the buildup of

fluid in different organs
(i.e. the lungs)

Tay-Sachs Disease Autosomal Recessive Inability to produce an

enzyme that breaks
down lipids (causes
buildup around the
brain)

Huntington’s Disease Autosomal Dominant Degenerative disease of

the nervous system

Hemophilia Sex-linked Recessive Inability to produce the

necessary proteins for
 blood clotting

Color Blindness Sex-linked Recessive Usually just an

inconvenience (inability
to see certain colors)
○
Chromosomal Pattern of Inheritance Description
Disorder

Down Syndrome An extra chromosome Mental disabilities and

21 characteristic
appearance

Klinefelter’s Syndrome Extra extra chromosome Causes abnormally

in a mle small testes (making the
man sterile)
 Molecular Genetics

● The Search for Inheritable Material

○ In 1927, Frederick Griffiths discovered transformation
■ The ability for a foreign genome to assimilate into bacteria (and
incorporate itself into its genome)
○ In 1944, Avery, MacLeod and McCarty found that DNA was the heritable material
being transferred in transformation
○ In 1952, Hershey and Chase proved that DNA is the heritable material
■ Tagged bacterial viruses (found that only DNA, not protein, entered the
foreign cell before infection)
○ In 1953, Maurice Wilkins and Rosalind Franklin found that DNA must be a helix
(by examining the x-ray crystallography picture of DNA)
■ This work helped Watson and Crick make their model
○ Watson and Crick described the DNA double helix
○ In 1953, Meselson and Stahl proved that DNA replicates in a semi-conservative
fashion (each strand is used as a template and attaches to the new one)
● Structure of Deoxyribonucleic Acid (DNA)
○ DNA is in the shape of a double helix
■ Consists of two complementary strands (running antiparallel to one
another)
○ Made up of nucleotide bases
■ Each nucleotide consists of a 5 carbon sugar, a phosphate group and a
nitrogenous base
● The nucleotides on opposite chains are paired together with
hydrogen bonds
● DNA Replication in Eukaryotes
○ DNA replication is used to make DNA genomes identical to those in the parent
cell
■ The DNA produced consists of one old strand and one new strand
● Called semiconservative replication (proved by Meselson and
Stahl)
○ DNA replication occurs during the S phase (in interphase)
■ Catalyzed by DNA polymerase (unzips the two strands, base pairs
nucleotides and proofreads for errors)
○ Each old strand of DNA serves as a template for new DNA
○ When DNA replicates, certain parts of the end of the genome can be lost
■ To protect the important genes, often genomes have telomeres on the
ends (nonsense sequences)
● Structure of Ribonucleic Acid (RNA)
○ RNA is a single helix
■ Polymer of repeating nucleotides
 ● Similar to in DNA, each nucleotide has a 5-carbon sugar, a
phosphate and a nitrogenous base
○ One of the nucleotides in RNA is uracil (instead of thymine)
○ The types of RNA are…
■ mRNA (messenger RNA)
● Carries messages from DNA to the nucleus (helps in protein
construction)
○ Made up of triplet nucleotide pairs called codons
■ tRNA (transfer RNA)
● Carries amino acids to an mRNA near the ribosome (to make
polypeptide chains)
○ Made up of complementary triplet pairs (to the codons)
called anticodons
■ rRNA (ribosomal RNA)
● Combined with proteins to make a ribosome
● Protein Synthesis
○ Transcription
■ The process of transforming DNA in RNA
● Catalyzed by RNA polymerase
■ Triplet sequences in the DNA are used to transcribe a codon sequence in
mRNA
○ RNA Processing
■ Before mRNA is allowed out of the nucleus, the pre-mRNA must be
altered
● The enzymes remove introns (noncoding regions)
○ Exons (coding regions) are joined together by DNA ligase
○ Translation of mRNA into Protein
■ The process transforming mRNA sequences into amino acid chains
● mRNA goes to the ribosome
○ tRNA brings the amino acids to the mRNA at the ribosome
■ The tRNA anticodon binds to the mRNA codon
● Gene Regulation
○ In the synthesis of new proteins, there are controls to synthesize proteins when
they are needed or save the macromolecules they are made of (if the protein is
not needed)
○ One important mechanism for regulation are operons
■ Cluster of genes with similar functions (that can be turned on or off to
regulate the synthesis of the entire molecule)
● Inducible (i.e. lac) operon
○ Usually turned off (unless it is turned on by something in
the environment)
● Repressible Operon
○ Usually turned on (unless it is inhibited by something in the
environment)
 ■ Most important parts are…
● Promoter
○ Binding site of RNA polymerase (controls synthesis)
■ If the promoter is obstructed, then RNA polymerase
cannot bind to it
● Operator
○ Binding site for repressor proteins
● TATA Box
○ Helps RNA polymerase bind to the promoter
● Mutations
■ Mutations are random changes in genetic material
● Can be spontaneous or caused by certain mutagenic elements
■ Raw material for genetic variation (and natural selection) within a
population
○ Gene Mutations
■ Point Mutations
● Simplest mutation (the substitution of one nucleotide in a DNA
sequence)
○ These mutations can be harmful (i.e. sickle cell anaemia)
or beneficial (or have no real impact)
■ Insertion or Deletion
● Results from the insertion or deletion of a single nucleotide in a
DNA sequence
○ If not inserted or deleted in a group of 3, these mutations
can result in a frameshift (entire sequence is altered)
○ Chromosome Mutations
■ Occur with changes in chromosome number or structure
● Aneuploidy = an abnormal number of chromosomes (i.e. Down’s
Syndrome -- have an extra chromosome 21)
■ Polyploidy = having entire sets of extra chromosomes
● Common in plants
■ Aneuploidy and polyploidy result from the incorrect separation of
chromosomes during division (nondisjunction)
● The Human Genome
○ The human genome is made up of about 3 billion DNA base pairs and 20,000
different genes (about 97% of this never ends up coding for proteins)
■ Some makes up regulatory sequences (control gene expression)
■ Some form introns
■ Some are present into repetitive or tandemly repetitive sequences
■ Some are pseudogenes (genes that resemble coding genes but have
been made obsolete by mutations)
● Genetic Engineering and Recombinant DNA
 ○ Recombinant DNA is made up of DNA from different sources that get combined
in one cell
■ Can be manipulated in genetic engineering
● Can help replace non functioning genes
● Can degrade/decontaminate harmful substances (i.e. oil spills)
■ There is widespread ethical concern about genetically modified
organisms (GMOs)
● Restriction Enzymes
○ Can be vital in the manipulation of DNA sequences
■ Cut DNA at specific recognition sites
● Make restriction fragments
● Gel Electrophoresis
○ Gel electrophoresis is a process to separate molecules of DNA based on their
rate of movement
■ The smaller the molecule, the faster their movement through the gel
○ The movement is measured in an agarose gel with an electrical field
● Polymerase Chain Reaction
○ PCRs can be used to make vast amounts of copies of a specific piece of DNA
 Evolution

