Chapter 1 pg.

49 12/28/14 7:43 PM
SECTION 1.1 WHAT IS BIOLOGY? PG. 49
Amphibian population: disappearing because of atrazine (from fertilizers)
- used in spring when they breed so it affects the young; feminized males; vocal structures
(used for mating) smaller; had eggs or female sex organs; or no sperm
- breeding plummeted and pop -; affected other orga. similarly
Archaea and Bacteria: might be unicellular but can also have structures more complex than that of other
prokaryotes.
BIOLOGY: study of living things
ORGANISMS: all descended from a common origin of life 4 bya
* Characteristics:
- made up of common set of chem comp, esp, carbs, lipids, nucleic acid, amino acids, and others
- building blocks are CELLS enclosed by plasma membranes
- cells convert molec obtained from environ into new bio molec
- cells extract E from environ and use it to do bio work
- org contain genetic info which uses universal code to specify assembly of proteins
- org share simil among a fund set of genes and rep this genetic info when reprod themselves
- org exist in pop that evolve thru changes in freq of genetic variants within pop over time
- living org self-reg their internal environ thus maintaining the cond that allow them to survive
obviously not all organisms meet all characteristics ex. seed & virus pg. 51
LIFE AROSE FROM NON-LIFE VIA CHEMICAL EVOLUTION: PG. 51
Earth formed 4.6-4.5 bya > 600 mil years later became hospitable
Earths atmosphere, climate, oceans all factored into how life arose
complex bio molec 1st came from random physical association of chem in environment.
NUCLEIC ACIDS: critical step for evo of life; molec that could reproduce themselves and also serve as templates
for the synthesis of proteins
PROTEINS: large molec with complex but stable shapes
variation in shape enabled them to participate in increasing #s and kinds of chem rxns with other molec

