Biology Notes

Biology 101 Notes
By Ethan Start
Original Artwork by: Ethan Start
Based on the Fall 2014 Lectures of Dr. Richard Showman
and Campbell’s Biology, 10th edition
Ethan Start’s Bio Notes, p.2
Chapter 2: Matter
 Matter is made of elements, which can’t be broken down into simpler substances
 Compounds are different elements in a fixed ratio
 Will have different properties than its elements
o Element’s properties depend on the structures of its atoms
 Atoms are made of
 Neutrons- mass, no charge
 Protons – mass, positive charge
 Electrons – no mass, negative charge
o Neutrons and Protons are in the nucleus, electrons form a “cloud” around the
nucleus
o Atomic number = number of protons
o Mass number = number of protons and neutrons
 Isotopes are atoms with the same number of protons but different number of neutrons
o Radioactive isotopes are unstable, nucleus decays spontaneously
 Radioactive tracing – tracks atoms in metabolism
 Energy levels of electrons
o Only electrons are directly involved in chemical reactions
o Energy is the ability to cause change
 Potential energy – energy possessed because of structure or location
o Electrons have potential energy due to distance from nucleus
 Farther from nucleus means more potential energy
 Electrons can only exist at certain energy levels, not in between
 Energy levels is average distance from nucleus
 Electrons are found in different electron shells
 Electrons can move from one shell to another, but only by absorbing or
losing an equivalent amount of energy
 The first shell has eight electrons, the rest have eight
 Valence electrons are only the electrons in the outermost shell
 Atoms with the same number of valence electrons behave similarly
 The formation and function of molecules depend on chemical bonds
o Covalent bond – sharing of a pair of valence electrons between two atoms
 Electronegativity is the attraction of an atom for the electrons in a covalent
bond
 Nonpolar – has the same elements, so the same electronegativity
 Polar – when an atoms is bonded to a more electronegative atom
o Ionic bond
 Ions form when a very electronegative atom strips an electron from
another atom to fill its valence shell
 This results in a cation (positive charge since it lost an electron)
and an anion (negative charge since it gained an electron)
 Since these two ions have opposite charges, they will be attracted to each
other, forming an ionic bond
 Compounds formed this way are called ionic compounds, or salts
o Weak Chemical Bonds
 Ionic bonds break up in water
 Hydrogen bonds
 When an hydrogen atoms is in a covalent bond, it has a partial
positive charge
 It will be attracted to an electronegative molecule
 Van der Waals interactions
 Electrons are not always evenly distributed
 As a result, there are ever-changing positive and negative regions
 These are weak, and only occur when the atoms or molecules are
very close together
o Geckos and adhere to surfaces because of their hairs on
their feet
 Molecular shape and function
o Shape is determined by the position of an atom’s orbitals
o Molecular shape determines how biological molecules recognize and respond to
each other
 Ex: opiates have the same shape as endorphins, allowing them to attach to
endorphin receptors
 Chemical Reactions make and break chemical bonds
 Ex: 2 H2 + O2  2H2O
Reactants product
o All atoms of the product must be accounted for in the reactants (et vice versa)
o All chemical reactions are reversible
 Concentration of reactants affects the rate of a reactions
 Eventually, the forward and reverse reactions stabilizes to a certain rate,
called chemical equilibrium
 The concentrations stabilizes to a particular ratio
Chapter 3: Water Supports Life

 Polar covalent bonds in water molecules result in hydrogen bonding
o In water, the oxygen is more electronegative, therefor the electrons spend more
time near it
 This results in a partial positive charge on the H
 The Hs become attracted to the negatively charged oxygens in nearby
water molecules
 These bonds are weak, and break and reform rapidly
 Four properties of water allow for life
o Cohesion of water molecules
 Hydrogen bonds hold water together – called cohesion
 This allows plants to transport water against gravity
o Water is in thin vertical tubes, when evaporation happens
up top, hydrogen bonds tug on the water lower down an
pull it up
 This creates surface tension, which is how some insects are able to walk
on water
o Moderation of Temperature by Water
 Kinetic energy – energy of motion
 Thermal energy – kinetic energy from random movements of
atoms and molecules
 Temperature – average kinetic energy
 Total thermal energy – dependent on volume
 Heat – thermal energy passing from one substance to another
o Measure in calories
 Water has a high specific heat – takes a lot of heat to change its
temperature
 This is because of its hydrogen bonds: to heat it up, the bonds must
be broken, which takes a good deal of energy to break them
 Large bodies of water can stabilize land temperatures by slowly storing
and releasing heat
 Evaporative cooling
 Water has a high heat of vaporization – heat that must be absorbed
for one gram of it to vaporize
 This stabilizes earth’s temperature – tropic heat is picked up by
evaporation and carried pole ward by winds
 As liquids evaporate, the surface of what remains cools
o This is why lakes have stable temperatures, and why we
sweat to cool off
o Floating Ice on Liquid Water
 Water is less dense as a solid than as a liquid
 When frozen, the hydrogen bonds stabilize far apart

 If ice sank, lakes would freeze solid, and only the upper few inches
would thaw
 Instead, when a deep body of water cools, the tice on top insulates
the water below, allowing fish to live
o Water is a solvent
 Solution – liquid homogenous mixture
 Solvent – dissolving agent (the thing that does the dissolving)
 Solute – the substance being dissolved
 Water is a very versatile solvent because of its polarity
 Ex: salt is made of sodium and chloride ions
o The oxygen in water is attracted to the Na+ and the
hydrogen is attracted to the Cl-
o Water molecules form spheres around the ions, separating
them and making hydrations spheres
 A compound doesn’t have to be ionic to dissolve
o Ex: sugar is not ionic, but is polar, and the water forms
hydrogen bonds with the polar regions
 Water dissolves in sap, blood, and the liquid within cells
 Hydrophilic – has an affinity for water
 Is not necessarily dissolved
o Ex: cotton has giant polar molecules
 Water forms hydrogen bonds with it, but the cotton
doesn’t dissolve
 Hydrophobic – no affinity for water
 These are non-ionic and non-polar
 Many are oils, which make up the cell membrane
 Solute concentrations in aqueous solutions
 Most chemical reactions in organisms involve solutes dissolved in
organisms
 We measure the number of molecules in moles (6.02×1023 is one
mole)
 Molarity is the number of moles divide by Liters of solution
 Acidic and Basic Conditions Affect Living Organisms
o Sometimes, a H atom in a hydrogen bond shifts from one molecule to the other
 When this happens, the H leaves its electron behind, leaving OH- and
becoming a hydrogen ion (H+), which immediately binds to a H2O
molecule, forming H3O+, called hydronium
 The equilibrium for this greatly favors H2O
 Only one in 554 million is disassociated
 The concentration of each ion is 10-7
 H+ and OH- are very reactive; changes in their concentrations drastically

affect a cell’s proteins
o Acids and Bases
 When acids dissolve in H2O, they add more H+
 Ex: HCl  H+ + Cl-
 When bases are added, they reduce hydrogen ion concentration
 Ex: NH3 + H+  NH4+
 Some bases act by breaking down to release OH-
 Ex: NaOH  Na+ + OH-
 The PH scale
o The product of the H+ and OH- concentrations is always 10-14
o When neutral, the concentrations are equal, and both equal 10-7
o pH = -log(H+ concentration)
 Buffers
o The internal pH of most cells is about seven (blood is 7.4)
o A slight change in pH can be very harmful
o Buffers minimize changes in the concentrations of H+ and OH-
 It accepts hydrogen ions when they are in excess and donate H+ when they
are depleted
 Most buffer solutions contain a weak acid and its corresponding base,
which combine reversibly with H+ ions
 Ex: Carbonic acid H2CO3
 H2CO3 ↔ HCO3- + H+
Chapter 4: Carbon as the backbone of life

o Carbon forms molecules complex enough for life
 Organic chemistry is the study of Carbon compounds
o “organic” really just means carbon based
 Carbon atoms can form diverse molecules
o Carbon has four valence electrons
o Carbon usually forms double and single covalent bonds
 When carbon forms four single bonds, is creates a tetrahedron
 However, if it forms a double bond, it will be a trigonal planar
o Carbon most frequently bonds with hydrogen, oxygen, and nitrogen
 CO2 is the source of carbon for all organisms
o Carbon skeletons can vary in four ways
 Length
 Ex: C-C vs C-C-C
 Branching
 Position of double bond
 Ex: C-C=C-C vs C=C-C-C
 Rings
o Molecular diversity arising from variation in carbon skeletons
 Hydrocarbons consist of only hydrogen and carbon
o Main ingredient in petroleum
 Not prevalent in living organisms, but cells do have molecules with
regions of just hydrogen and carbon
o Fats have long hydrocarbon tails
o Petroleum and fats are hydrophobic because the majority of
their bonds are nonpolar C-H bonds
o These bonds undergo reactions that release lots of energy
 Isomers are compounds with the same number of atoms and elements, but
with different structures and properties
 Structural isomers
o Differ in the covalent arrangement of atoms
 Cis-trans isomers
o Differ in arrangement around a double bond
o Single bonds can rotate, double bonds cannot
o Trans means same side, cis means opposite
 Enantiomers
o Mirror each other
o Have an asymmetric carbon
o Methamphetamine, albuterol, and ibuprofen all have less
effective enantiomers
 A few chemical groups are key to molecular function

o The properties of an organic molecule depend not only on the carbon skeleton, but
also the chemical groups attached to it
 Some molecules have chemical groups that are important because they affect
shape, indirectly affecting the body
 Other chemical groups, called functional groups, are directly involved in
chemical reactions, because of properties like shape and charge
 Important chemical groups
 Hydroxyl - OH
 Carbonyl – CO
Chemically Reactive
 Carboxyl – COOH
Hydrophobic
 Amino – NH2
 Phosphate – OPO32-
 Sulfhydryl – SH
 Methyl – CH3
 ATP – Adenosine Triphosphate

o Source of energy for cellular processes
o When ATP reacts with water, it releases energy
 In the reaction with water, a phosphate splits off
 This leaves an inorganic phosphate ion and ADP
 This reaction gives off 7.3 kcal of energy
Chapter 5: The Structure and Function of Large Biological molecules