● Intro
○ Evolution = the change in the gene pool of a population over long periods of time
■ Microevolution (changes in the gene pool of one population)
■ Macroevolution (the formation of new species)
● Evidence for Evolution
○ Fossil Record
■ Reveals the existence of extinct species (or those that have evolved)
● Help illustrate how old the earth actually is
● Shows progression from prokaryotes to eukaryotes over time
● Transitional fossils (link ancient species with those alive today)
○ Comparative Anatomy
■ Often, organisms with similar anatomies can be related (through a
common ancestor)
● Homologous structures
○ Same structure in different species (with different functions
that came about as emergent properties)
○ Help prove evolution from a series of common ancestors
● Analogous structures
○ Structures that have the same functions in different
organisms (but not the same structure)
■ Similarity came about as a result of adaptation to
the environment
● Vestigial Structures
○ Ancient structures (i.e. appendix)
■ Show how anatomy has evolved (some organs are
not needed)
○ Comparative Biochemistry
■ Organisms related through the existence of a common ancestor tend to
have common biochemical pathways
● The more similar the biochemistry, the more related two
organisms are
○ Comparative Embryology
■ Because of the evolution from a common ancestor, related organisms
tend to go through similar stages in the development of their embryos
● I.e. All vertebrates have gill pouches on their throats (change into
other things during development)
○ Molecular Biology
■ All organisms have cytochrome c (a polypeptide used in cellular
respiration)
● The more similar the cytochrome c is in different organisms, the
more closely related they are
 ○ Biogeography
■ Originally, the continents were locked together into pangaea
● With its separation, some species were able to move to other
continents
● Lamarck vs. Darwin
○ Lamarck also studied evolution
■ He believed that, due to environmental conditions, individuals have the
capacity to change
● These individuals can then pass these acquired characteristics
down to their offspring
○ Darwin believed in natural selection (consisting of…)
■ (Malthus) Populations grow exponentially/overpopulate (exceed the
resources they have)
● This creates competition and a struggle to survive
■ In any given population, different individuals have different traits that
make them more favorable/able to better survive and reproduce in a
given environment
● These most fit individuals tend to have their traits represented in
disproportionate amounts in future generations
○ Over time, these traits accumulate in the population
■ I.e. Giraffe necks
● Darwin believed that the giraffes started out with short necks
○ Over time, the giraffes with longer necks could better
survive and were able to pass down the trait to more
offspring
■ This created longer necks for the entire population
of giraffes
■ I.e. Moths in Industrial England
● Before 1840, moths in England were white (because that provided
the advantage)
○ With industrialization (and dark smoke and soot) darker
moths became favorable
■ By 1950, all the moths in industrialized regions
were dark
● Evolution and Drug Resistance
○ Depending on the generation lengths of different organisms, natural selection
can act upon populations faster
■ I.e. Bacteria resistant to antibiotics (antibiotics allow immune bacteria to
proliferate)
○ I.e. AIDS is treated with a drug cocktail to slow the progression of the disease
■ At some point, AIDS can become resistant to the drugs (viruses particles
immune to the drugs can proliferate)
● Types of Natural Selection
○ Stabilizing Selection
 ■ Selection that favors the status quo (eliminates extreme phenotypes)
● I.e. Keeps babies between 6 and 9 pounds
○ Disruptive/Diversifying Selection
■ Limits the frequency of traits at the status quo
● Favors movement of the population towards extreme traits (on
either end of the spectrum)
○ Directional Selection
■ Favors the movement of gene frequency to one extreme (can happen
with changing environmental conditions)
● I.e. Moths in England
● Diversity within a Population
○ Natural selection can only act on variation
■ Variation comes about because of mutation, genetic drift and gene flow
● Mutation
○ Changes in genetic material
■ Can be spontaneous or induced by certain mutagenic substances or
events
○ Create variation (allows natural selection to operate)
● Genetic Drift
○ Change in the gene pool of a population based on random, chance events
■ The Bottleneck Effect
● Chance events (like natural disasters) can decrease population
size non selectively
○ This creates a smaller population (not representative of
the original one)
■ This can make certain alleles over represented
(and therefore overrepresented in future
generations)
■ The Founder Effect
● If a small group breaks off from a larger population to colonize a
new area, it is likely not representative of the original population
○ Different alleles can be overrepresented (purely by
chance)
● Gene Flow
○ The movement of alleles in or out of a population (can occur as a result of
migration in or out of a population)
■ Can lessen the expression of certain alleles within a population
● Population Stability (Hardy-Weinberg Equilibrium)
○ Hardy and Weinberg described the conditions for a non evolving population
(called Hardy-Weinberg equilibrium when the conditions are met)
○ The conditions are…
■ The population must be large
 ● The smaller the population, the more significant random changes
in the gene pool are
■ No gene flow (population must be isolated)
● Alleles can be gained or lost through migration (can alter
frequencies in the population)
■ No mutations
● Mutations can change the gene pool (introduce a new allele and
change frequencies)
■ Random mating
● If mates select individuals with certain traits, those traits will be
more prevalent in future generations
■ No natural selection
● Natural selection causes change in allele frequencies over time
○ Equation (p = dominant allele) (q = recessive allele)
■ 𝑝 + 𝑞 = 1
■ 𝑝 2 + 2𝑝 + 𝑞 2 = 1
● Isolation and New Species Formation
○ Species = population of individuals who can interbreed and produce viable
offspring
■ New species can form in a number of different ways
○ Geographic Isolation
■ Geographic isolation occurs with the physical separation of a population
● Can cause speciation
○ Polyploidy
■ Mutations that result from errors during meiosis (disjunction)
● Have abnormal numbers of chromosomes
○ Isolated from non-polyploid individuals in a population
○ Habitat Isolation
■ Habitat isolation can occur when two different organisms live near each
other but rarely interact
● I.e. Two types of snakes (one living in the water, the other on the
land)
○ Behavioral Isolation
■ Behavioral isolation can occur from the specific tendencies or behaviors
associated with the reproduction of a specific species
○ Temporal Isolation
■ Temporal isolation can occur when different species may become
separated because of time
● I.e. Different mating season, different maturation, different growth,
etc.
○ Reproductive Isolation
■ Although two species may be closely related, they can be kept from
mating by incompatibility of their sex organs
● Patterns of Evolution
○ Divergent Evolution
■ Divergent evolution occurs when a population becomes isolated from the
rest of the species and evolves to better fit the new environment
● Over time, natural selection can act enough to create a totally new
species
○ Convergent Evolution
■ If totally unrelated species occupy similar environments, than natural
selection will act to favor similar traits in either group
● I.e. Whale and fish (both have a normal aquatic appearance, but
the whale’s bone structure is much more similar to that of a
mammal)
○ Parallel Evolution
■ Parallel evolution is when, after their divergence from a common
ancestor, two species continue to evolve similarly
● I.e. Tasmanian wolf and gray wolf (diverged from a common
ancestor and evolved in similar environments)
○ Coevolution
■ Coevolution are the adaptations that arise from two different species
interactions with one another
● I.e. Honeybees feed on the nectar of Scottish broom flowers
○ These flowers have developed a mechanism to give the
bees pollen
○ Adaptive Radiation
■ Adaptive radiation is the emergence of different species from a common
ancestor
● I.e. Galapagos finches
○ 14 species of finches came about in response to different
environmental conditions on the different islands
○ Theories about Evolution
■ Gradualism
● Theory that over time, new species have come about because of
the gradually compounding evolutionary adaptations
○ Big change = accumulation of small changes
■ Punctuated Equilibrium
● The theory most compatible with recent findings and the fossil
record
○ Proposes that speciation occurs during short spurts of
great change, with long periods of stasis in between
■ Spontaneous Generation
● The theory that living things can randomly emerge from nonliving
objects
○ Disproved by Francesco Redi
● How Life Began
○ Using dating techniques, experts have found that the Earth is around 4.6 billion
years old
■ At first, the atmosphere likely lacked free oxygen (energy provided by
heat, lightning and radiation)
○ They were also likely able to make organic compounds in these conditions
■ A.I. Oparin and J. B. S. Haldane hypothesized this
● Stanley Miller and Harold Urey tested this hypothesis (proved that
organic molecules could have been made)
■ Sidney Fox was even able to produce membrane bound structures in
these early Earth conditions
● The Heterotroph Hypothesis and the Theory of Endosymbiosis
○ The Heterotroph hypothesis (first cells were anaerobic prokaryotes)
■ They adsorbed organic molecules from the environment
● Eukaryotic cells then evolved from early prokaryotes as bacteria
took up residence inside of them
○ The Eukaryotes thrived because the bacteria performed important functions
■ This resulted in the formation of membrane bound organelles (theory of
endosymbiosis)
○ From about 565 million years ago to about 525 million years ago, the Cambrian
explosion created speciation to fill all areas of the environment
■ Many animals moved to land
● Developed lungs, skin, limbs, new fertilization techniques and
shells to protect their eggs
■ Many plants also moved to land
● Developed roots, cells that enable them to absorb light, tissue that
can carry water, mechanisms to protect the leaves from drying,
and seeds to package the embryo
○ The first mammals arose relatively recently (210 million years ago)
■ Humans (as we know them) did not arise until around 150,000 years ago
● Mass Extinctions
○ According to the fossil record, around 99% of the organisms that have ever lived
are extinct
○ Major extinctions…
■ Permian extinction (250 million years ago)
● Occurred with volcanic eruptions in Siberia (climate increased and
life was wiped out on a massive scale)

■ Cretaceous extinction (65 million years ago)

● Occurred when an asteroid crashed into the Earth
○ Created a cloud of debris that blocked the sun (resulting in
widespread death)
● Important Concepts of Evolution
○ Evolution does not have to be slow (depending on the generation length of a
species/population)
■ Occurs at different rates in different organisms
○ Evolution does not have to make organisms more complex
■ Can make simpler organisms
○ Populations evolve, not individuals
○ Evolution/natural selection only can act on environmental conditions and
variations in a population’s gene pool
 Biological Diversity