CELLULAR STRUCTURE EVOLVED IN THE COMMON ANCESTOR OF LIFE
Enclosure of complex proteins & other bio molec by membranes another critical step
FATTY ACIDS: enclosed complex prot and bio molec incompact internal environ; dont dissolve in
water, form membranous films that form spherical structures.
These were the first cellular org that could reprod.
Enclosure of all these molec and their reactions opened up possibility that all can be integrated and controlled in
the tiny environment
PROKARYOTES: unicellular and enclosed by single membrane; ex. bacteria
BACTERIA
ARCHAEA
Both are single-celled prokaryotes but fundamentally diff metabolic processes
Eventually both types merged to form (because they lived dependent):
EUKARYOTES: outer membranes, internal membranes that enclosed specialized organelles within their cells,
nucleus (contained genetic material), mitochondria
glitch in cell / led to two euk. getting stuck and then working together > led to multicellular euk
because of:
CELLULAR SPECIALIZATION: cells to specialize in certain funct. While other cell specialized in
another funct = more efficient gathering of resources and adapting to specific environment
Emdosymbioses of bacteria: can also explain orgin of Eurkaryotes
PHOTOSYTHESIS ALLOWS SOME ORGANISMS TO CAPTURE ENERGY FROM THE SUN PG. 52
cells got E from METABOLISM: (E transf) take small molec directly from environ and break down to component
atoms to > release and use E
PHOTOSYNTHESIS: 2.5 bya; transf sunlight into bio E that powers synthesis of large molecules > broken
down > release E > E captured and used to provide metabolic E
Cyanobacteria most like 1st photosyn. cell
eventually became so abundant that O2 (product of photosyn) accumulated in atmos.
O2 was actually poisonous to many prokar so as it inc. only the ones that could tolerate it survived
Led to new methods of metabolism
AEROBIC METABOLISM: used O2 to extract E from nutrient molec; way more efficient than anaerobic (which
was what was occurring before it)
allows org to grow larger
ANAEROBIC METABOLISM: occurs without O2
Oxygen kept accumulating in the atmosphere and began forming the OZONE LAYER: O3; blocked UV radition
 Oxygen kept accumulating in the atmosphere and began forming the OZONE LAYER: O3; blocked UV radition
from sunlight from killing org not in H2O
about 500 mya, Ozone layer dense enough to protect life on land and life moved to land as well
BIOLOGICAL INFO IS CONTAINED IN A GENETIC LANG COMMON TO ALL ORG PG. 53
GENOME: sum total of all DNA molec cont. wi/in each of orgs cells
DNA: (deoxyribonucleic acid) molec of long sequ of 4 diff subunits
NUCLEOTIDES: 4 diff ones make up DNA; contains: 5-C sugar, Nitrogenous base, and phosphate group
adenine, thymine, guanine, cytosine, (and uracil)
GENES: specific seg. Of DNA that encode info used to create amino acids and form them into proteins
AMINO ACID: 26 diff ones. Building blocks of protein
PROTEIN: govern the chem rxns wi/in cells and form much of orgs struct.
all cells have same genes but still create diff protein as per their function = concept of gene expression
org contain 1000s of genes and they must all be replicated > not perfect so errors, mutations, arise;
MUTATIONS: can arise spontaneously or be induced by outside factors; inc. chem and radiation
o Harmful, no effect, or very rarely beneficial
POPULATIONS OF ALL LIVING ORGANISMS EVOLVE PG. 54
POPULATION: is a group of indivi of same type of org (SPECIES) interact wth one another
EVOLUTION: acts on popu; change in the genetic makeup of bio pop over time
major unifying principle of bio
Charles Darwin: 1859 On the Origin of Species; natural selection could account for much of
evolution of life.
NATURAL SELECTION: differential survival and repd among individuals in a population
if trait enhances survival = the org will survive and trait will spread in the population and vice versa
natural selection leads to adaptation
ADAPTATION: structural, physiological, or behavioral traits that enhance orgs chances of survival and reprod. in
environ
Biodiversity:
Natural selection
SEXUAL SELECTION: selection due to mate choice (looks, singing, fighting)
GENETIC DRIFT: random fluct of gene freq in a pop due to chance events
And much more
BIOLOGISTS CAN TRACE THE EVOLUTIONARY TREE OF LIFE
Species that share a recent evol history are genetically more similar to each other
PHYLOGENETIC TREE: portray evo hist of diff groups of org; constructed by analyzing and quantifying smili
and diff btw species
BIONOMIAL: two Latinized names assigned to all org that ever lived
GENUS (genera): 1st name; group of species that share a recent common ancestor; Homo (man)
SPECIES: specific to the org within the family (genus); sapiens (wise)
Genome sequencing: helped biologists back up phylo tree with molec evidence
CELLULAR SPECIALIZATION AND DIFFERENTIATION UNDERLIE MULTICELLULAR LIFE PG. 57
As cells became specialized in multicellular orgs they lost other functions and BIOLOGICAL HIERARCHY:
emerged; cells tissues organs org sys indi.
TISSUES: groups of same differentiated cells organized
ORGANS: Different tissue types are organized to form organs
ORGAN SYSTEMS: Diff organs interrelated to run certain functions
LIVING ORGANISMS INTERACT WITH ONE ANOTHER (Hierarchy)
internal hierarchy of org matched by external hierarchy of world
POPULATION: is a group of indivi of same type of org (SPECIES) interact wth one another
COMMUNITY: populations of all species that live and interact in a defined area
ECOSYSTEM: communities together with their abiotic envrion
interaction btw individuals in pop: competition (for food, mates), killing, cooperation (forming social units) >
Resulted in social behave as communi and courtship displays.
Plants also depend on partnership with fungi, bacteria, and animals; compete with each other for sunlight and
resources; protect against predation
NUTRIENTS SUPPLY ENERGY AND ARE THE BASIS OF BIOSYNTHESIS PG. 58
living org get nutrients from environment > nutrients supply org with E and materials to carry out biochem rxns
TYPES OF WORKS CELLS DO:
Mechanical: moving molec from one loc to another (moving cells, tissues, or even the org)
Synthesis: of complex molec(carbs), struct(protein), or even the org itself
RXNS are related: products of one rxn is raw material for another rx
LIVING ORGANISMS MUST REGULATE THEIR INTERNAL ENVIORNMENT
INTERNAL ENVIRONMENT: made up of extracellular fluids in which cells, tissues, and org sys exist in
HOMEOSTASIS: maintenance of narrow range of cond of internal environment; stable environ means cells can
funct efficiently even when cond outside of orgs body become unfavorable for cellular processes.
Orgs regulatory sys obtains infor from sensory cells (about internal and external cond) > process and
integ. Info > send signal to component of physiological sys> change in response to these
signals> internal environ maintained
 signals> internal environ maintained
Homeostasis applies to unicellular orgs to > need to maint physiological parameters (acidity, salinity0 wi/in
range so cells can survive and funct
indi cells do this is plasma membrane that encloses them
self-regulation is general attribute to livin orgs