 Four important large molecules
 Carbohydrates, Proteins, and Nucleic Acids are macromolecules, Lipids
are not
 Macromolecules are polymers, made from monomers
o Monomer – repeating unit that makes up polymers
o Polymer- long molecule made up of many similar or
identical building blocks linked by covalent bonds
 Synthesis and Breakdown of Monomers
o Enzymes facilitate the construction and breakdown of
polymers
o Dehydration reactions are used in assembly
 Monomers are connected through a reaction in
which two molecules are bonded covalently
together with the loss of a water molecule
 On monomer provides a hydroxyl group, the other
provides a hydrogen
o Hydrolysis is the disassembly of polymers
 A water molecule is introduced, and the bond
between the monomers is broken, one takes the H
and the other takes the OH
o Carbohydrates are fuel and building material
 Sugars can be monosaccharides or disaccharides
 Monosaccharides are a multiple of CH2O
o Have a carbonyl group and multiple hydroxyls
o Aldose sugars have a carbonyl on the end
o Ketone sugars have a carbonyl within the skeleton
o Sugars can have different rotations around an asymmetric
carbon
 They forms rings
o Monosaccharides are major nutrients for cells
 Used in cellular respiration as fuel
o Their carbon skeletons are raw material for the synthesis of
other small organic molecules, like amino acids or fatty
acids
o Other monosaccharides are used for the synthesis of
disaccharides and polysaccharides
 Disaccharides are two monosaccharides joined by a glycosidic
linkage
o Glycosidic linkage is a covalent bond because of a
dehydration reaction
o The most common type of disaccharide is sucrose (Table

Sugar), which is composed of a glucose and a fructose
 Polysaccharides are hundreds to thousands of monosaccharides
 Their structure and function are determined by its
sugar monomers and the positions of the glyocsidic
linkages
o Storage polysaccharides store sugar for later use
 Starch – made only by plants, stores glucose, which
is withdrawn by hydrolysis
 All in the alpha configuration
 Helical
 Two forms:
o Amylose: all 1-4 linkages,
unbranched
o Amylopectin: has 1-6 linkages, and
branches
 Glycogen – made by animals, stores glucose in the
liver and muscles, also withdrawn by hydrolysis
 Stores are used up quickly in about one day
o Structural polysaccharides – used to build strong materials
 Cellulose – strong material in plant cells, is the most
abundant material on Earth
 Has only beta linkages; each is upside down
relative to its neighbor
 Straight, never branches
 Hydrogen bonds to parallel molecules
 Holds together in units called microfibrils
 Key ingredient in paper and cotton
 Enzymes that digest starch can’t digest
cellulose because of the beta linkages
o However, it does stimulate the
intestines to secrete mucous
 Chitin is found in exoskeletons
 All beta linkages
 Composed of a glucose and an acetyl group;
named N-acetyl glucosamine
o Lipids are a diverse group of hydrophobic molecules
 Not big enough to be considered macromolecules or polymers
 Mostly consist of hydrocarbons
 Fats – made of a glycerol and fatty acids
 Typical formula: C1H2O<1
 Glycerol – an alcohol – has a hydroxyl group on each of its three

carbons
 Fatty acid – long carbon skeleton (16 or 18 C)
o A carbon on the glycerol end is part of a carboxyl group,
which makes the structure an acid
o C-H bonds are relatively nonpolar
 Water molecules don’t hydrogen bond to the fatty
acid tails, instead the water molecules just hydrogen
bond to each other
 The three fatty acids attach to glycerol with an ester linkage
o Ester linkage – dehydration reaction between a hydroxyl
group and a carboxyl group
o This creates a triglycerol
o Fatty acids in a fat can have the same or different structures
 Saturated fats have no double bonds between the carbons in the
fatty acids, since they are saturated with hydrogen
o Most animal fats are saturated
o Solid at room temperature (like lard and butter)
o Hydrogenation is synthetic process that makes unsaturated
fats saturated
 Partial hydrogenation creates trans fats, which are
bad since they can cause atherosclerosis
 Unsaturated fats have cis double bonds
o The cis double bonds cause a kink, keeping the molecules
from packing together
o Liquid at room temperature
o Come from plants and fish, called oils
 Purpose
o Energy storage for animals
 Store twice the amount of energy that starch does
 Plants are immobile; they don’t benefit from
more compact storage
 Animals use lipids because the compactness
increases their mobility
o Insulation for whales, pregnant women, etc.
o Play role in formation of compartments
 All biological processes must take place in a
specific environment, or a compartment.
 Lipids in general preserve the integrity of the
compartment by preventing water-dissolved
particles from entering
 Phospholipids
 Two fatty acids and a phosphate group attached to a glycerol

 Phosphate group has a negative charge
 The fatty acids have no charge
 This results in a hydrophilic head with two hydrophobic tails
 Can ( and sometimes does on its own ) be arranged to form
compartments – this is its lowest energy state
 Phospholipid bilayer
o Stuff dissolved in water is kept out because the
hydrophobic (neutral) tail reject the polar water
 Carotenoids – made only in plants, is an orange and yellow pigment
o Seen in fall when chloroplasts die
 Made out of isoprenes
 The central isoprene unit is turned into vitamin A in animals
o Vitamin A is used in vision
 Doesn’t dissolve in water, but is assimilated into cell membrane
 Steroids
 Four fused rings
 Distinguished by the chemical group attached to the rings
 Used for cellular communication, but doesn’t affect the structural
composition of the cell
o They do provide information that changes the function of a
cell
 Since they are neutral molecules, they can pass through the
phospholipid bilayer with no difficulty
o Proteins include a diversity of structures, resulting in a wide variety of functions
 Account for more than fifty percent of the dry mass of cells
 All enzymes are proteins
 Serve as catalysts- chemical agents that selectively speed up
reactions without being consumed themselves
 All are constructed from around twenty amino acids in unbranching
polymers
 Bond with other amino acids in a peptide bond, making proteins
into polypeptides
 Have 100-300 subunits
 Amino acids have the same structure, except for a varying R-group
 The R-group determines what kind of amino acid it is
 The amino acid is made out of C, H O, N, and sometimes Sulfur
 Sulfur is only used in proteins
 Polypeptides – amino acid polymers
 Formed by a carboxyl group interacting with an amine group in a
dehydration reaction, creating a peptide bond
 Repeating sequence of amino acids= polypeptide backbone

 Side chains (R groups) extend from this
 Has one free amine end (N-terminus) and a free carboxyl end (C-
terminus)
 Structure of a polypeptide determines how it functions
o Ex: morphine looks like endorphins
 Levels of organization
 Primary Structure – sequence of amino acids
o The order that amino acids appear in a linear chain
 Secondary Structure – coiling or bending
o Result of hydrogen bonds among polypeptide backbone (no
the side chains)
o Forms alpha helixes – a coil because of hydrogen bonds
between every fourth amino acid
o Forms beta pleated sheets – two or more segments of
polypeptide chain being parallel
 Creates a core of globular proteins, which are very
strong (ex: silk)
 Tertiary Structure – overall shape of polypeptide
o Results from interactions between side chains
 Hydrophobic interactions – misnomer
 amino acids with nonpolar side chains are
forced together by their repulsion to AAs
with polar side chains
 Disulfide bridges – permanent and hard to destroy
 Covalent bonds between two sulfurs
 Stabilize the shape of the overall molecule
 Ionic bonds
 Electrostatic attractions between charged
side chains
 Quaternary Structure – association of multiple polypeptides
o Ex: hemoglobin – two heme groups plus two alpha chains a
two beta chains
 Oxygen binds to the heme group, which contains
iron
 Denaturation
 Except for disulfide linkages, tertiary structure comes from weak
bonds
 If in a bad environment, they can be denatured – unraveled
 And be caused by excess heat or being put in a highly acid or basic
substance
 Most cannot be renatured into a useful shape
 Proteins are formed in specifically designed and controlled

environments
o Chaperonins are protein molecules that help the proper
folding of the proteins
o The protein’s environment during initial folding is
manipulated such that a protein’s lowest energy state is the
proper shape
o If denatured, the lowest energy state will result in a
nonfunctional shape
 Disulfide bonds are less affected by heat: they are
more likely to renature properly
 Hormones can be proteins
 Since most proteins are polar, they cannot enter through the
phospholipid bilayer
 Instead they communicate indirectly through receptors
 Modifications to amino acids
 Other molecules can be attached to amino acids
o Sugars – makes glycoproteins
o Metals- makes metal proteins
 Ex: hemoglobin- has iron to hold oxygen
o Lipids – makes lipoproteins
o Nucleic acids – makes nucleoproteins
o Nucleic acids store, transmit , and help express hereditary information
 An amino acid sequence is recorded by a gene (3 base pair: 1 AA)
 Genes are made of DNA, a type of nucleic acidic
 Nucleic acids are polymers made of long chains of polymers called
nucleotides
 The roles of amino acids
o Two types- DNA and RNA- enable living animals to
reproduce their complex components from one generation
to the next
 DNA
o Controls RNA synthesis
 DNA’s genes synthesize mRNA
 mRNA goes to a proteins production factory to
direct production of a polypeptide
o Genetic material inherited from parents
 When a cell divides to reproduce, the DNA is
copied
o Contains information that controls all of a cell’s activities
 However, the actuals tool that do stuff are proteins
 The components of nucleic acids
 Polynucleotides made of nucleotides

o A nucleoside is a nucleotide without a phosphate group
 Nucleotides are phosphates plus a sugar and a nitrogenous base
o Sugar – two types
 Deoxyribose–has no oxygen on the second carbon–
DNA
 Ribose – has oxygen on the second carbon – RNA
o Nitrogenous base
 Pyrimidine – six member ring of carbon and
nitrogen
 Cytosine
 Thymine (only in DNA)
 Uracil (only in RNA)
 Purine – six ring fused to a five ring
 Adenine
 Guanine
 These can have three phosphates, and serve
as an immediate energy source
 Nucleotides polymers – nucleotides linked together
o Linked by phosphodiester linkage
 Phosphate group linking two sugars
 The 5’ end connects to the 3’ end – you can only
attach nucleotides to the 3’ end
o If the nucleotide had three phosphates (like ATP or GTP),
two would break off to release energy for the
phosphodiester linkage to form
o A gene’s meaning is coded in the sequences of bases
 The structure of DNA and RNA molecules
 DNA has two polynucleotide strands, each thousands to millions of
base pairs long
o Form a double helix
o Strands are antiparallel
o Held together by Hydrogen bonding between the base pairs
 A bonds to T, forming two hydrogen bonds
 G binds to C, forming three hydrogen bonds
o Since they are complementary, a cell can make two copies
of the DNA at once
 RNA is single stranded
o Some complementary base pairing can occur between two
RNAs or even with itself, but overall, it’s a versatile
tangled mess
o A binds to U
Chapter 6: Cells, the Fundamental Unit of Life