● Intro
○ Taxonomy is the system used to classify all organisms
■ First developed by Carl Linnaeus
○ The modern system is that of binomial nomenclature
■ Every organism has a two part name
○ Linnaeus classified organisms into different levels (or taxa)
■ Kingdom, phylum, class, order, family, genus and species
● Starting from kingdom, these get progressively more specific
○ Today, most scientists use the three-domain system (based on DNA)
■ Bacteria, archaea and eukarya
● The Three-Domain Classification System
○ Domain Bacteria
■ All are prokaryotic (with no internal membranes/membrane bound
organelles)
■ Can be anaerobic or aerobic
■ Have a thick/rigid cell wall
■ Has no introns
■ Many function as decomposers or pathogens
○ Domain Archaea
■ Unicellular (prokaryotic)
● Includes organisms that live in extreme environments
(extremophiles)...
○ Methanogens (obtain energy by producing methane)
○ Halophiles (live in environments with high salt
concentrations)
○ Thermophiles (thrive in high temperatures)
■ Sometimes have introns
○ Domain Eukarya
■ All have membrane bound organelles/a nucleus (eukaryotic)
● Include the kingdoms Protista, fungi, plantae and animalia
● The Four Kingdoms of Eukarya: Protista, Fungi, Plants, Animals
○ Kingdom Protista
■ Includes many different types of organisms (all eukaryotes)
● Mostly single celled (some basic multicellular ones as well)
● Includes many organisms that do not fit into the other kingdoms
(i.e. seaweed and slime molds)
■ Can be heterotrophs (i.e. amoeba and paramecium) or autotrophs
(euglenas)
■ Some carry out conjugation (sexual reproduction)
■ Can move using a variety of different things (i.e. pseudopods, cilia,
flagella, etc.)
 ■ Can be pathogens (i.e. malaria and amoebic dysentery)
○ Kingdom Fungi
■ All are eukaryotic and all are heterotrophic
● Can be unicellular or multicellular
● All carry out extracellular digestion (to break down things outside
of the cell and absorb the nutrients)
○ Function in nature as decomposers
■ Fungi obtain nutrients from decaying organic matter (saprobes)
● Important in recycling nutrients in nature
■ Have thick cell walls made of chitin
■ Can form symbiotic relationships with algae to make lichen (can help
them survive in tough environments)
■ Reproduce asexually
● By budding (i.e. yeast), spore formation (i.e. mold), or
fragmentation (a parent breaks into parts which can grow into new
individuals)
○ Can also reproduce sexually in some cases
○ Kingdom Plantae
■ All are multicellular, autotrophic, and eukaryotic
● With thick cell walls of cellulose
■ Carry out photosynthesis to make food
● Store carbohydrates as starch
■ Reproduce sexually (by alternating generations)
● Alternate between gametophyte (n) and sporophyte (2n)
generations
■ Can have vascular tissue (tracheophytes) or no vascular tissue
(bryophytes)
○ Kingdom Animalia
■ All are heterotrophic, multicellular, and eukaryotic
● Most can move on their own
■ Most reproduce sexually (with 2n diploids)
● Usually a sperm fertilizes an egg
■ Grouped into 35 phyla
● Only nine are important (porifera, cnidaria, platyhelminthes,
nematodes, annelids, mollusks, arthropods, echinoderms and
chordates)
○ Evolutionary Trends in Animals
■ The first organisms were small prokaryotes living in the ocean
● Each phylum in animals represents the evolution of a new body
plan (i.e. specialization of tissues, germ layers, body symmetry,
development of a head end and body cavity formation)
● Specialized Cells, Tissues and Organs
○ Tissues are groups of cells with similar functions
 ■ Organs are groups of tissues that work together to perform similar
functions
○ Sponges (porifera) consist mostly of unspecialized cells (not really tissues)
■ Cells can react to the environment
○ Cnidarians (i.e. hydra and jellyfish) consist of the most primitive tissues
■ Over time, tissues evolved to be really complex (and eventually organs
and organ systems)
● Germ Layers
○ Germ layers form tissues and organs in the body
■ They are vital (formed during embryonic development)
○ Include three important layers…
■ Ectoderm (outermost layer) develops into the skin and nervous system
■ Endoderm (innermost layer) becomes the digestive system
■ Mesoderm (middle layer) develops into the blood, muscles and bones
○ Some animals only have two cell layers (i.e. porifera and cnidarians)
■ Instead of a mesoderm, they have a mesoglea (holds the two layers
together)
○ Triploblastic = having three true cell layers
● Body Symmetry
○ Over time, animals evolved to have bilateral symmetry (instead of radial
symmetry)
■ Bilateral symmetry dictates that the right and left sides will mirror each
other
○ Most animals with bilateral symmetry are also triploblastic
● Development of a Head (Cephalization)
○ Animals who have bilateral symmetry also have to develop a head (anterior) and
a rear end (posterior)
■ At the anterior end, some sort of sensory apparatus and a brain (or
ganglia) can be found
■ At the posterior, digestive, excretory and reproductive structures can be
found
○ The simplest animals (porifera and cnidarians) do not have a head end
■ Beginning with flatworms, the evolution of heads on animals begins
● Body Cavity Formation
○ Coelom = fluid filled body cavity surrounded by mesoderm tissue
■ The evolution of the coelom provides a space for complex organ systems
○ Primitive animals without coelom are called acoelomates
■ Their bodies are flat
■ All of their cells come in contact with the moist environment
○ Somewhere in the middle (i.e. nematodes and roundworms) are
pseudocoelomates
■ They have a tube filled with fluid in between the endoderm and the
mesoderm (acting as a skeleton to support the animal)
○ Coelomates are more complex animals (with a coelom)
 ■ Includes several phyla (annelida, mollusca, arthropoda and chordata)
●
Primitive Animals Complex Animals

No symmetry or radial symmetry Bilateral symmetry

No head end Head with a sensory apparatus/brain

Mesoglea (middle glue) holds ectoderm Three cell layers (triploblastic)

and endoderm together

No coelom (acoelomate) Pseudocoelomate and coelomate

No true tissues/specialized groups of cells True tissues/organs/organ systems

Don’t move on their own Move on their own (motile)

Not very specialized Specialized

● Characteristics of Animals
○ Porifera (sponges)
■ The least specialized/advanced
● No symmetry
● No specialized nerve or muscle tissues
● Unable to move (sessile)
● Take nutrients from water that is drawn into a central cavity
● Only have an ectoderm and an endoderm
○ Connected by a mesoglea
● No true tissues/organs
● Reproduce asexually with fragmentation
○ Can reproduce sexually as well (hermaphrodites)
○ Cnidarians (hydra and jellyfish)
■ Radial symmetry
● Can be vase shaped (polyp) and be mostly sessile
● Or upside-down bowl shaped (medusa) and be mostly motile
● Can go through two reproductive stages
○ Asexual (polyp) and sexual (medusa)
● Only have an ectoderm and an endoderm
○ Connected by a mesoglea
● Have a gastrovascular cavity (where extracellular digestion
occurs)
○ Carry out intracellular digestion in lysosomes
● Cnidocytes contain stingers (nematocysts)
○ Platyhelminthes (flatworms and tapeworms)
■ Simplest animals with bilateral symmetry
● Have an anterior end
● And are triploblastic (three cell layers)
 ■ Only have one opening in their digestive cavity (food cannot be
processed continuously)
■ Have a solid body (no room for digestive or respiratory systems)
● Instead, flatworms have cells that can exchange nutrients with the
environment (by diffusion)
○ Nematodes (roundworms)
■ Have bilateral symmetry but a very primitive sensory apparatus
● Can be parasites (trichinella can cause trichinosis)
■ C. elegans are used to study genes and embryonic development in
animals
○ Annelids (segmented worms)
■ Bilateral symmetry (sensory apparatus still primitive)
● Digestive tract is essentially a tube inside of a tube (with a crop,
gizzard and intestine)
■ Use nephridia for excretion
■ Have a closed circulatory system (heart with five pairs of aortic arches)
■ Have blood that can carry oxygen (with hemoglobin)
■ Oxygen and carbon dioxide can diffuse in and out through moist skin
■ Hermaphrodites (both female and male reproductive organs)
○ Mollusks (squids, octopuses, slugs, clams and snails)
■ Have a soft body (with a hard calcium shell)
■ Open circulatory system
● Blood filled spaces (called hemocoels or sinuses)
■ Have bilateral symmetry (splits the body up into three parts)
● Head-foot (anterior and posterior) containing both sensory and
motor organs
● Visceral mass (contain organs for digestion, excretion and
reproduction)
● Mantle (tissue that surrounds the visceral mass and secretes the
calcium shell)
■ Have radula (almost like a tongue with teeth)
■ Usually have gills and nephridia (for excretion)
○ Arthropods (grasshopper, shrimp, crab, spider)
■ Bilateral symmetry
● Split into the head, thorax and abdomen
■ Have jointed appendages
■ Have a relatively advanced sensory apparatus
● Can move (motile)
■ Have a thick exoskeleton made of chitin
■ Have an open circulatory system with a heart made up of tubes (and
blood filled spaces called hemocoels or sinuses)
■ Have malpighian tubules for excreting nitrogenous wastes/uric acid
■ Have trachea (air ducts) to bring air to the blood/hemocoels
○ Echinoderms (starfish and sea urchins)
 ■ Usually sessile or slow in movement
■ During embryonic development, they have bilateral symmetry
● As an adult, they take up radial symmetry
■ Reproduce sexually (external fertilization)
● Can reproduce asexually I(with fragmentation and regeneration)
○ Pieces of the starfish with parts of the central canal can
grow into their own organisms
■ Sea Stars have a calcium endoskeleton that grows with the body
● Exoskeletons must be shed periodically
○ Chordates (fish, amphibians, reptiles, birds, mammals)
■ The most complex of all of the phyla
● Have a notochord (rod that extends over the entire body and is
flexible)
● Have hollow nerve cords
● Have tails that help in movement and in balance (in humans,
coccyx bone)
● Birds and mammals are homeotherms (consistent body
temperatures)
● Fish, amphibians and reptiles are cold-blooded (endotherms)
● Characteristics of Mammals
○ All belong to the phylum chordata
■ Babies get nutrients from their mother’s milk (produced by the mammary
glands)
■ Mammals have hair or fur
■ Most are eutherians (have placenta)
● The babies develop in a uterus (connected to the mother by the
placenta) where nutrients can be transferred
■ Marsupials have babies born very early
● Complete development in their mother’s pouch
■ Egg-laying mammals (monotremes) get nutrients from a shelled egg
● Classification
○
Taxa Human