SECTION 1.2 HOW DO BIOLOGISTS INVESTIGATE LIFE? PG. 59

OBSERVING AND QUANTIFYING ARE IMPORTANT SKILLS
DATA: quantified information (that is observed)
mathematical models and calculations allow for comparative investigations of all other aspects of an
orgs body
SCIENTIFIC METHODS COMBINE OBSERVATION, EXPERIMENTATION, AND LOGIC
INDUCTIVE LOGIC: involves taking observations and creating new statement/ tentative prop that is compatible
with the observations
HYPOTHESIS: new statement or proposition formed thru inductive logic; uses know info to come up with
answer to question (educated guess); needs to be tested
DEDUCTIVE LOGIC: starts with statement believed to be true (hypothesis) and then goes on to predict what
facts would also have to be true to be compatible with the statement
GOOD EXPERIMENTS HAVE THE POTENTIAL TO FALSIFY HYPOTHESES PG. 60
CONTROLLED EXPERIMENT: manipulates one or more factors being tested
COMPARATIVE EXPERIMENTS: compare unmanip data gathered from different sources
we cannot control the variables; sometimes we cannot even identify all variables; but compare data
INDEPENDENT VARIABLE: manip variable
DEPENDENT VARIABLE: response that is measured (in exp and contr group)
STATISTICAL METHODS ARE ESSENTIAL SCIENTIFIC TOOLS PG. 61
Significance of collected data can be determined by using statistics > statistical tests determine probability of
randomness in data
STATISTICAL TEST: starts with a NULL HYPOTHESIS: premise that any observed diff r simply
result of random diff tat arise from drawing two finite samples from same pop
If less than 5% or lower then, the data is significant (good)
DISCOVERIES IN BIOLOGY CAN BE GENERALIZED PG. 62
MODEL SYSTEMS: findings from these systems can be generalized to other orgs
NOT ALL FORMS OF INQUIRY ARE SCIENTIFIC
Scientific observation and evaluation is the most pow way man devised to learn about world and how it functs
Scientific explanations r reliable because hypotheses can be tested and it must have a potential for being rejected
amost all experiments are repeated
science depends on strict objectivity and absolute dependence on evidence based on reproducible and quantifiable
observations

1.3 WHY DOES BIOLOGY MATTER PG. 63

MODERN AGRICULTURE DEPENDS ON BIOLOGY
even in pre-historic times, ppl selectively bred crops
understanding bio and plant helped planet support of large pop
BIOLOGY IS THE BASIS OF MEDICAL PRACTICE
biology helped us understand disease and our bodies (how it funct and why we get disease)
BIOLOGY CAN INFORM PUBLIC POLICY PG. 64
knowledge of how things work can help with addressing ethical issues
ex. tracking bluefinned tuna to see how it interacts w/ other fish enact fishing policy for the
endangered species etc
BIOLOGY IS CRUCIAL FOR UNDERSTNADING ECOSYSTEMS PG. 65
world always changing but humans affect rate of change; ex. our activities released CO2 into atmos and warming
rate increased
BIOLOGY HELPS US UNDERSTAND AND APPRECIATE BIODIVERSITY
our curiosity could be an adaptive traits; new discoveries help us understand and appreciate