 Cell Theory
o All living matter is made up of cells
o The chemical reactions of life take place inside the cell
 Both synthetic or energy making
o Cells come from other cells
o Cells contain the genetic or hereditary information of the organism
 Two types of cells:
o Prokaryotic cells – bacteria and Archean
 DNA is not membrane enclosed, but is in a region called the nucleoid
 Generally smaller than eukaryotes
 Only has one plasma membrane, which folds inward to form
compartments
o Eukaryotic Cells – Protists, Fungi, Plants, and Animals
 Have nucleus, which is a double membrane-enclosed organelle, which
contains the DNA
 Have internal membranes – enclosed organelles – in the cytoplasm
 Cytoplasm is the space between the plasma membrane and the
nucleus
 Cytoplasm is filled with organelles suspended in cytosol, a jelly-
like substance
 (Both Eukaryotes and Prokaryotes) have a plasma membrane that
selectively lets oxygen, nutrients, and waste through
 This membrane requires that cells be small; mathematically, the
surface to volume ratio decreases as size increases
 This means that if the cell is too big, there will not be enough
surface area to support its massive volume
 It won’t be able to get enough of the nutrients it needs to survive
 Most membranes are double layers of phospholipids and other
lipids, with proteins embedded in it
 Tour of the Eukaryotic cell
o The eukaryotic cell’s genetic information is stored in the Nucleus and carried out
by ribosomes
 Nucleus – contains most of the genetic material of the cell
 Enclosed by a nuclear envelope
o Double membrane
o Perforated with pores – let proteins and RNA through
o Lined by nuclear lamina – proteins that maintain its shape
 Within the nucleus, DNA is organized into chromosomes
o Each chromosome has one long DNA molecule associated
with many proteins
o Chromatin is the complex of DNA and the proteins making

up a chromosome
 Inside the nucleus is the nucleolus (can be multiple)
o Ribosomal RNA is synthesized here based on instructions
from DNA
o Proteins are brought in and added to rRNA to make
ribosome
 Directs protein synthesis
o Makes mRNA, which is transcribed from the DNA
o mRNA goes through nuclear pores to the cytoplasm
o Ribosomes translate the mRNA’s message into the
structure of a polypeptide
 Ribosomes are made of rRNA and proteins
 Carry out proteins synthesis in two
locations:
o Free ribosomes – floating in the
cytoplasm
 Proteins made stay in the cell
for its own use
o Bound ribosomes – attached to ER or
nuclear envelope
 Proteins are released from the
cell
o The Endomembrane System regulates protein traffic and performs metabolic
functions in the cell
 Endoplasmic Reticulum – accounts for half of the total membrane in cells
 Network of membranous tubules and sacs
o The sacs, called cisternae, are used to store stuff
 Membrane is continuous with the nuclear envelope
o Since it is surrounded by a plasma membrane, it is
technically outside the cell
 The Lumen is the cavity inside
 Two types of ER
o Smooth ER – outer surface lacks ribosomes
 Makes lipids and steroids (hormones)
 In the liver, the SER is used for
 Lipid and complex carbohydrate metabolism
 Detoxification
o When a drug is injected, the amount
of SER and detoxification proteins
rapidly increases (p450 is one of
these proteins)
 Stores Calcium ions

 Calcium ions are used as messengers
o Receptors fire when they receive Ca+
+
o Ca++ must be withdrawn once

deployed
 Calcium is never free in the cell
 Sarcoplasmic Reticulum is the SER in muscle cells
o Rough ER – has ribosomes on the outside
 Ribosomes on it make many important proteins
secreted outside the cell
 Makes proteins
 mRNA attaches to a ribosome on the surface
 a signal sequence on the N-terminus of the
Sugar
mRNA is translated onto the protein
(methionine is the first amino acid)
 As the Polypeptide chain is produced, a hole
Lipid opens in the ER. A protein complex on the
ER membrane mechanically threads the
polypeptide chain through
 An enzyme cuts of the signal sequence from
the protein
Growing polypeptide  The proteins has lots of ASP R-groups,
chain  A lipid, which has a row of phosphates, in
the RER anchors the protein
Motor for o Carbohydrates on the phosphate are
bringing attached to the ASPs
in protein o Different sugars are specially placed
mRNA on the proteins; requires energy from
Enzyme for
phosphates or ATP
cutting off signal
o Proteins can be identified by these
sequence
sugars
 The RER forms a bulge, which the protein
goes into
Ribosome  The bulge breaks off as a transport vesicle
and is directed (because of its “tag”) to the
Golgi
 Produces membranes
 Makes proteins and phospholipids, which
RER grow in the rough ER’s membrane
membrane Signal  Portions of the RER’s membrane are taken
Sequence to other parts of the system
 Golgi Apparatus – shipping and receiving center

 Products of the ER are sent here in vesicles
 Vesicles attach and fuse to the cis side (same side as the ER and
the nucleus)
 The products move from the cis side to the trans side, high
turnover rate
o Products are usually modified in transit
 Products are sorted and targeted for specific areas of the cell
o Some go to lysosomes to be recycled
o Some are released from the cell
 Products are dispatched by budding vesicles on the trans side
 Golgi also makes polysaccharides
 Lysosomes – sac of hydrolytic enzymes
 Digest (hydrolyze) macromolecules
 Made by the rough ER
 Phagocytosis – lysosome fuses with a food vacuole and digests it
 Recycles the cells own organic material (autophagy)
 Vacuoles – large vesicles (made by ER and Golgi)
 Have selectively permeable membranes
 Used for storing all sorts of stuff
o Mitochondria and Chloroplasts change energy from one form to another
 Mitochondria – chemical energy conversion through the Krebs Cycle
 Found in almost all eukaryotic cells
 Site of cellular respiration (Krebs cycle)
o Uses oxygen to make ATP by taking energy from sugars,
fats and other stuff
 Chloroplasts – perform photosynthesis
o Contain green pigment called chlorophyll
o Absorb sunlight and use it to turn carbon dioxide and water
into organic molecules, like sugars (not ATP)
 Peroxisomes
 Make hydrogen peroxide
 Used to break down fatty acids and alcohols
o The cytoskeleton is a network of fibers that organizes structures and activities in
the cell
 Gives mechanical support and maintains the cell’s shape
 Anchorage for many organelles
 Can be dismantled and relocated to change shape
 Cells move by the cytoskeleton interacting with motor proteins
 Cytoskeleton is made of
 Microfilaments – smallest, about 3-6nm
o Twisted double chain of actin proteins

o Bears tension (pulling)
o Used in
 Microvilli – increase surface area of small intestine
 Muscle- interacting with myosin to contract the
muscle
o Can be used for a crawling movement
o In cell division, it forms a ring around the cell, which then
subtracts in length, squeezing the cell in half
o Can add and subtract subunits
 Intermediate Filaments – 8-12 nm
o Made of different proteins and sequences
o Very strong, can stretch and handles stress – key in
desmosomes
o Permanent, stable, and insoluble
o Types
 Keratin – in skin, nails, and hair
 Vimentin – in muscle
 Neurofilaments – in nerves
 Fibronectin – covers the outside of regions of
developing animals to prevent attachment of
unwanted things
 Used in development to guide stuff where to
go
 Microtubules – largest, 20-25nm in diameter
o Made from alpha and beta tubulin
 Interlocks and coiled with hole in center
o In cell division, pulls chromosomes apart (by shortening)
o Movement of flagella and cilia
 Bend and whip to create force
 Requires lots of strength and energy to move
o Compression resistance
o Can add or subtract
o Primary highway for stuff in the cell
o Cellular Junctions
 Cells adhere and communicate with each other
 Desmosomes – stretching and strength
 Filaments anchor between cells
 Dominant filaments connect between two cells; these dominant
filaments have a linkage to long filaments inside the cell
Long filament
 Septa are the spaces between filaments (think rungs on a ladder)
 Any force applied will be distributed through all cells in the

desmosomal network, preventing tearing
 Tight Junctions – create physiological compartments
 The plasma membrane of two cells fuse (by binding together with
specific proteins) to create an impermeable layer
 Watertight and prevents leakage
o Uses
 Bladder – toxic nitrogen in the urea cannot be
released into the body because of tight junctions in
the bladder
 Eye – contains ascorbic acid which can’t leak
 Blood Brain Barrier
 Protects brain and spinal cord from toxins,
viruses, and bacteria in your blood
o Meningitis- inflammation of the
brain and spine
 Barrier of tight junctions gives the cells
which it is composed of the ability to choose
what it lets in
 Gap Junctions – communicate between the cytoplasm of two cells
 Tiny tube between two cells
o Allows for direct transmission instead of diffusion
o Can only send small things, like Ca++
 Can’t send large steroids, etc.
 Allows a decision be cell A to be executed in unison by cell B
o Seen in shell development – all start at once
o Seen in electric eels – open all gap junctions at once to
release a massive charge, shocking their prey
Chapter 7: Membranes
 Membranes are not an inanimate wall
 Membranes constantly adjust
 Four functions
o Regulating passage of material
 Compartmentalization  life
o Receives Information
 Lipids (steroids) can easily pass through
 Proteins bind to receptors
o Structural
 Supports parts
 Can deform its shape to stay intact
o Specialized functions
 Ex: sodium inrush to change electrical current
 Fluid Mosaic Model
o Proteins “float” like solids on a “fluid” lipid layer
o Only neutral molecules can exist in the central neutral region of the phospholipid
bilayer
o Types of Proteins
 Integral proteins – anchored in the plasma membrane, amphipathic
 Will left behind if membrane is dissolved
 Peripheral proteins – on the outside, not anchored
 Interact with charged outer surface of the PM
 Charged and soluble in water
 Will break off if enough salts are added
 Passage Through the Membrane
o Selectively permeable – lets what it wants when it wants in or out
o A cell regulates its composition through its membrane
 Two ways to get stuff in
o Physical Process – doesn’t expend ATP
 Energy comes from the random movement of molecules
 Quantified by temperature
 Diffusion – movement of particles from high concentration to low
concentration using the kinetic energy of the particle itself
 Factors affecting diffusion over membrane
o Size and shape of entering molecules
 Compactness means faster diffusion
o Charge of molecule
 Neutral molecules can slip through
o Speed (temperature) of the molecule
 Faster means higher likelihood of entry
o States of matter
 Solids take forever to get through
 Size of cell is limited by diffusion
o Volume increase faster than surface area
o If cell is too big, it won’t have enough surface are to let
everything in it wants
o Large organisms must actively transport stuff
 Ex: oxygen in humans goes from the lung, to
hemoglobin in the blood, to the target
 Ex: sea anemones do better in rough water because
more water moving through
 Ex: plants use roots with high surface area to grab
stuff and use their vascular system to bring it up
 Artificial Dialysis – remove nitrogenous waste (urea) from blood
o Use a selective membrane - lets urea and anything smaller
across
o Sodium and other small stuff must be in equal
concentrations in dialysis fluid to prevent the necessary
minerals from diffusing out of you blood
o Uses reverse flow to make it more efficient
 Facilitated Diffusion – uses only kinetic energy
o Form of mediated transport – protein assisted
o Charged molecules can’t get across; some other molecule
must help
 Osmosis – diffusion of water from areas of high solvent
concentration to areas of low solute concentration
o Isotonic solution – same concentration in cell and solution
 No net change, cell is fine
o Hypertonic solution – more solute outside the cell
 Water diffuses out, cell shrivels up and dies
o Hypotonic solution – more solute inside
 Water floods in, cell pops (lyses)
 However, plants have cell walls, which are strong
and exert backpressure on the water
 This backpressure causes a plant to stand firm,
called turgor pressure
o Physiological Process – uses ATP
 Works against the gradient (pushes stuff from high to low concentration)
 Form of mediated transport – have to use proteins
 Highly specific for what’s being transported
o Works independently of everything else
 Can be blocked (poisons and pesticides block specific transport