Domain Eukarya

Kingdom Animalia

Phylum Chordata

Class Mammalia

Order Primate

Family Hominid
 Genus homo

Species Sapiens
● Characteristics of Primates
○ Primates (i.e. humans/gorillas/monkeys in general) are descendants of small
mammals
■ Have opposable thumbs (make fine-motor tasks possible)
● Nails replaced claws
● Fingers/hands have many nerve endings (making them sensitive)
■ Have forward facing eyes
● Eyes are also set close together (enhance depth perception and
hand-eye coordination)
■ Most dedicated/direct in terms of parenting
● Primates usually nurture their young for long periods of time
● Cladograms and Phylogenetic Trees
○ All living things have evolved from a common ancestor
■ Cladograms/phylogenetic trees can be used to illustrate evolutionary
history based on DNA
● Does this by distinguishing between shared traits (that organisms
have in common) and derived traits (new traits not shared with
common ancestors)
 Plants

● Intro
○ Plants are eukaryotic, multicellular autotrophs (who carry out photosynthesis)
■ They have cell walls made of cellulose
■ Store carbohydrates as starch
○ Likely evolved from algae (chlorophyta) that lived in freshwater
● Classification of Plants
○ Bryophytes
■ Less advanced/primitive plants
● Have no vascular tissue
■ Need to live in moist environments
● No roots/xylem (can only absorb/transport water through osmosis)
■ Tend to be very small
● Lack the lignin-fortified tissue that is needed to support tall plants
■ Include mosses, liverworts and hornworts
○ Tracheophytes
■ More advanced plants
● Has transport vessels, xylem and phloem (vascular tissue)
■ Include seedless plants (i.e. ferns) that can reproduce with spores
● Also include plants that reproduce with seeds
○ Plants that reproduce are further divided into
gymnosperms and angiosperms
○ Gymnosperms
■ Gymnosperms are plants that produce seeds on the surface of cones
(conifers)
● Different modifications (i.e. needle shaped leaves, waxy/thick skin,
and specially located stomates to limit water loss) all help to make
gymnosperms more resistant to different environmental conditions
■ Include…
● Cedars, sequoias, redwoods, pines, yews and junipers
○ Angiosperms
■ Angiosperms are plants that having seeds developing inside of the
ovaries of their flowers (flowering plants)
● When pollinated, the ovary becomes the fruit
■ Angiosperms are the most diverse/prevalent plants
● I.e. flowers, fruits, nuts, grains and grasses
■ Split into monocotyledons (monocots) and eudicots (including complex
dicots)
●
Characteristic Monocots Dicots

Seed leaves One Two

 (cotyledons)

Vascular bundles in Scattered In a ring

stem

Leaf venation Parallel Netlike

Floral part Usually in 3s Usually in 4s or 5s

Examples Wheat, corn, oats, Most flowering

law grass and rice plants (i,e, roses,
(provide most food) carrots, cherries,
oak and walnut)
● Evolutionary Developments That Enabled Plants to Move to Land
○ Plants (beginning as green algae living in water) moved to land because of
increasing competition in the sea
■ They could do this because…
● Cell walls (made of cellulose) helped reinforce their shape
● Roots/root hairs allowed for water and nutrients to be absorbed for
soil
● Stomates (pores) open to release gases (produced by
photosynthesis) and close to reduce water loss
○ Waxy coating (cutin) also helps prevent water loss
● Some gametes/zygotes form with protective jackets (gametangia)
that prevent them from losing water and drying out
○ Spores and pollen also have protective coats that prevent
them from drying out (also help disperse offspring)
● Sporopollenin (found in spores and pollen) is resistant to almost
all environmental damage
● How Plants Grow
○ Plants grow throughout the duration of their lives
■ Meristem tissue continuously divides (generating new cells in the plant)
○ Primary Growth
■ Primary growth = vertical growth (of the roots into the soil and the plant
into the air)
● New cells continuously arise from the apical meristem (located at
the tips of roots)
■ Root growth mainly occurs near the root tip
● At the root tip, the zone of cell division (apical meristem), the zone
of elongation and the zone of differentiation are all located
■ The root tip is covered in a protective root cap
● The root cap helps secrete different substances that digest the
surrounding earth/soil (allowing the roots to continue growing)
■ In order from the root cap…
 ● Root cap - zone of cell division (meristem layer) - zone of
elongation - zone of differentiation/specialization
■ Zone of cell division
● Contains meristem cells/tissues that continuously divide
○ Responsible for producing the new cells that grow down
into the soil
■ Zone of elongation
● Where cells elongate
○ Push down on the root cap (get it deeper into the soil)
■ Zone of differentiation/specialization
● Where cells undergo differentiation (to determine whether they will
in the primary meristems that give rise to the epidermis, ground
tissue, or xylem and phloem)
○ Secondary Growth
■ Secondary growth = lateral growth (increase in girth)
● New cells are created through division in the lateral meristem
■ In woody plants (like trees), secondary growth enlarges the trunk
● Each year, another ring is added
● Roots
■ Roots are vital in absorbing nutrients from soil, anchoring the plant, and
storing food
○ Structure
■ Roots have specialized tissues/structures to carry out different functions
○ Epidermis
■ Covers the surface of the root (modified to increase absorption)
● Tiny root hairs extend from each epidermal cell (increase surface
area available for absorption)
○ Cortex
■ The main function of the cortex is in storage
● It has parenchyma cells (with plastids in them) that can store
starch and other organic substances
○ Stele
■ Stele = vascular cylinder
● Main function is in transport
■ Consists of the vascular tissues (xylem and phloem) that are surrounded
by one or more layers of tissue (pericycle)
● From the pericycle, lateral roots can grow
○ Endoderm
■ The endodermis surrounds the vascular cylinder
● Each endoderm cell is wrapped in a Casparian strip (waxy
material that does not allow water or nutrients to pass)
■ The endoderm is selectively permeable
● Mainly functions in choosing what minerals/nutrients can enter the
vascular cylinder and which can’t
● Absorption of Nutrients and Water
■ The roots are used by plants to absorb nutrients/water from the soil
● These nutrients must then be absorbed by the cells in the plant
○ Apoplast and Symplast
■ Lateral movement (the movement of water and solutes across a plant)
are the main functions of the apoplast and symplast
● Symplast = the channels between neighboring cytoplasms
connected by plasmodesmata
● Apoplast = the network (of connected cell walls and intercellular
spaces) that allows water/nutrients to move within the plant
○ Mycorrhizae
■ Often as plants age, parts of their roots start to lack root hairs
● In these situations, mycorrhizae help supply the plant with water
and nutrients
■ Mycorrhizae essentially are the plants roots in a symbiotic relationship
with the filaments (hyphae) of a fungus
● This fungus allows the plant to absorb substantially more nutrients
and water from the soil
○ Rhizobium
■ Similarly to the mycorrhizae, rhizobium are bacteria that develop a
symbiotic relationship with specific parts of the roots
● The rhizobium is vital in taking nitrogen gas from the air (and
transforming it into a type of nitrogen the plant needs)
● Types of Roots
○ Taproot = single, large root that gives rise to lateral branch roots
■ Many dicots have their primary root as a taproot
● Taproots can either take water from deep in the soil, or be
modified for storage purposes
○ In monocots, fibrous root systems help hold the plant in place
■ Adventitious roots = roots that arise above the ground
● I.e. Aerial roots (trees growing in swamps have roots that stick out
of the water (and give air to the root cells)
● I.e. Prop roots (tall plants use prop roots to support the base of the
plant)
● Stems
○ The main function of a stem is usually for support
■ This is vital in allowing the leaves to receive most of the light
■ They are also vital in transport (water/minerals from the soil and nutrients
from the leaves)
○ Structure
■ In the stem, vascular tissues run in strands
● Each bundle of vascular tissue has phloem on the outside, xylem
on the inside and meristem tissue between them
 ○ In monocots, these bundles are scattered throughout the
stem
○ In dicots, these bundles are found in rings along the stem
■ In the ground tissue of the stem (in dicots), parenchymal tissues (cortex
and pith) are used for storage
● The Leaf
○ The different parts of the leaf are organized to optimize sugar production and
limit water loss
■
Parts of Leaf Function