systems)
 Can be saturated to the point at which the rate of transfer cannot be
increased
 Common transport molecules
 Sodium/Potassium pump (in brain, consumes 70% of ATP)
o All cells want an electrical charge across the membrane –
called membrane potential
o Made by pumping three sodium ion out for every two
potassium ions in
 Creates a gradient, with 10 Sodium outside : 1
sodium in and 35 potassium in for every one outside
 Uses phosphorylated intermediate – by attaching a
phosphate group to the transport protein, it changes
shape to push the potassium in and sodium out
o Glucose Pump
 Pumps glucose in
o Amino Acid Pump
 Has separate pump for each amino acid
Chapter 8: Metabolism
 An organism’s metabolism transforms matter and energy, subject to the laws of
thermodynamics
o The totality of an organisms chemical reactions is its metabolism
o Metabolic pathways are a series of reactions to achieve a certain product
 Catabolic pathways – break stuff down to release energy
 Ex: cellular respiration
 Anabolic pathways – build complicated molecules
o Forms of energy (energy is the ability to cause change)
 Kinetic energy – relative movements of objects
 Thermal energy – random movements of molecules
 Heat – thermal energy in transfer
 Potential energy – energy by virtue of location or structure
o The Laws of Thermodynamics
 First Law: Energy can be transferred and transformed, but cannot be
created or destroyed
 Second Law: Every energy transfer increases he entropy of the universe
 Entropy is disorder or randomness – heat
 Spontaneous process – one that increases entropy
 Nonspontaneous process – leads to a decrease in entropy
o Requires energy to run, some of which will be lost as heat
o Organisms make complex structures by taking stuff in and
releasing it in a less ordered form
 The Free-Energy change of a reaction tells us whether or not the reaction occurs
spontaneously
o Free energy change = ΔG
o Free energy is the portion of a system’s energy that can perform
 ΔG = ΔH - T× ΔS
o H = enthalpy
o T = temperature
o S = entropy
 If ΔG is negative, the reaction will run
 If ΔG is positive, energy must be added for the reaction to occur
 In order to keep the reaction going one way, a product must be
removed
 ATP powers cellular work by coupling exothermic reactions with endothermic reactions
 Uses an exothermic process to drive an endothermic one
o ATP + H2O  ADP + Pi ΔG = -7.3 kcal/mole
 The reactants have higher energy than the products
o How hydrolysis of ATP performs work
 ATP breaks into ADP and a Pi
 The phosphate is transferred to a molecule in the reaction

 This forms a phosphorylated intermediate
 This intermediate reactant now has more energy than the product,
so it can now run spontaneously
 Enzymes speed up reactions by lowering the activation energy
o Spontaneous process can take a long time
o Enzymes are catalysts, which speed up reactions without being consumed
themselves
o Activation Energy is the energy required to start a reaction
o The transition state is the point where molecules have absorbed enough energy to
break their bonds and change shape
o Enzymes lower the activation energy, not the total ΔG
 The substrates (reactants) bind to a special active site on the enzyme
 The enzyme works only on specific substrates because of their
shape
 The enzyme changes shape, changing the shape of the substrate into the
product, and spits it out
 Cofactors enable the substrate to enter the active site
 Apo enzymes – enzymes that require cofactors
 Metals are one type of cofactor
 Coenzymes – organic non-protein cofactors (ex: vitamins, NADH)
Transition  Things that affect enzymes activity
state o raising temperature increases the rate of the reaction
Activation
 However, when it denatures, the rate basically drops
energy
to zero
ΔG o Low pH means too many protons, messes up enzyme
structure
 Hydrogen bonds get messed up
o Substrate concentration – higher concentration means
higher reaction rate, until the enzyme is saturated
 Inhibitors block the function of certain enzymes
 Irreversible – covalently bond to active site, enzyme won’t work
again
 Reversible – not permanent, will work again when removed
o Competitive inhibitors – enter the active site, delaying and
slowing the enzyme’s function
 Adding more substrate will speed up the reaction
 Competitive inhibition can result from a feedback
loop
 Ex: ABCD
 If D looks like A, it will enter the active site
and competitively inhibit
 However, this will decrease D production,

and as D is consumed, the enzyme will be
less blocked and will run faster
o Noncompetitive inhibitors – binds somewhere else, not in
the active site, called the allosteric site
 Causes a shape change
 This temporarily blocks function until the
inhibitor pops out
 Adding something with a higher binding
constant (a measure of a how long
something will bind) will cause the inhibitor
to bind to the new chemical (ex: EDTA)
instead of the allosteric or active site
 Regulation of Enzyme activity helps control metabolism
o The cell needs to be able to regulate when ,where, and how much enzyme activity
occurs
o Allosteric Regulation of enzymes
 When a protein’s function at one site is regulated by the binding of
a regulatory molecule to a separate site
 Allosteric Activation and Inhibition
 Most allosterically regulated enzymes have two or more subunits,
each with its own polypeptide chain and subunits
 The complex bounces between an active and an inactive shape
 The binding of an activator will stabilize the enzyme in the active
configuration, while an inhibitor will stabilize it in the inactive
shape
o ATP acts as an inhibitor on catabolic enzymes
 When lots of ATP is present, the cells slows down
energy production
o ADP acts as an activator on catabolic enzymes
 When there is little ATP, the cell increases energy
production
 Cooperativity
 He binding of a substrate to a multi-subunit enzyme triggers a
shape change that increases the activity of the other subunits
o One molecule primes the enzyme to act on other substrates
o Ex: hemoglobin – has four subunits, each carrying an
oxygen
 The binding of an oxygen at one site increases the
oxygen affinity of the other sites
 Thus, in the lungs and gills, hemoglobin readily

picks up oxygen, but in oxygen deprived areas, it
drops off the O2
Chapter 9: Cellular Respiration and Fermentation

 Respiration – breaking down organic food molecules for ATP
o Three parts of respiration: Glycolysis, Krebs Cycle, and Oxidative
Phosphorylation
 Catabolic Pathways yield energy by oxidizing organic fuels
o Potential energy in organic compounds comes from the arrangement of electrons
in their bonds
o In aerobic respiration, oxygen and organic fuel are consumed to release carbon
dioxide, water, and energy
o C6H12O6 + 6O2  6CO2 + 6H2O ΔG= -686 kcal/mole
o Oxidation of Organic Fuel during Cellular Respiration
 Potential energy is lost when an electron moves from a less
electronegative atom to a more electronegative atom (oxygen is very
electronegative)
 Oxidation – having one’s electrons move farther
 Reduction – electrons moving closer
 C6H12O6 + 6O2  6CO2 + 6H2O
 Organic molecules with lots of hydrogen are great fuels because their
electrons will fall down an energy gradient when transferred to oxygen
 Activation energy prevents from all of your glucose from going off at
once; enzymes are required to make it break down
o Stepwise Energy Harvest via NAD+ and the Electron Transport Chain
 Cellular respiration does not oxidize glucose all at once
 Instead, it is broken down into a series of steps, catalyzed by enzymes
 At key steps, electrons are stripped from the glucose
 These electrons are tacked onto protons, forming hydrogen atoms
 The hydrogen atoms are transferred to an electron carrier called NAD+
(nicotinamide adenine dinucleotide)
 NAD+ traps electrons from glucose
 Dehydrogenases remove two hydrogen atoms (two protons and
two electrons) from the glucose, oxidizing the glucose
 The enzyme takes one proton and two electrons and tacks it onto
its coenzyme, NAD+, forming NADH
 The electrons go down a chain of redox reactions, losing energy,
which is used for ATP synthesis
 At the end, they are reunited with protons and tacked onto oxygen,
making water
o Substrate level phosphorylation – alternative to oxidative phosphorylation
 90% of ATP is from oxidative phosphorylation, but this makes a little
ATP
 Phosphate is taken from a substrate molecule and tacked on to an ADP by
an enzyme. This happens in glycolysis (steps 3, 7 , and 10) and in the
Krebs cycle (step 5)
 The majority of the ATP produced, however, comes from the oxidative
phosphorylation of the electrons in the NADH and FADH
 Three Stages of Cellular Respiration
o Glycolysis – in cytoplasm – breaks up glucose into two pyruvate
 Intermediate Step: pyruvate is turned into Acetyl CoA
o Krebs Cycle – in mitochondria
o Oxidative phosphorylation – electron transport chain – on mitochondrial
membrane
 Glycolysis – oxidizes glucose into two pyruvate
o Occurs in the cytoplasm
 Two ATP are invested into the glucose
 The adenine splits into two products, which can be change between
each other
 Two NAD+s pick up electrons, making 2NADH
 Twice, two ATP are made from ADP and a Phosphate on the
product
 Pyruvate is formed, no oxygen is used or carbon dioxide released
 Net result: +2ATP, +2NADH, +2 pyruvate, +2H2O