Epidermis (lower and upper) Protection

Waxy cuticle (of cutin on the Limits water loss

exterior of the epidermis)

Guard cells (epidermal cells with Control the opening and closing of
chloroplasts) the stomates

Palisade mesophyll (tightly Mesophyll tissues are important in

packed) photosynthesis (where pigments
are)

Spongy mesophyll (loosely Allows for the diffusion of gases in

packed) and out of the mesophyll cells
(during photosynthesis)

Veins (in the mesophyll tissue) Transport nutrients/water from the

roots to the leaves (and take sugar
from the leaves to the rest of the
plant)
● Stomates
○ During photosynthesis, plants take in carbon dioxide and release oxygen and
water vapor
■ These gases can diffuse in and out of spongy mesophyll cells through the
stomates
○ The stomates must be open and closed when needed to prevent water loss
■ Open stomates during the day (when photosynthesis can run) and close
them at night (when photosynthesis isn’t necessarily running at the same
rate)
○ Guard cells function in opening and closing the stomata
■ Can do this in response to changes in water pressure
● When water is absorbed and cells become turgid, the stomata are
opened (because of the curves in guard cells)
● When water is allowed to leave and the cell becomes flaccid, the
stomates close again
● Types of Plant Tissue
○ Dermal Tissue
■ Dermal tissue tends to make up the outer covering of plants (for
protection)
● Often come in the form of a single layer of epidermal cells
○ On leaves, the waxy cuticle protects the dermal tissue
under it
○ Some other leaves can also be covered with small spikes
(trichomes) that also can protect the leaf
● Usually, the only epidermal cells that can carry out photosynthesis
are guard cells
○ Vascular Tissue
■ Vascular tissue is vital in transporting nutrients and water up and down
the plant
● Vascular tissue is made up of xylem and phloem
○ Xylem = tracheids and vessel elements (water)
○ Phloem = sieve tube elements and companion cells (food)
○ Ground Tissue
● Ground tissue makes up all of the tissue in a plant (spare the
vascular and dermal tissue)
■ Parenchyma Cells
● Parenchyma cells are standard plant cells in structure (with a
primary cell wall and a cytoplasm with one or two large central
vacuoles)
○ These cells help in storage (when they are turgid and filled
with water, they help support the plant)
● Parenchyma cells are found all over the plant
■ Collenchyma Cells
● Collenchyma cells are tissue cells with unevenly thick primary cell
walls
○ Make up the strings in celery
■ Important providers of support
■ Sclerenchyma Cells
● Sclerenchyma cells also function in support
○ They have thick primary and secondary cell walls
(reinforced by lignin)
● Transport in Plants
○ Xylem
■ Xylem are made up of elongated tracheid and vessel element cells
● Tracheids have secondary cells walls (reinforced by lignin) to offer
support and transport value
■ Xylem help transport water and nutrients from the roots to the leaves
without using energy (using transpirational pull and cohesion tension)
 ● Water molecules have attraction to each other (cohesion), so
when one evaporates (transpiration) others are pulled up
■ Different factors can decrease/increase the rate of transpiration (and
therefore the rate of transport)
● The higher the humidity, the slower the rate of transpiration
○ Wind can reduce humidity (increasing rate)
● Increased light can increase the rate of photosynthesis
○ This increases rate
● When the stomates are closed, transpiration stops
○ Phloem
■ Phloem are made up of sieve tube elements and companion cells
● Carry the sugar (made during photosynthesis) from the leaves to
the rest of the plant
■ Sugar is transported through translocation and can be stored in the roots
● This process requires energy
● Plant Reproduction
○ Asexual Reproduction
■ A process called vegetative propagation allows plants to reproduce
asexually
● A piece of the plant (specifically the root, stem, or leaf) can
produce a plant that is identical to the parent
○ Sexual Reproduction in Flowering Plants
■ Sexual reproduction plants is enabled by the flower
■ Each part of the flower has important functions in sexual reproduction
● Petals (bright coloration attracts animals that can pollinate the
plant)
● Sepals (outermost circle of leaves that protect the flower during
development and enclose the bud before it opens)
● Pistils/Carpels (have an ovary, stigma and style that work together
to produce the female gametophytes)
● Ovary (part of the pistil containing the ovule where ova are
produced during division)
● Ovule (structure inside of the ovary that fosters the development
of the female gametophytes)
● Style (thin/long part of the pistil)
● Stigma (sticky part of the style where pollen lands)
● Stamen (the male part of the flower that consists of anther and
filament)
● Anther (part of the stamen where sperm, in the form of pollen, is
produced during division)
● Filament (threadlike structure that supports the anther)
○ Pollination and Fertilization in Flowering Plants
■ Pollination is a vital step in initiating sexual reproduction in plants
● First, pollen lands on the stigma
 ○ The pollen takes moisture and germinates
● Next, the pollen forms a tube down into the ovary
○ The two sperm nuclei (brought in the pollen) travel into the
ovary
■ These sperm then enter the ovule
● One of the sperm fertilizes the egg (ova) and becomes a diploid
embryo
○ The other fertilizes two polar bodies (becoming a triploid
endosperm)
■ This endosperm provides the food for the embryo
○ Both of the processes = double fertilization
■ After fertilization occurs, the ovule becomes the seed and the ovary
becomes the fruit
● The monocots maintain food storage in the endosperm
○ The mature dicots lack the endosperm
○ The Seed
■ The seed is made up of a protective coat surrounding the embryo and the
endosperm (food for the embryo)
● The embryo itself is made up of several different parts
○ The hypocotyl will develop into the lower portion of the
stem and the roots
○ The epicotyl will develop into the upper portion of the stem
○ The radicle (embryonic root) develops into the first organ
that emerges from the seed
■ Dicot seeds split in half (and feed on cotyledon)
● Monocot seeds do not split in half (feed on endosperm)
● Alternation of Generations
○ Haploid and diploid generations alternate in the generations of plants
■ Haploid gametophytes come together during fertilization to make diploid
zygotes
● These diploid zygotes develop into sporophytes
○ These diploid sporophytes produce haploid spores through
division
○
Term Definition

Antheridium Structure on the gametophyte that

produces sperm

Archegonium Structure on the gametophyte that

produces eggs

Gametophyte Haploid plant

Megaspores Haploid spores produced by large

 female cones (that will eventually
become female gametophytes)

Microspores Haploid spores produced by small

male cones (that will eventually
become male gametophytes or grains
of pollen)

Protonema Unicellular filaments produced by

moss spores (eventually becoming a
moss gametophyte)

Sporangia Where meiosis occurs on the

sporophyte (eventually producing
haploid spores)

Sporophyte Diploid plant

Sori Clusters of sporangia (in the form of

spots) on the bottom of sporophyte
ferns
● Mosses and Other Bryophytes
○ Mosses are primitive plants (bryophytes)
■ Gametophyte (haploid) generations dominate the life cycle
● For most of its life, the organism is haploid (with the diploid
sporophyte dependent upon it)
■ The gametophyte receives nutrients through photosynthesis
● The sporophyte gets nutrients through the gametophyte
● Ferns
○ Ferns are an intermediate plant between bryophytes and flowering vascular cells
■ The fern itself is seedless, but containing vascular tissue
○ In ferns (unlike in moss), the sporophyte generation is longer and independent
from the gametophyte generation
■ Both the gametophyte and the sporophyte are able to sustain themselves
by carrying out photosynthesis
● Seed Plants
○ Seed plants are relatively advanced (have vascular tissue)
■ The two main groups of seed plants are flowering plants (angiosperms)
and conifers (gymnosperms)
○ In angiosperms (flowering plants), the gametophyte is totally dependent on the
sporophyte
■ In gymnosperms, the gametophyte generation can only develop from the
haploid spores produced by the sporophyte
● Plant Responses to Stimuli
○ Hormones
 ■ The production of hormones in plants help coordinate many processes
(i.e. growth/development) and respond to volatile conditions in the
environment
● Even though they are only produced in small quantities, they can
have significant effects (because the signal is amplified)
○ Auxins
■ Unequal distributions of auxins affect the growth of a plant (so that it can
best absorb sunlight)
● Auxins usually favor growth upward (lateral growth is suppressed)
■ By softening the cell wall, auxins can help stimulate the growth of the
stem
● One example of an auxin is an Indoleacetic acid (IAA)
● Auxin 2,4-D can be used as a weed killer
● Can also be used to speed up the development of roots to
optimize planting
● Some can produce fruits without pollination (makes seedless fruit)
○ Cytokinins
■ Cytokinins are hormones secreted to stimulate cell division (and
cytokinesis)
● Can also delay aging (i.e. give flowers a longer life)
○ Gibberellins
■ Gibberellins are hormones secreted to stimulate stem/leaf growth
○ Abscisic Acid (ABA)
■ Abscisic acid is a hormone secreted to stop growth (can send seeds into
dormancy)
● Closes the stomates (helps plants survive droughts)
○ Ethylene
■ Gas hormone that is secreted to stimulate growth/ripening
● When ripe, more ethylene gas is produced
● Tropisms
○ Tropism = the growth of a plant in reaction to a stimulus (towards or away from it)
■ I.e. Thigmotropism (touch), geotropisms/gravitropism (gravity) or
phototropisms (light)
○ Positive tropisms are growth towards a stimulus
■ Negative tropisms are growth away from a stimulus
○ Phototropisms (responses to light) are caused by the distribution of auxins (which
tend to build up away from the light)
■ This means that the plant cells on the side away from the light will
enlarge/grow (because auxins stimulate growth)
○ Geotropisms/gravitropism result from the unique interactions of auxins and
statoliths (starchy plastids)
 Animal Physiology

● Intro
○ Animals are multicellular/eukaryotic and are heterotrophs (get nutrients through
ingestion)
● Movement and Locomotion
○ All animals are motile (can move) in some way
■ Locomotion = the ability to move from place to place
● Some animals (i.e. hydra) can’t move
○ Different types of animals have different structures to allow movement/protection
■ Some mollusks (i.e. clams) can secrete a shell for protection
■ Some arthropods (i.e. grasshoppers) have chitin exoskeletons
● These must be shed periodically (because they do not grow with
the organism)
■ Some nematodes (roundworms), flatworms (planaria) and annelids
(earthworms) have hydrostatic skeletons (filled with fluid)
● Working in tandem with muscles that change the shape of the
hydrostatic skeletons, they can help the animals move
■ Chordates (i.e. humans) have endoskeletons of bone and cartilage
● These can grow with the animal
● Body Temperature Regulation
○ The majority of organisms can only survive from around zero degrees celsius to
about fifty degrees celsius
■ Animals need to live in suitable environments (oceans are ideal because
of stable temperatures)
○ On land, temperature is volatile
■ Animals have different mechanisms to regulate body temperature
● I.e. Snakes go into the sun for warmth and go into the shade to
cool off
● I.e. Bees swarm together in a hive to raise temperature
● I.e. Humans shiver to keep warm/sweat to lower temperatures
● Important Terms
○ Ectotherm (like cold blooded)
■ Heated from the outside
○ Endo/homeothermic (warm blooded)
■ Body temperature remains constant (despite fluctuations in the outside
environment)
● Excretion
○ Excretion is the process of removing metabolic waste from the body (usually
water, carbon dioxide, or one of three nitrogenous bases)
● Ammonia
○ Water soluble (toxic)
■ Excreted by organisms that live in the water
● Urea
○ Toxic (but not nearly as much as ammonia)
■ Excreted by earthworms and humans
○ Comes from the ammonia in the livers of mammals
● Uric Acid
○ Not water soluble (non toxic)
■ Excreted by insects, reptiles and birds
● Methods for Excretion
○
Organism Structures Nitrogenous Waste

Hydra None Ammonia

Platyhelminthes Flame cells Ammonia

Earthworms Nephridia Urea

Insects Malpighian tubules Uric acid

Humans Nephrons Urea

● Hydra (Cnidaria)
○ Nutrition
■ Cnidarians conduct digestion in the gastrovascular cavity
● There is only one opening (so food enters through the same
opening that waste exits)
■ Cells lining the gastrovascular cavity secrete enzymes to help in
extracellular digestion
● Cnidarians also have lysosomes that help in digestion
○ Body Plan and Symmetry
■ Hydra tend to be in the form of a polyp (vase shaped)
● Jellyfish tend to be in the form of a medusa
■ Cnidarians have primitive, radial symmetry
■ There are only two cell layers (the ectoderm and the endoderm)
● These are held together by the mesoglea (glue in the middle)
■ There is no circulatory system (all cells are in contact with the
environment)
○ Nervous System
■ Cnidarians have cnidocyte cells with nematocyst stingers
■ A primitive nerve net is used to respond to the environment
● The entire body of the cnidarian responds to each stimulus from
the environment
○ Reproduction
■ Cnidarians can reproduce sexually or asexually through budding
● The bud is identical to the parent (forms in the parent or on the
parent)
 ○ It grows and eventually breaks away from the parent
● Earthworm (Annelida)
○ Nutrition
■ Earthworm's digestive tracts are long tubes
● Food is first stored in the crop and then is grinded up by the
gizzard
■ After food has been grinded, it is digested and absorbed
● Absorption is stimulated by a large fold (the typhlosole) that
increases the surface area available for absorption
○ Nervous and Transport Systems
■ Earthworms exchange gases by diffusion through their skin
● They have an external respiratory system
■ Earthworms have a closed circulatory system and a heart with five pairs
of aortic arches
○ Excretion
■ Earthworms have nephridia in each of their body segments
● These nephridia excrete urea
○ Reproduction
■ Earthworms have both female and male sex organs (hermaphrodite)
● Grasshopper (Arthropoda)
○ Nutrition
■ Grasshoppers have a digestive tract that resembles a straight tube
● The grasshoppers have advanced mouths with increased
capability
○ The food is then stored in the crop and grinded by a
gizzard (reinforced with chitin)
■ The digestive system also uses malpighian tubules to excrete uric acid
○ Nervous and Transport Systems
■ Grasshoppers have open circulatory systems (no capillaries)
● Blood moves through the hemocoels around organs
○ Blood cannot carry oxygen
○ Exchange of Respiratory Gases
■ Gas exchange occurs inside of grasshoppers
● Air travels through tracheal tubes to the hemocoels
○ Diffusion occurs and can be carried by hemocyanin (similar
to hemoglobin)

Human Physiology

● Digestion
 ■ The digestive system functions in breaking down large food molecules
into smaller ones and absorbing these smaller food molecules (nutrition)
● Different molecules are broken into their respective monomers
■ The smooth muscle populating the digestive tract moves food through
peristalsis
● These muscles are controlled by the nervous system
○ Mouth
■ Digestion begins in the mouth
● Salivary amylase (an enzyme in saliva) initiates the breakdown of
starch
○ Along with different enzymes, the tongue and teeth also
break down food (depending on diet, different animals
have different types of teeth)
○ Esophagus
■ The esophagus only functions in the transport of food towards the
stomach
● No actual digestion occurs in the esophagus
○ Stomach
■ The main part of both chemical and mechanical digestion occurs in the
stomach
● The muscular wall of the stomach churns food (breaking it down)
and releases gastric juice )to break down molecules further)
■ Hydrochloric acid can start breaking down muscle (and activates
pepsinogen to break down proteins)
● Having too much acid is known to cause ulcers (that arise from
heliobacter pylori)
○ Small Intestine
■ In the small intestine, digestion is completed and food is absorbed
● The pH of the small intestine returns to a normal level of around 8
■ Digestion occurs in the beginning of the small intestine (called the
duodenum)
● Enzymes aid in finishing digestion…
○ Pancreatic amylases digest starch
○ Peptidases break down protein
○ Nucleases break down nucleic acids
○ Lipases break down fats
■ Once broken down, food monomers can be absorbed by the microvilli
lining the small intestine
● Inside of each villi is a capillary (which absorbs nutrients into the
bloodstream)
○ Liver
■ The liver produces bile (not an enzyme)
 ● Bile is extremely basic and can break down fats (also neutralizes
the acidic food from the stomach before it enters the small
intestine)
■ Vital in other processes…
● Breaks down and recycles blood cells
● Detoxifies the bloodstream
● Produces cholesterol (for cell membranes)
● Produces urea (nitrogenous waste)
○ Gallbladder
■ Stores bile (produced by the liver)
● Not a necessary organ in the body
○ Pancreas
■ The pancreas is a gland
● Produces the enzymes that break down carbohydrates, proteins,
lipids and nucleic acids
○ Secretes these enzymes into the small intestine when
stimuli are received
● Produces basic sodium bicarbonate (to neutralize stomach acid
and allow the enzymes to work)
○ Large Intestine or Colon
■ Can only indirectly function in digestion
● Vital in egestion (removing undigested waste)
■ Produces vitamins (bacteria in the colon make important vitamins and
acids)
■ Reabsorb water to maintain balance
● Constipation (body absorbs too much water)
● Diarrhea (too little water is absorbed into the body)
○ Rectum
■ Final step in egestion (removing undigested waste) after the colon
● Stores feces until its release from the anus
● Gas Exchange
■ In humans, enters through the nasal cavity and travels through the larynx
down the trachea (through to the bronchioles)
● The air is then taken in by tiny sacs (alveoli)
■ Humans have internal respiratory systems
● Air can be drawn into the lungs with the movement of the
diaphragm (through negative pressure)
■ Breathing is monitored by the medulla (in the brain)
● The medulla monitors Co2 levels in blood and pH fluctuations in
the bloodstream
○ Lower pH means higher Co2 levels (which triggers
increased breathing)
○ Transport of Oxygen and Carbon Dioxide
 ■ Once it has diffused into the bloodstream, oxygen is carried by
hemoglobin (forming oxyhemoglobin)
● Carbon dioxide (product of cellular respiration) is released into the
blood as well (makes up the carbonic acid-bicarbonate ion buffer)
○ Circulation
■ Circulation is conducted through arteries, veins and capillaries
●
Vessel Function Structure