Glucose A phosphate is tacked of from an ATP
by the enzyme hexokinase
Glucose 6-phosphate
It is rearranged into a five part ring
Fructose 6-phosphate
Another phosphate is added
Fructose 1,6-biphosphate
The Fructose 1,6 biphosphate is split half, forming

Glyceraldehyde G3P and DHAP, which change between each other.
3-phosphate By using up all of the G3P, eventually all of the DHAP
G3P becomes G3P and is used. This split uses a lot of
energy, which allows a free phosphate to tack on and
NAD to take a hydrogen and become NADH
1,3 biphosphoglycerate
ADP picks up a phosphate, becoming ATP
3 phosphoglycerate
2 phosphoglycerate ADP picks up a phosphate, becoming ATP
An H2O is pulled out
Phosphoenol-
pyruvate (PEP)
Pyruvate
 Intermediate Step – pyruvate oxidation

o As the pyruvate enters the mitochondria, it goes through a transport protein, loses a
CO2, and an electron to NADH, and Coenzyme A attaches to it, forming Acetyl CoA
 Krebs cycle – oxidizes fuel from pyruvate – occurs in mitochondria

o Acetyl Coenzyme A (two carbon) attaches to oxaloacetate, and loses the CoA,
forming citrate
o Citrate goes through the citric acid cycle, losing two carbon dioxide, which break off.
In the process, one GTP, three NADH and an FADH are made
 NADH has the most energy; it can pump six protons, which is worth about 3
ATPs
 FADH can pump four protons, making about two ATPs
Summary thus Far ATP NADH FADH2

Glycolysis +2 +2
Intermediate Step +2
Krebs Cycle +2 +6 +2
Total +4 ATP +10 NADH +2 FADH2
 Oxidative Phosphorylation, or the Electron Transport System
o High energy electrons from NADH are sent through the ETS, going through multi-
protein complexes as they lose energy, pushing protons into the intermembrane space
to build up a gradient such that protons will want to diffuse back into the
mitochondrial matrix
 These complexes are embedded in the inner membrane, which is folded to
increase surface area
 The electron goes downhill towards more and more electronegative proteins,
eventually attaching to oxygen, and forming water.
 The NADH drops off the electron at a molecule called a flavoprotein, which
has a prosthetic group (non-protein cofactor) called Flavin mononucleotide
 The electron then is passed on to an Iron-sulfide protein, then to a
compound called ubiquinone (Q)
 The rest of the chain is composed mostly of cytochromes, which have
an iron-containing heme group, which can grab or release electrons
 In complexes I,III, and IV, two proteins are pushed across the
membrane into the intramembranous space
 FADH2’s electrons have less energy; therefore, they enter at complex II,
where no protons are released, then continues down the chain
 While NADH pushes 6 protons, FADH pushes 4
2H+
2H+
2H+
 ATP Synthesis
o Protons are allowed to diffuse back through the membrane, but as they do, they spin a
“turbine,” called the rotor, causing it to spin in such a way that catalyzes ATP from
ADP and a free phosphate
 The proton gradient supplies the energy
o Theoretically, two protons yields one ATP
 Why we don’t get 38
 In theory, one glucose should yield thirty eight ATP
 In reality, we get 30-32 ATP, and about 26-28 in the brain
 Glucose is worth ~686 kcal, the 32 ATP is worth ~230kcal
 About 34% efficient
 We don’t just burn a glucose all at once (even though it would be more
efficient) because we can’t handle all that energy at once
o Entropy
o Energy used tom move NADH, pyruvate, and ATP across mitochondrial membrane
 NADH is formed in the mitochondria in two ways
 1) The energy from NADH is used to form malate, which can cross
o On the other side, the malate is used to form or itself forms into
NADH
 Glycerophosphate is used as the intermediate, which crosses and forms
FADH2, which is less efficient
o It can take more than two protons to make an ATP
Chapter 10: Photosynthesis

 Photosynthesis uses light energy to convert CO2 + H2O into sugars
o Chloroplasts are the site of photosynthesis
 Chloroplasts have two membranes, and are filled with stacks of thylakoids
surrounded in fluid stoma.
 Chlorophyll is in the thylakoid membranes
 Photosynthesis Overview
Light Energy + 6 CO2 + 6 H20 -> C6H12O6 + 6 O2
o 2 Stages of Photosynthesis
 Light Reactions
 Light energy is used to transfer electrons to NADP+
 Also generates ATP through chemiosmosis in a process called
photophosphorylation
 Calvin Cycle- light independent
 Turn CO2 into organic compounds powered by NADPH and ATP
 Light Reactions
 Convert solar energy into NADPH and ATP
o Light can be reflected, transmitted, or absorbed
 Pigments absorb light; the color you see is what is not absorbed
o Chloroplasts have three types of pigments
 Chlorophyll a – main pigment – deep blue and far red
 Chlorophyll b – blue, yellow, and medium red
 Carotenoids
 Carotenes- yellow and orange
 Xanthophyll- red
o When a photon hits, an electron is elevated to a higher orbital
 Certain compounds only absorb photons of certain wavelengths
o Chlorophyll is set up in photosystems on the thylakoid membrane
 Has a reaction-center complex surrounded by light harvesting complexes
(chlorophyll a or b)
 Light harvesting complexes act as an antenna for the reaction-center
complex.
 When a photon hits, energy is transferred randomly bouncing around from
pigment to pigment until it is passed into the reaction-center complex.
 There, a chlorophyll a gets excited, and transfers and electron to a primary
electron acceptor
o Two types of photosystems
 Photosystem I – absorbs 700nm light (association with different proteins
causes different absorbing properties)
 Photosystem II – loads Photosystem I
o Linear Electron Flow
1) Photon hits PSII, energy is relayed to reaction center complex, electron is

excited and picked up by primary electron acceptor
2) H2O is split into 2 H+ , 2 e- , and oxygen
 H+ are released into thylakoid space (space inside thylakoid)
 O- bonds with another to make O2
3) Electron goes down an electron transport chain from PS II to PS I,
pumping protons into the thylakoid space; proton gradient is later used for
chemiosmosis (making ATP)
4) Meanwhile, light has gone to PS I, and an electron has gone to a primary
acceptor
5) Electron goes down ETS to make NADPH
o Cyclic Electron Flow- uses just PS I to make ATP
 Instead of going to make NAPDH, PS I’s electron is used to make ATP by
pumping protons, and is sent back to PS I
 Calvin Cycle
o Phase One – CO2 is attached to a five-carbon sugar called RUBP
 This forms an unstable six-carbon that splits immediately into two
molecules of 3-phosphogylcerate
o Phase Two
 Each 3-phosphoglycerate receives a phosphate from ATP and an electron
from NAPDH, popping off that phosphate and forming glyceraldehyde 3-
phosphate (G3P)
 There were 15 carbons in the 3 RUBPs at the beginning, adding 3 CO2
now means there are 18 carbons in the 6 G3P. For the cycle to continue,
only one G3P can be used, the rest must return to being RUBP
o Phase Three
 Three ATP are used to turn 5 G3P into 3 RUBP
o Summary
 For one G3P, 6 NADPH and 9 ATP are used
 The G3P then goes down several different pathways, to make glucose,
sucrose, or other carbohydrates
o Different approaches to the Calvin Cycle:
 C3 plants- most plants
 Run the Calvin Cycle as described above
 Process CO2 slower than C4 plants
 C4 plants- sugarcane corn, grasses
 Twice the yield of C3 plants
 Has two types of cells: mesophyll cells and bundle sheath cells
 Mesophylls pump CO2 into bundle sheath cell to increase CO2
concentration in the bundle sheath cells, where the Calvin cycle
occurs, thus increasing the efficiency
 CAM plants- cacti
 Close stomata during, open to let CO2 in at night

o At night, the humidity increases, decreasing the amount of
water lost when the stomata open
 Store CO2 , use in the Calvin Cycle during the day
Chapter 11: Signal Transduction

o Paracrine signaling- messages to cells close by
o Hormonal signaling- messages to cells far away
 Three Steps – found by Sutherland
o Reception
o Transduction- passive change across membrane
o Response
 Most signal transduction is a signal molecule -a ligand- binding to a receptor on the
membrane
o Then the receptor changes shape and stuff happens
 Receptors are integral proteins
 Reception
o Three common kinds of receptors
 G-proteins – bind GTP, not ATP
 Three parts- a G Protein-coupled receptor (GPCR), a G
protein, and an enzyme
 When inactive, the G protein has GDP attached
 When the ligand attaches to the GPCR, the GPCR binds the G
protein, kicking the GDP off and replacing it with a GTP
o This actives the G protein
 The G protein then detaches from the GPCR and binds to an
enzyme, altering the enzymes shape and activity.
 Eventually, the G protein turns its GTP into GDP (which it
keeps) and a Phosphate, allowing the G protein to be used
again
 Tyrosine Kinase Receptors
 Attaches a Phosphate to a tyrosine inside the cell; relay
proteins recognize the activated tyrosine and come do their
thing
 Ion Channel Receptors
 When the ligand binds to the receptor, it lets ions in (like Ca++
and Na+)
o Side note: some ion channels are controlled by voltage
changes- crucial to the nervous system
 Pathways – Three major types
o Multistep Operation
 Can exponentially amplify
 Most parts of this process are proteins

 Called a protein-kinase phosphorylation cascade
o (recall: kinases add or remove phosphates from
ATP/GTP)
1) Receptor activates
2) Relay turns an active protein kinase (pk1) on
3) Pk1 slaps a phosphate onto pk2, activating it, and allowing
pk2 to likewise activate pk3
4) Eventually activates a proteins that results in a cellular
response
o Dephosphorylation at one of these points will stop the
process
o Second Messenger Pathways
 Small, water-soluble non-proteins molecules diffuse through the cell
 Initiated by G-proteins or protein kinase receptors
 Cyclic AMP is the most common example
1) An arriving ligand triggers a G-protein
2) Adenylyl Cyclase is activated by the G-proteins
3) Adenylyl Cyclase turns ATP into cAMP
4) cAMP transmits its message to the cytoplasm
5) Phosphodiesterase cleans up by turning cAMP into AMP
o Calcium Pathways
 Ca++ is used as a second messenger
 Can be activated by a G protein or a protein kinase
 Used heavily in fertilization and development
1) Ligand attaches to G protein receptor activating
phospholipase C
2) Phospholipase C turns a membrane lipid called PIP into
DAG and IP3
o DAG is used elsewhere for protein synthesis
3) IP3 binds to and opens a calcium channel to the smooth
endoplasmic reticulum
4) Ca++ flows out of the SER, activating the next proteins in the
pathway
 One molecule can release multiple responses, resulting in an exponentially huge
response
 Different cells can react differently to the same hormone
o This is because these cells have different relay molecules
 Ex: The liver uses epinephrine to for glycogen metabolism, while the
heart uses it for contraction
Chapter 12: Cell Reproduction

 Cell Cycle – has four stages
o G1 – cell checks itself, examining to see if DNA is correct
o S – copies its chromosomes
o G2 – self checks to see if DNA replication worked correctly and is ready to go
into mitosis
o M – Mitosis – four sub stages
 Prophase
 DNA is condensed into chromosomes
 Spindle apparatus forms
 Prometaphase- nuclear envelope dissolves, microtubules attach to
centromeres
 Metaphase
 Tension from kinetochore microtubules lines up the chromosomes
in the middle of the cell
 Anaphase
 Kinetochore microtubules pull the sister chromatids apart and back
to their respective sides
 Telophase
 Chromosome have reached the poles
 Tubulin that had been used for microtubules returns to the
cytoskeleton
 Nucleolus and nuclear envelope reform
 Cytokinesis – splitting of the cytoplasm
 Set up by formation of spindle apparatus
 In plants: (which have cell walls)
o Enzymes are released to loosen cell wall
o Cell doubles in size
o Golgi apparatus makes huge vesicles
o Vesicles line up in center and fuse to form a plasma
membrane, splitting the cell
o New cell is formed between the two cells
 In animals:
o Actin microfilaments form a contractile ring, embedded in
the matrix
o Actin compresses (through subtraction), squeezing the cell
in half until it splits in two
Chapter 13: Meiosis

o Two types of cells
 Somatic cells – all cells except gametes
 Gametes – reproductive cells that transmit genes from one generation to
the next
 Fertilization and Meiosis alternate in sexual life cycles
o In humans, each somatic cell has 46 chromosomes
 Karyotype – ordered display by length of all chromosomes
 Homologous chromosomes – the two chromosomes of a pair, with the
same length, centromere position, and staining pattern
 The 46 chromosomes we have are two sets of 23; a maternal set and a
paternal set
o Gametes contain a single set of chromosomes (haploid – 1n)
 Diploid cells have two sets – 2n
o In fertilization, a haploid sperm and a haploid egg fuse nuclei, resulting in a
diploid zygote
 Mitosis of the zygote then generates all of the somatic cells
 Meiosis must happen, or else the chromosome number would double with
each successive generation
o Meiosis makes each sperm and egg haploid
o Three big types of sexual life cycles
 Animals – gametes are the only haploid cells produced
 Meiosis occurs during the production of gametes, which undergo
no cell division before fertilization
 Plants and some algae – multicellular diploid and haploid stages
 Multicellular diploid stage (sporophyte) makes spore, which divide
mitotically, creating a multicellular haploid stage
 Gametophytes become gametes by mitosis; 2 gametes fuse,
creating a diploid zygote, a new generation of sporophyte
 Most fungi and some protists
 Gametes fuse to become diploid zygote
 But the zygote doesn’t grow; it undergoes meiosis to become
haploid cells, which do divide by mitosis and live as haploid adults
o Meiosis reduces the number of chromosome sets from diploid to haploid
 Meiosis I
 DNA duplicates
 Prophase I – DNA condenses
o End up with four chromatids together in tetrad
o DNA is “exchanged” between maternal and paternal
chromosomes
 Metaphase I
o Both chromosomes from one homologue are connected to

one pole, both from the other are attached to the other pole
 Anaphase I
o Homologues (mom’s vs dad’s) separate, but sister
chromatids stay together
 Telophase I and Cytokinesis
o Each half is haploid with duplicated DBA
o No duplication occurs between Meiosis I and Meiosis II
 Meiosis II
 Prophase II – spindle apparatus forms
 Metaphase II
o Sister chromatids line up
 Because of crossing over in Prophase I, sister
chromatids are not genetically identical
 Anaphase II
o Sister chromatids separate and move to poles
 Telophase II and Cytokinesis
o Nuclei form, cell splits
o End up with four total genetically distinct haploid daughter
cells
o Differences in meiosis between men and women
 Women
 Make all of their eggs while in the womb and store them
 Make only one egg for each meiosis
o In Meiosis I, they create a large cell and a small polar body
o In Meiosis II, the polar body divides into two and the large
cell again divides into a large cell a polar body
o End up with one large cell and three polar bodies, which
die
 Men
 Continuously make sperm throughout their lives
 Make four sperm for each meiosis
 Lots of cytoplasm is lost in the making of each sperm
Chapter 16: Inheritance through DNA

 The Discovery of DNA as the genetic material
o Mendel – 1850’s
 Discovered function of genes (Punnett squares, etc.)
 Rediscovered in 1900’s
 However, people thought genes were proteins
o Griffith – 1928
 Was working with two strains of bacteria
 Smooth strain was lethal, the rough strain was harmless
 When the smooth bacteria, which had been killed by boiling, was
added to living rough bacteria, the resulting bacteria was lethal
 Conclusion – nonliving material from the smooth strain affected the
function of a cell
o Avery, McCarty, and MacLeod – 1944
 Broke strep down into proteins, lipids, carbohydrates, and DNA
 DNA was the only one that affected other strep
 However, they were not believed- people thought the DNA was
contaminated with proteins
o Hershey and Chase – 1942
 T2 is a virus that attack E. coli bacteria (called a bacteriophage)
 The virus is made of just proteins and DNA
 Tagged the proteins in the T2 virus with a sulfur radioactive isotope, 35S
 Tagged the DNA in the T2 virus with a phosphorous radioactive isotope,
32
P
 Infected bacteria with the viruses, found that the DNA and the 32P entered
and were incorporated into the cell
o Chargaff – 1952
 Found that the ratio of bases is constant
 The number of A ≈ T, G ≈ C
o Watson and Crick – 1953 (side note: Watson is a shmuck)
 Found that DNA was an antiparallel double helix, where A connects to T
and G connects to C
o Meselsohn and Stahl – late 1950’s
 Looked into how DNA replicates
 Added 15N to one group of E. coli and 14N to another
 Three possibilities were considered for how DNA replicated
 Conservative
o When a double helix of 15N DNA replicates in the presence
of the 14N isotope, the two original strands would end up
together (15N) and both strands of the new helix would have
the isotope 14N
 Semi conservative
of the 14N isotope, the resulting two helixes would each
have a 14N strand and a 15N
 Dispersive
of the 14N isotope, each strands would have sections of the
original 15N and the new 14N isotope
 When combined and centrifuged, the first replication resulted in one band
between where the 15N and the 14N would be
 Couldn’t be conservative; the conservative model would expect
there to be a band at 15N and a band at 14N
 The second replication resulted in one band at 14N and one band between
where the 15N and the 14N would be
 Couldn’t be dispersive; dispersive would expect one line between
where the 15N and the 14N would be
 Conclusion: DNA replicates semi conservatively
 DNA Replication
o Many proteins work together in DNA replication and repair
 When a cell copies a DNA molecule, each strand serves as a template for
ordering nucleotides
 Replication begins at sites called origins of replication
 Proteins separate the two strands, making a bubble
o In eukaryotes, there are many “bubbles”, and the resulting
produced DNA fuses
o At each end of the bubble is a replication fork, where the
parental strands are being unwoven by helicases
o Single-strand binding proteins keep the parental DNA
strands from rejoining
o The untwisting of the double helix causes tighter twisting
and tension ahead of the replication fork
 Topoisomerase relieves this tension by breaking,
swiveling, and rejoining DNA strands
 A short (5-10 nucleotides) RNA primer chain is laid down
o Recall: you can only add DNA to the hydroxyl group on
the 3’ end
 The DNA chains are antiparallel; replication is going both
directions from the origin, but DNA can only be added to the 3’
end
o Thus, there is a leading strand and a lagging strand
 Leading strand
o DNA-dependent DNA polymerase III adds DNA

nucleotides onto the RNA primer, and keeps on laying
DNA onto the 3’ ends
o The leading strand elongates in one continuous DNA strand
 Lagging strand
o The lagging strand is made discontinuously is a series of
segments, called Okazaki fragments
 Primase lays down RNA as a primer a small
separated segments
 DNA-dependent polymerase III adds DNA to the
RNA’s 3’ end, forming Okazaki fragments (about
100 nucleotides long)
 DNA-dependent polymerase I replaces the RNA of
the primer with DNA
 DNA ligase joins the sugar-phosphate backbones of
the Okazaki fragments into one continuous strand
 All of these proteins form one large complex
 Mutations
o Point mutations – one wrong nucleotides is laid down in
place of the correct one, only affects one amino acid
 This mistake is found and fixed frequently by the
polymerase
 A wrong nucleotide results in a “bump” in the helix,
which the polymerase notices, and quickly replaces
the nucleotide
 However, some like Sickle Cell Disease, get
through and can be deadly
o Insertion mutations – a nucleotide is added between to right
ones
 Offsets the triplet frame of the genetic message
(called a frame shift)
 All nucleotides downstream will be improperly
grouped into codons
 Protein is almost guaranteed to be nonfunctional
o Duplication mutations
 Occurs during crossing over in meiosis
 Very bad, end up with an extra and a missing set of
genes
Ex: AA 1234 5678 9AG AA 1234 1234
9AG
↑↓ 
AA 1234 5678 9AG AA 5678 5678

9AG
o Inversion mutations – caused by a loop forming
 AA 1234 5AG  AA 4321 5AG
o Translocation
  