Artery Carry blood away Thick smooth

from the heart muscle walls (that
can withstand high
pressure)

Veins Carries blood back Located within

to the heart muscles (to propel
blood with muscle
contraction)

Has no thick
muscular walls (no
need to withstand
pressure)

Constructed with
valves to
concentrate flow

Capillary Vessels that allow Blood travels slowly

nutrients/waste to (allowing time to
diffuse in or out diffuse)
○ Blood
■ Blood consists of red blood cells, white blood cells, platelets all
suspended in a liquid plasma
●
Component Scientific Name Properties

Plasma Liquid of the blood

(made mostly of
water) containing
many vital
nutrients/wastes

Red blood cells Erythrocytes Carry

hemoglobin/oxygen

Produced in bone
marrow and
 recycled in the liver

White blood cells Leukocytes Fight infection

(important in the
immune system)

Platelets Thrombocytes Important in blood

clotting
○ The Mechanism of Blood Clotting
■ Blood clotting involves a complex series of reactions (first set off by the
release of clotting factors from platelets/damaged tissue)
● First, thromboplastin (with calcium) is released by platelets
○ This stimulates the inactive prothrombin to activate (and
become thrombin)
● The thrombin stimulates the inactive fibrinogen to activated into
fibrin
○ This fibrin can then form the clot
○ The Heart
■ The main function of the heart is to receive blood without oxygen,
oxygenate it and then pump it into the rest of the body (through the aorta)
● The sinoatrial node sets a pace for heart contractions
○ Different factors/signals can stimulate the node to go faster
or slower
■ Blood pressure is lowest in veins and highest in arteries
● Normal pressure is 120/80
○ 120 = systolic (when ventricles contract)
○ 80 = diastolic (when the heart relaxes)
○ Pathway of the Blood
■ Veins carry blood into the vena cava
● The blood then travels to the right atrium, down to the right
ventricle, into the pulmonary artery, to the lungs
■ The blood is then oxygenated in the lungs
● The pulmonary vein brings the oxygenated blood back into the
heart (left atrium)
○ The blood then goes down to the left ventricle, into the
aorta, and then to the rest of the body
■ Blood can circulate through the heart (coronary), the kidney (renal) and
the liver (hepatic)
● Endocrine System
○ The endocrine system can release signals (often in the form of hormones) that
work with the signals of the nervous system (in the form of neurotransmitters) to
maintain homeostasis
■ Different signals can function as both hormones and neurotransmitters
○ Hormones are produced and secreted from endocrine (ductless) glands
 ■ These hormones move through the blood to specific targets
● Different hormones can have temporary effects or stimulate long
term developments in an animal
○ Tropic hormones are secreted and stimulate target glands to release other
hormones (i.e. Thyroid stimulating hormone is secreted by the gland to stimulate
the production of thyroxine by the thyroid)
■ Pheromones can transport messages between individuals of the same
species
● Other signals can travel between neighboring cells through
diffusion
● The Hypothalamus
○ The hypothalamus is a vital part of the brain
■ Helps connect the nervous and endocrine systems
● Endocrine Glands
○
Gland Hormones

Anterior Pituitary ● Growth Hormone (stimulates

the growth of bones)
● Luteinizing hormone
(stimulates the ovaries and
testes)
● Thyroid-stimulating hormone
(stimulates the production of
thyroxine in the thyroid)
● ACTH (stimulates the adrenal
cortex)
● Follicle-stimulating hormone
(stimulates the production of
sperm and ova)

Posterior Pituitary ● Oxytocin (stimulates uterus

contractions during labor and
stimulates the production of
milk by the mammary glands)
● Antidiuretic hormone (keeps
water in the kidneys)

Thyroid ● Thyroxin (controls the

metabolism)
● Calcitonin (lowers calcium
concentration in the
bloodstream)

Parathyroid ● Parathyroid hormone (raises

calcium concentration in the
bloodstream)
 Pancreas ● Insulin (lowers sugar levels in
the bloodstream)
● Glucagon (raises sugar levels
in the bloodstream)

Adrenal cortex ● Glucocorticoids (raises sugar

levels in the blood)

Adrenal medulla ● Epinephrine/norepinephrine

(adrenaline; raise blood sugar
levels)

Thymus ● Thymosin (stimulates part of

the immune system)

Pineal ● Melatonin (reacts to rhythms in

the environment and body)

Testes ● Androgen (produce

sperm/stimulate secondary sex
characteristics in males)

Ovaries ● Estrogen (develop secondary

sex characteristics in females)
● Progesterone (stimulates
growth of the uterine lining)
● Feedback Mechanisms
○ Positive Feedback
■ When something enhances an already existing response
● More of whatever is causing the response creates more of the
response
○ Negative Feedback
■ Maintains homeostasis
● Reacts to fluctuations in what is needed (stimulates hormone
secretion when there is too little, stops hormone secretion when
there is enough)
● Nervous System
■ Vertebrates have nervous systems composed of two main parts
● The central nervous system = the spinal cord and the brain
● The peripheral nervous system = all of the other nerves in the
body
○ The Peripheral Nervous System
■ Sensory = conveys/interprets information picked up on nerve
endings/sensory receptors
■ Motor = stimulates movement in voluntary or involuntary muscles
● Consists of…
○ The somatic system (voluntary muscles)
 ○ The autonomic system (involuntary muscles)
■ Sympathetic Response
● Heart and breathing rate increase
● Glucose levels in the bloodstream increase
● Adrenaline (fight or flight response)
■ Parasympathetic Response
● Calms the body
● Lowers heart and breathing rate
● Enhances digestion
○ Opposite of sympathetic
○ The Neuron
■ Neurons are the basic units used by the nervous system to transport
messages
● Consist of cells with two types of cytoplasmic extensions
○ Dendrites receive messages (sensory) and transport the
message to the cell body
○ Axons send messages from the cell body to other cells
■ Usually only one on each neuron (wrapped in a
myelin sheet for protection/efficiency)
○ The Reflex Arc
■ Reflex arcs are the simplest (natural/instinctual/protective) nerve
responses
● I.e. (knee is hit with a hammer and your foot flies up)
○ The message is only going from the sensory neuron (that
is hit) to the motor neuron (that responds)
■ Reflex arcs are more complex when they involve an
interneuron/association neuron
● Sensory neurons send a signal to the interneurons in the spine
(which signal the brain and the appropriate motor neuron)
○ How a Neuron Functions
● All cells have membrane potential (difference in electrical charge
between the cytoplasm (in the cell) and fluid outside of the cell
○ The inside of the cell is usually negative relative to the
outside
■ Resting Potential
● Neurons at rest have the polar gradients maintained by sodium-
potassium pumps
○ The stronger the gradient/membrane potential, the
stronger the signal must be to reach the nerve and create
a response
■ Action Potential
● Action potential = an impulse
○ Impulses can only be generated through the axons
 ■ This occurs when the axon is stimulated and able
to pass through the membrane potential
● A wave of depolarization occurs and the
impulse is able to be sent
○ Shortly after, a period of repolarization (refractory period)
restores the membrane potential
■ During the refractory period, neurons are unable to
respond to other signals
● This insures that the impulse only passes in
one direction
○ The impulse is able to keep moving because action
potential sets off a chain reaction
■ Only strong stimuli can set off the initial action
potential
■ The Synapse
● Impulses can cross synapses chemically
○ During depolarization, vesicles with neurotransmitters are
able to fuse with the membrane and release the
neurotransmitter into the synapse
■ This then sets up a similar action with another
neighboring cell
● Nitric oxide (NO) can also be release to stimulate other cells
● The Eye and the Ear
○ The Eye
■ Cones = light receptors that help distinguish colors
■ Cornea = clear/glossy covering that protects the eye (allows light to pass)
■ Humor = fluid that maintains the shape of the eyeball
■ Iris = colored part of the eye (that controls light absorption)
■ Lens = focuses light onto the retina
■ Pupil = opening in the iris
■ Retina = converts light into signals that can be interpreted by the nervous
system and taken to the brain
■ Rods = sensitive light receptors (do not distinguish colors)
○ The Ear
■ Auditory canal = hole where sound enters
■ Tympanum (ear drum) = vibrates when hit by sound
● Ear bones (hammer, anvil and stirrup) = send vibrations to the
oval window
○ Oval window = turns vibration into pressure waves (sends
to the cochlea)
■ Cochlea = fluid in the inner ear (interprets sound
into nerve impulses that can be transported to the
brain)
 ■ Eustachian tube = balances pressure differences between the inner ear
and the environment
■ Semicircular canal = fluid filled canals that help maintain balance
● Excretion
○ Intro
■ Excretion is the process of removing metabolic wastes from the body
● Can excrete salts, CO2/water (from cellular respiration) and
nitrogenous wastes
○ The Human Kidney
■ Kidneys produce urine
● Change it depending on salt and water intake (and the
subsequent production of urea)
■ Kidneys also filter blood
● Depending on what the body need, the kidneys can respond
because they are controlled by hormones
○ The Nephron
■ Nephrons are the vital units in the kidneys
● Filtration = everything small enough diffuses into the Bowman’s
capsule
○ The filtered blood moves into the loop of henle
○ The waste moves to the ureter (in preparation for urine)
● Secretion = active/selective process (removes what could not be
taken out of the blood through filtration)
● Reabsorption = because filtration is not selective, the blood often
needs to reabsorb some of what was lost
● Excretion = removal of metabolic wastes
○ After all of these processes, the wastes that end up in the
collecting tubule are excreted out of the body
● Muscles
○ Types
■ Smooth (involuntary) muscles are found in blood vessels and on the
digestive tract
● Can absorb stuff (controlled by the autonomic nervous system)
■ Skeletal muscles (voluntary) are large and work together (contract/relax)
■ Cardiac muscle is found in the heart
● Makes its own action potential (can continue to beat even after
removal from the body)
○ The Sliding Filament Theory
■ Myofibrils run parallel to each skeletal muscle cell
● Myofibrils are made of different size filaments (thin = actin,
thick=myosin)
■ It is thought that muscles contract when the thick and thin filaments slide
over one another
 Reproduction and Development

● Intro
○ Most animals show cycles in reproduction (controlled by hormones and the
environment)
■ Animals can reproduce asexually or sexually (or alternate between either)
○ Some eggs are not fertilized and are haploid adults (parthenogenesis)
■ Male honeybees do this
○ Some animals that do not move are hermaphrodites
■ Mate with any member of their species
○ Sexual reproduction creates variation (helpful in changing environments)
■ Sperm (haploid) fertilizes an egg (haploid)
● Form a diploid zygote
■ Fish and amphibians carry out external fertilization
● Eggs laid in the open to be fertilized
■ Birds, reptiles and mammals carry out internal fertilization
● Less zygotes = more parental care
● Asexual Reproduction
○ Asexual offspring is a mechanism that produces offspring that are identical to
their parent
■ In some ways, asexual reproduction is advantageous
● Can reproduce without a mate
● Can reproduce at a faster rate
○ No elaborate cycle
○ No complex hormones
● Works in stable environments
● Examples of Asexual Reproduction
○ Fission = separation into two new cells (found in amoeba and bacteria)
○ Budding = new individuals split off from old ones (hydra)
○ Fragmentation = parent breaks into parts that become new individuals (sponges,
planaria, sea star)
○ Parthenogenesis = egg develops without fertilization (haploid adult)
■ Seen in honeybees
● Sexual Reproduction
○ Sexual reproduction creates variation in a gene pool
■ Each offspring is the random product of both parents
● Helpful in changing environments (some better fit than others)
● The Human Male Reproductive System
○ Testes = male gonads (where sperm is produced)
○ Vas deferens (carry sperm during ejaculation)
○ Prostate gland = gland that secretes semen into the urethra
○ Scrotum (sac that holds the testes)
○ Urethra (tube that carries semen and urine)
● The Human Female Reproductive System
○ Ovary = site of meiosis
○ Fallopian tube = site of fertilization
○ Uterus = where the embryo develops
○ Vagina = where the baby comes out
○ Cervix = the mouth of the uterus
○ Endometrium = lining of the uterus
● The Menstrual Cycle of the Human Female
○ The menstrual cycle is the result of changes in the ovary and uterus (controlled
by hormones)
■ Release gametes every 28 days
○ Happens in four stages…
■ Follicular Phase
● Follicles grow and secrete estrogen (in response to the release of
follicle stimulating hormone)
■ Ovulation
● Luteinizing hormone is released and the oocyte leaves the ovaries
■ Luteal Phase
● The corpus luteum forms
● Estrogen and progesterone are released (thickening the lining of
the uterus)
■ Menstruation
● If the egg is not fertilized (and the embryo is not implanted) the
lining of the uterus (endometrium) is shed
○ Blood is discharged (period)
● Hormonal Control of the Menstrual Cycle
○ The hormonal cycle is vital in the female reproductive cycle
■ First, the hypothalamus releases GnRH
● The GnRH stimulates the release of FSH and LH (from the
anterior pituitary)
■ FSH and LH stimulate the ovaries
● The ovary releases estrogen and progesterone
○ This thickens the lining of the uterus
● Spermatogenesis
○ Spermatogenesis = sperm production
■ Begins when LH is released and the testes produce testosterone is
released
● The testosterone works with the FSH to produce sperm in the
testes
○ The cells then undergo division
■ The spermatognium cells divide by mitosis
● The primary spermatocyte and secondary spermatocyte divide
with meiosis
○ This yields four haploid spermatids
● Oogenesis
○ Oogenesis = production of ova (begins before birth)
■ Oogonium cells divide with mitosis to form two diploid primary oocytes
● These are activated by hormones
○ When the primary oocytes are activated, they go through meiosis I (producing
secondary oocytes)
■ These secondary oocytes are released during ovulation
○ Meiosis II only occurs when sperm fertilizes the secondary oocyte
■ During meiosis, the egg keeps most of the cytoplasm (creating polar
bodies that disintegrate)
● This means that only one egg cell forms in each cycle
● Embryonic Development
○ During fertilization, a haploid sperm fuses to a haploid egg
○ This zygote then undergoes three stages of development…
■ Cleavage = divisions of the zygote through mitosis
● Happens so fast that cells are unable to grow
○ The end of cleavage = blastula (fluid-filled ball of cells)
production
■ Individual cells in the blastula = blastomeres
■ Fluid filled center of the blastula = blastocoel
■ Gastrulation = continuation of cleavage
● The blastula is rearranged into a gastrula
○ The gastrula has a three layered embryo (with an
ectoderm, endoderm and mesoderm)
● Eventually…
○ The ectoderm = the skin and the nervous system
○ The endoderm = the viscera (lungs, liver, digestive organs)
○ The mesoderm = muscles, bones and blood
■ Primitive animals have a mesoglea
■ Organogenesis = the process of cell differentiation (produce the end
products of the three germ layers)
● Once this occurs, the embryo starts increasing in size (eventually
becoming a fetus)
● Extraembryonic Membranes of the Bird Embryo
○ Bird embryos develop four membranes (outside of the embryo)
■ Chorion = under the shell (allowing gases to diffuse through)
■ Yolk sac = encloses the yoke (food for the embryo)
■ Amnion = (protective fluid that encloses the embryo)
■ Allantois = placenta (where nitrogenous waste accumulates and gases
can go to the embryo)
 Animal Behavior

● Intro
○ Behavior = how organisms respond to different stimuli in its internal or external
environment
■ Can be learned or innate
● Study of behavior = ethology
● Fixed Action Pattern
○ Fixed action patterns are innate behavior (have to be continued until completion)
■ FAPs are initiated by sign stimuli (external)
● Can be released between members of the same species
(releasers)
● Learning
○ Learning is when organisms respond differently as a result of experience
■ Ability to learn is often paired with the complexity of the brain
● Short life span -- no time to learn (rely on fixed action patterns)
● Long life span -- behavior can be dependent on learning from prior
experience
● Habituation
○ Habituation is a simple form of learning (animals start to ignore persistent stimuli)
● Associative Learning
○ When organisms link persistent stimuli with other experiences
● Classical Conditioning
○ Associative learning where organisms can be trained to react to different stimuli
● Operant Conditioning
○ Trial and error learning
■ Animals associate certain behaviors with success or failure
● Learns to do what leads to a reward
● Imprinting
○ Learning that happens during critical stages of early life (irreversible in the future)
■ I.e. Mother-offspring bonding tends to revolve around parental care
● In many cases without bonding, the offspring will die (because the
mother won’t care for it)
● Social Behavior
■ Social behavior = interactions between two or more animals (generally in
the same species)
○ Cooperation
■ Cooperation involves allowing individuals to work together in order to
carry out a behavior
● I.e. Hunting in a pack
○ Agonistic Behavior
■ Agonistic behavior = aggressive behavior
 ● Threats/fighting to settle disputes between different individuals
○ Dominance Hierarchies
■ Behavior that dictates the hierarchy among a group of individuals
● Alpha animal controls the behaviors of all the animals
○ As you go down, each animal controls the behavior of the
animals under them
○ Territoriality
■ Territories are areas that an organism defends (other communities are
excluded)
● Territories are established by agonistic behavior
○ Altruism
■ Altruistic behaviors reduce reproductive fitness while increasing the
fitness of the group
■ I.e. When a worker bee stings something it usually dies, but it increases
the fitness of the queen bee (by protecting it)
● This is spread over generations through kin selection (offspring of
parents who are altruistic have similar genes that allow them to do
the same)