F
 The sister chromatid which a section of DNA is on
is actually very important
 Things happening in other locations will impair its
function, even if it’s in the right spot on the wrong
side
 Structure of a Chromosome
o DNA binds to specific proteins, forming chromatin
o Chromatin has three parts
 DNA – negatively charged
 Histones – basic proteins, positively charged
 H1 – fills in space between nucleosomes
 H2A
 H2B Form a nucleosome, a
 H3 ball which the DNA
 H4 wraps itself around
 Acidic proteins – negative charge
 Fine tuners, allow DNA to make RNA
o DNA can wind up tightly around nucleosomes
 Stabilizes, gets it ready for mitosis
 But when wound tightly, the genes can’t be used or
expressed
o DNA can unwind and be loosened
 Example of epigenetics – level of control of gene
expression greater than the sequence of nucleotides
 Tight vs. Loose is controlled by adding methyl or
acetyl groups to histones
 When loosened, the enzymes can come and make
RNA and proteins
o Three kinds of DNA
 Single-strand DNA – structural proteins- basically
all enzymes
 Moderately repeated DNA – makes rRNA and
histones
 Highly repeated – stabilizes chromosomes
Chapter 17: From Gene to Protein

o DNA  RNA  Protein
 Transcription – Turning DNA into mRNA
o RNA is single stranded, has oxygen on C2’
o Original DNA is used as a template
o DNA dependent RNA polymerases are used
 Three types of polymerases are used
 Pol 1 – makes rRNA for making ribosomes – about 14000 base
pairs
 Pol 2 – makes mRNA – about 103-104 base pairs
 Pol 3 – makes tRNA
o DNA loosens by adding methyl and acetyl groups to histones
 Only one strand of DNA is replicated
 The other is opposite and backwards of the desired message, it’s
basically gibberish
o Some bacteria are the exception, having useful DNA on the
same portion of both strands
 A strand of DNA will have template and non-template sections
o Eukaryotic RNA synthesis is more complicated than prokaryotic
 Prokaryotic RNA synthesis
 Prokaryotic RNA polymerase lands on the promoter – a sequence
on the DNA that tells the RNA polymerase where to land
 Polymerase lays down RNA with the help of transcription factors
 At the end, the polymerase reaches a terminator sequence - signals
the end of transcription
o Causes polymerase and the new RNA to detach
o The RNA cuts itself off the DNA
 Afterwards, prokaryotic RNA is ready for use
o However, in eukaryotes, lots of stuff happens after RNA
detaches
 Eukaryotic RNA synthesis
 Eukaryotic Initiation Factors (EIFs) land on TATA box- where the
appropriate polymerase lands
o Need the right polymerase – want right kind of RNA
o TATA box is about 25 base pairs long before start site
 Enzyme splits the two strands, starts transcribing from template
strand at start site
o Only about 10-20 RNA nucleotides are exposed at a time;
RNA strand peels off in the wake of the polymerase and the
DNA strands rejoin
 First segment after start site is the 5’ UTR – untranslated region

which gives instruction to ribosome as to how fast to proceed, etc.
 After UTR, methionine is laid down, which is used to let protein
into the endoplasmic reticulum, and the polymerase keeps on
transcribing region that contains protein coding segments
 As it approaches the end, the polymerase transcribes the
polyadenylation signal – AAUAAA – where several proteins
attach
o 10 to 35 base pairs later, these proteins cut the pre mRNA
from the polymerase
o However, the pre-mRNA is not ready for use – in
eukaryotes, lots of post transcription modifications occur
o Polymerase keeps going, but these proteins destroy RNA
and eventually disconnect the polymerase from the DNA
 Post transcription modification
o Polyadenylation – addition of 50 – 250 A’s onto the 3’ end
 Helps the mRNA leave the nucleus
 Protects mRNA from degeneration by hydrolytic
enzymes
 Enzymes chew down the A’s, when the A’s
run out, the RNA “dies” (like a fuse)
o Splicing
 In eukaryotes, only certain sections of the mRNA,
called the exons, are needed for the final product
 The rest, called introns, are not needed
 The introns are clipped off and the exons are
connected by a spliceosome
 x This allows for multiple combinations of RNA
 Thus, there is a greater variety of proteins
than number of genes coding for them
 Ex: egg albumin – 1800 out of 7700 base
pairs are used
o Capping
 The 3’ end is protected by the poly-A tail
 The 5’ end is protested by a 5’ cap – a modified of
guanine – called 7-methylguanosine
7-methylguanosine
 Prevents ribonucleases from destroying the
RNA
5’ UTR
Tri-phosphate Bridge
 mRNA Translation into Proteins

 Transfer RNA (tRNA) is used in the ribosome to interpret the mRNA and
chain together amino acids accordingly
o An amino acid attaches to a tRNA
 An amino acyl-tRNA synthetase pops two phosphate off an ATP (leaving
AMP) and puts them on the tRNA, then pops them back off to add the
appropriate amino acid
 There is a tRNA with an anticodon – the corresponding RNA
sequence – for each mRNA codon
 Each mRNA codon codes for an amino acid, but often multiple
mRNAs can code for the same amino acid
o The third nucleotide in the codon is often not as important
Where amino as the first two
acid attaches
o The tRNA adds the amino acid to the growing polypeptide chain as instructed by
the mRNA
5’  This occurs in the ribosome
 Ribosomes are about 1/3 protein and 2/3 rRNA
3’  Ribosomes are made of three subunits
o Size: measured in Svedberg units
 Prokaryotes: 16, 23, 5
 Eukaryotes: 18, 28, 5
 Conclusion: Eukaryotes have bigger ribosomes
o The large and small subunits only join together one of the
Growing polypeptide Next amino acid
chain is attached to the
anticodon small subunits mRNA
to be added
 An initiator tRNA attaches to the mRNA, carrying
tRNA exiting formyl methionine
from the E site
tRNA
A
E P
o Using the mRNA as a template, the ribosome allows tRNA to form a

corresponding amino acid chain
 A tRNA enters the A site carrying an amino acid and pairs with the
complementary mRNA codon
 The polypeptide chain binds to the tRNA’s amino acid
 This removes the chain from the tRNA in the P site
 The tRNA moves to the P site, while the previous tRNA goes to the E site,
where it is expelled, bringing the next tRNA into the A site
 All of this requires lots of GTP
 When the mRNA gets to the “stop codon”, the A site accepts a “release
factor,” which cuts off the polypeptide chain and breaks apart the
ribosome into its three subunits and the mRNA
 Post Translation Modifications
o Folding- result of primary structure
o Add lipids, sugars, phosphates, metals, etc.
o Cutting it up
 A polypeptide is rarely cut up to result in two functional proteins
 Cutting most often happens to activate the protein
 The active site will be covered by a section of the protein, by
cutting it off, the protein will function
o Ex: Digestive proteases are manufactured in the cell in an
inactive state, it’s activated by cutting off the section
covering the active site
o Joining multiple proteins together
 Results in quaternary structure (ex: hemoglobin)
o Methylation and acetylation
Chapter 18: Regulation of Gene Expression

o In order to survive, organisms must maintain homeostasis
o This is done by regulating how genes are expressed
 Operon Concept – by Jacob and Monod
 Explains how genes are regulated in E. coli
1) All genes start out repressed
 This makes things efficient – processes only run when they need to
2) When we want to do something, we derepress the gene
o The primary mechanism for all gene regulation is through RNA transcription
 Regulation can occur at all four levels
 Transcription
 Post-transcription – increase mRNA degeneration rate
 Translation – increase rate of synthesis
 Post-translation – increase stability
o Operons consist of (in bacteria)
 An operator – an “on/off switch”
 The promoter
 Multiple genes – when the polymerase runs, it makes multiple enzymes
 Ex: E. coli makes three enzymes at once for digesting lactose
o Beta galactosidase
o Gal. permetase
o Gal. transacetylase
 Negative Gene Regulation
o Uses a repressor to bind reversibly to the operator site,
stopping the polymerase from running
o The repressor is a molecule made elsewhere on a regulatory
gene
o There are strong repressors and weak repressors
 Strong repressors, like for the lactose gene, rarely
fall off, keeping the gene from running 99% of the
time
 Weak repressors, like for Trp, fall off the operator
site frequently, allowing the polymerase to run 90%
of the time
 Inducible Operons – usually off, can be stimulated to turn on
o A strong repressor is bound to the operator site until an
inducer binds to the repressor
 When the inducer binds to the repressor, the
repressor changes shape, and is no longer able to
bind to the operator site
 Repressor falls off, and the polymerase can run
o Ex: Lactose operon

 E. coli eat mostly glucose when in the
stomach
 However, if pooped out and carried by a fly
into a bucket of milk, they must be able to
digest lactose
 Lactose serves as the inducer, kicking off the
repressor, and allowing the Lac gene to produce
lactose-digesting enzymes
 When all of the lactose is digested, the repressor can
again bind to the operator site (inducer is absent)
 Repressible Operons – usually on, but can be turned off
o Repressible operons have weak repressors
o To turn them off, a corepressor binds to the repressor,
changing the repressor’s shape into a strong repressor
 The resulting repressor will be able to stay on the
operator site, shutting down production
o Ex: tryptophan operon
 Tryptophan is a protein not consistently
consumed by animals, thus, E. coli must
make its own tryptophan most of the time
 But, if a deer kills and eats a turkey (which
is rich in tryptophan), it does not need to
produce any tryptophan of its own in the
short term
 The Trp operon is usually on, but when tryptophan
is consumed, the tryptophan serves as a corepressor,
shutting Trp mRNA production
 Positive Gene Regulation
o Used when E. coli has both glucose and lactose
 E. coli will preferentially digest glucose and turn off
the lactose digestion
o There are strong and weak promoters
 The polymerase is not likely to bind to a weak
promoter; it will fall off a majority of the time
 The polymerase will almost always bind to a strong
promoter
o Lactose has a weak promoter; if glucose is present, it won’t
run
o Catabolite Activator Protein (CAP) can bind upstream of
the promoter, allowing the polymerase to bind mush more
frequently
 However, CAP only takes its active form when

cyclic AMP binds to the CAP
 cAMP levels rise when glucose levels drop
o Thus, when glucose is in short supply:
 cAMP binds to CAP
 CAP binds to the promoter
 Polymerase binds to the promoter and makes the
mRNA
 Eukaryotic Gene Regulation
o No multigene organization; 1 promoter : 1 protein
o Lots of regulator proteins can bind upstream of the promoter to affect the
transcription rate
 Multiple proteins can attach; some speed it up, some slow it down
 This allows for fine tuning of the transcription rate
Chapter 38: Plant Reproduction and Development

 Flowering plants (angiosperms) are the most common type of plant
 Co-evolved with (mutually dependent on) insects
 Show alternation of generations
 Sporophyte diploid (2n) stage – majority of life
 Gametophyte haploid (1n) stage – sperm and egg
o General Anatomy
 Sepal – outermost – calyx is all of the sepal together
 Green miniature leaves under petals
Anther  Petals – corolla is all of the petals together Stigma
 Have ultraviolet-visible landing markings for insects to see
 Stamen (male) – has two parts
 Filament Style
 Anther
o Has four chambers Ovule
Filament o Contains pollen grains – male gametophyte
 Carpal (female) – has three parts Ovary
 Stigma – landing pad for pollen
2n  Style
 Ovary – contains ovule, where the egg is stored
o Gametophyte Development
 Male – Pollen
1n  A diploid cell in the anther, called a microsporocyte, under goes
meiosis, resulting in
1n  Four haploid microspore, which undergo mitosis resulting in
Gen.  One generative nucleus and one tube nucleus for each microspore
 Each generative nucleus undergoes mitosis, resulting in two sperm
nuclei for each generative nucleus
1n 1n 1n  The walls of two sperm nuclei and one tube nucleus thicken and
Tube Sperm Sperm
fuse together, forming a pollen grain
 Female
 A diploid megasporocyte undergoes meiosis, resulting in
 Four haploid megaspores, three of which are tiny and die; the last
one is huge and under goes mitosis three times, resulting in
 Eight haploid nuclei
o Three antipodal nuclei
o Two polar bodies
o One oocyte (egg)
o Two synergids
o Pollination and Fertilization
 Pollen lands on the stigma

 Tube nucleus forms tube under and into the ovule
 Two sperm nuclei come in through the tube
 One fertilizes the egg
 One fertilizes two polar bodies
 This results in a diploid sporophyte – the seed – and a triploid endosperm
 Endosperm serves as food for the seed
o Divides mitotically to become a milky “super cell”
 The seed grows to become the adult plant
o As the plant grows, it makes one or two embryonic leaves,
called cotyledons
o If it has one cotyledon, it’s a monocot (ex: corn)
o If it has two cotyledons, it’s a dicot (ex: peanuts)
 Plant growth and development
o Only certain parts of a plant undergo mitosis – called meristematic tissue, or
growing tips
 Meristematic tissue is like a stem cells: it can be removed from a
plant, reproduced (called a callus), and then be used to make more
plants
o Is done with orchids or with certain non-reproducing
manmade plants like the one the Hungarian guy is working
on
 Shoot Apex – at the top of the plant and the ends of the branches
 Root Apex – at the ends of each root
 Branch Apex – at the junctions of branches
 A ring around the branches
 The outer surface of a tree is dead material
 Underneath is a layer of meristematic tissue, compressing the
wood inside and growing it outside
o Everything else can’t divide, instead it just grows in size up to a certain point
 Not all plants make seeds
o Some colonize with runners (ex: strawberries, bamboo, aspen trees)
 The runners can go aboveground or belowground
o Some use tubers
o Some plants use parthenogenesis – no fertilization (ex: dandelions)
 Minimizes diversity – offspring are genetically identical and can cause
genetic disorders
 Allows many plants to be made all at once
o Some plants are totally sterile – human made (ex: seedless watermelon and
bananas)
 Grown from meristematic tissue
Acrosome
Chapter 48: Animal Development
Actin
Jelly Coat
Nucleus
Vitelline Envelope
Mitochondria
Cortical granules
Plasma Membrane
Flagella
 Fertilization
o Contact
 The egg releases jelly coat proteins, creating a gradient, which the sperm
follows – called chemotaxis
 Sperm comes into contact with the jelly coat
 In mammals, when sperm are initially released, they are not fully
capable of penetrating the egg. On the way, enzymes inside the
reproductive track act on the sperm, giving it that capability
o Sperm Entry
 The sperm nucleus has to get through two plasma membranes (the egg’s
and its own), the jelly coat, and the vitelline envelope
 Acrosomal reaction
 Sperm touches the jelly coat, and receptors bind to it
Hydrolytic enzymes  Sperm releases Ca++ , causing it to pump in Na+ and pump out K+
and H+
o Pumping protons changes the pH
Polymerized Actin
 Acrosome “ruptures” – dehiscence – the acrosomal membrane and
the plasma membrane fuse
o This forms little balls, which float away, leaving the
hydrolytic enzymes
 Ca causes:
++
o Hydrolytic enzyme release

o Exposes Bindins – proteins that hold the sperm and the egg
together for the plasma membrane to fuse
 Have to hold them together for a fusogenic protein

to fuse the plasma membranes
 Shift in pH causes:
o Activation of dynein ATPase
 Dynein is in the flagella, which enables the flagella
to twist
 Activation of dynein ATPase causes the
flagella to push the sperm really hard
o Mitochondrial activity increases 50%
 More ATP being made for dynein
o Actin polymerizes, forming a long acrosomal filament
 The filament is covered in the hydrolytic enzymes
 Chews its way through into the cytoplasm, and the
nucleus is pushed in
 Cortical Reaction
o Prevents polysermy – having multiple sperm nuclei enter
the egg
o Two ways to prevent polyspermy
 Kill all but the ones you don’t want
 Birds do this
 Only let one in (everyone else, see below)
 When the acrosomal reaction occurs, the sperm releases Na+ into
the egg
 Na+ release causes a cascade
o Fast Block (technically part of the acrosomal relation)
 Na+ inrush changes the membrane potential, the
charge across the membrane
 Membrane potential is normally negative;
adding the Na+ makes it positive
 When the membrane potential is positive, the
fusogenic proteins are unable to bind the sperm to
the egg, and the unwanted sperm fall off
 Discovered by two experiments
o Holding the membrane potential at
-80 caused polyspermy
o Holding the membrane potential at
+20 prevented fertilization
 The membrane potential returns to normal
(negative) after two minutes, so the slow block
prevents polyspermy after the fast block fades
o Slow block
 Na+ causes releases of Ca++ from the smooth

endoplasmic reticulum
 Ca++ only hangs around for a few seconds,
before being sucked back into the SER
 Ca++ causes the plasma membrane and cortical
membranes to fuse
 The cortical granule itself releases Ca++ into the
base between the plasma membrane and the
vitelline envelope, which triggers the fusion of other
cortical granules
 Enzymes in CG cause four simultaneous actions:
 Enzymes break the vitelline envelope free
Hydroscopic – attracts from the plasma membrane
and brings in water o Breaks the bindin, and all of the
other sperm break away
Fertilization  Hydroscopic enzymes cause water uptake
Vitelline
envelope o Water is drawn into the space
envelope
between the vitelline envelope and
the plasma membrane, inflating the
region
 Ovoperoxidase sticks to the new fertilization
envelope and crosslinks tyrosines
PM o Creates covalent bonds between
tyrosine side chains, turns the
envelope from soft to a very tough,
hard plastic fertilization envelope
 Hyaline layer coats the egg with a strong
elastic barrier so that the cells will hold
together before tight junctions are formed
 Metabolic Zygote Activation
 Calcium is released (for some, the Ca++ comes from the
environment)
 Ca++ release causes”
o Activation of NAD Kinase – makes NADP
 NADP makes fats and hydrogen peroxide
 Hydrogen peroxide allows Ovoperoxidase to work
o Increase in oxygen consumption
 Oxygen is used to make hydrogen peroxide, by
adding it to the water which was brought in by the
hydroscopic enzymes
o Drop in H concentration, from pH 6.5 to 7.0
 Ca++ and low pH increase protein synthesis
 Animal development after fertilization

o Egg
o Zygote
 Goes from one cell, to two, four, eight, and sixteen
Mesomere
Macromere
Micromere
o Blastula
 Forms a hollow sphere
Blastocoel
o Gastrula – shows the three germ layers

Ectoderm – will
form the skin
Mesoderm – will form

bones, muscle, and limbs
Endoderm – will form

the digestive track

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Biology 101 Notes

Chapter 3: Water Supports Life

 When frozen, the hydrogen bonds stabilize far apart

 H+ and OH- are very reactive; changes in their concentrations drastically

Chapter 4: Carbon as the backbone of life

 A few chemical groups are key to molecular function

 ATP – Adenosine Triphosphate

Chapter 5: The Structure and Function of Large Biological molecules

o The most common type of disaccharide is sucrose (Table

 Glycerol – an alcohol – has a hydroxyl group on each of its three

 Two fatty acids and a phosphate group attached to a glycerol

 Repeating sequence of amino acids= polypeptide backbone

 Proteins are formed in specifically designed and controlled

 Polynucleotides made of nucleotides

Chapter 6: Cells, the Fundamental Unit of Life

o Chromatin is the complex of DNA and the proteins making

 Stores Calcium ions

o Ca++ must be withdrawn once

 Golgi Apparatus – shipping and receiving center

o Twisted double chain of actin proteins

 Any force applied will be distributed through all cells in the

 Can be blocked (poisons and pesticides block specific transport

 The phosphate is transferred to a molecule in the reaction

 However, this will decrease D production,

 Thus, in the lungs and gills, hemoglobin readily

Chapter 9: Cellular Respiration and Fermentation

 C6H12O6 + 6O2  6CO2 + 6H2O

It is rearranged into a five part ring

Another phosphate is added

The Fructose 1,6 biphosphate is split half, forming

ADP picks up a phosphate, becoming ATP

2 phosphoglycerate ADP picks up a phosphate, becoming ATP

An H2O is pulled out

 Intermediate Step – pyruvate oxidation

 Krebs cycle – oxidizes fuel from pyruvate – occurs in mitochondria

Summary thus Far ATP NADH FADH2

Chapter 10: Photosynthesis

1) Photon hits PSII, energy is relayed to reaction center complex, electron is

 Close stomata during, open to let CO2 in at night

Chapter 11: Signal Transduction

 Most parts of this process are proteins

Chapter 12: Cell Reproduction

Chapter 13: Meiosis

o Both chromosomes from one homologue are connected to

Chapter 16: Inheritance through DNA

o DNA-dependent DNA polymerase III adds DNA

AA 1234 5678 9AG AA 5678 5678

Chapter 17: From Gene to Protein

 First segment after start site is the 5’ UTR – untranslated region

 mRNA Translation into Proteins

o Using the mRNA as a template, the ribosome allows tRNA to form a

Chapter 18: Regulation of Gene Expression

o Ex: Lactose operon

 However, CAP only takes its active form when

Chapter 38: Plant Reproduction and Development

 Pollen lands on the stigma

o Hydrolytic enzyme release

 Have to hold them together for a fusogenic protein

 Na+ causes releases of Ca++ from the smooth