Ch. 2 Small Molec & Chem of Life pg. 69 12/28/14
7:43 PM
SECTION 2.1 HOW DOES ATOMIC STRUCTURE EXPLAIN THE PROPERTIES OF MATTER? PG. 70
ATOMS: tiny, consists of positive, neutral, and negative charged part
MASS: measure of quantity of matter present (weight depends on gravity, changes with planet, etc)
DALTON: mass of proton that serves as a standard unit of measure; proton and neutron = 1 Dalton = 1.7X 10^-24
grams
ELEMENT: pure substance that cont only 1 kind of atom; 94 elements in nature
 ELEMENT: pure substance that cont only 1 kind of atom; 94 elements in nature
ATOMIC NUMBER: number of protons in element; unique
MASS NUMBER: (# of prot and neut)
ISOTOPES: same element but diff # of neutrons = diff mass
PG. 71
ATOMIC WEIGHT: avg of weight of all isotopes and their freq
RADIOISOTOPES: unstable and spontaneously give off E in form of ALPHA, BETA, or GAMMA radiation
from atomic
used in research to track brain activity, track molecule, date fossils
RADIOACTIVE DECAY: release of E that transf original atom
w/ instruments, radiation can be used to study brain funct etc
MOLECULES: stable associations of atoms in living org
THE BEHAVIOR OF ELECTRONS DETERMINES CHEMICAL BONDING AND GEOMETRY PG. 72
#of e- determines boding; chem rxns change atom comp. & prop.
ORBITAL: region of space where e- is found at least 90% of time
ELECTRON SHELLS: E levels around nucleus
s has lowest E level
VALENCE SHELL: outermost shell determines how atom reacts
o Atoms with unpaired e- in VS, is unstable reacts more
OCTET RULE: tendency to bond to have 8 e-s in VS

SECTION 2.2 HOW DO ATOMS BOND OT FORM MOLECULES? PG. 74

CHEMICAL BOND: attractive force that link 2 atoms together in a molec
COVALENT BONDS CONSIST OF SHARED PAIRS OF ELECTRONS
COVALENT BOND: when 2 atoms share one or more pairs of e-
strong because take a lot of E to break them
COMPOUND: pure substance made up of two or more diff elements bonded in a fixed ratio
MOLECULAR WEIGHT: sum of atomic weights of all atoms in molec
Orientation of molec affects 3-D shape of molec/comp
phenomenon: molec can twist around covalent bonds
o molec in body can change shape to fit other molec
MULITPLE COVALENT BONDS PG. 76
sign, double, and triple bonds
UNEQUAL SHARING OF ELECTRONS
when 2 diff elements covalent bond, unequal sharing
ELECTRONEGATIVITY: attractive force than an atomic nuc exerts on electrons in a covalent bond
depends on: how many + charges it has & distance btw nuc and e- in VS
closer the e- = greater electroneg pull
NON POLAR COVALENT BOND: share e- = ; 2 atoms closer to each other in electroneg
POLAR COVALENT BOND: e- drawn more to 1 nuc than to another
POLAR: opposite charges are separated at two ends or pole of bond
polar bonds greatly inful. Interact btw polar molec and np molec
IONIC ATTRACTIONS FORM BY ELECTRICAL ATTRACTION
IONIC BOND: when one much more electroneg, transfer of e- occurs
IONS: electrically charged part. that form when atoms gain/lose e-
CATIONS: + ANIONS: -
COMPLEX IONS: NH4+, SO42-, etc
once formed ions r stable and no gain or loss of e-s
IONIC ATTRACTIONS: bonds formed as a result of electrical attract btw ions bearing oppo charges
when 2 ions bonds = salt forms
interact with polar molec since both are charged; ex. how liquid water interacts with NaCl
strength of ionic bonds greatly reduced when emmersed in liquid
HYDROGEN BONDS MAY FORM WITHIN OR BTW MOLEC WI/ POLAR COVALENT BONDS PG. 78
HYDROGEN BOND: bond resulting from attraction btw charged O atom in H2O and + charged H atom
Not restricted to water molec only
H Bond weaker than most ionic attract cuze formation due to partial charges
Do play a role in determining and mainting 3D struct of gaint molec; ex. DNA and proteins
HYDROPHOBIC INTERACTIONS BRING TOGETHER NONPOLAR MOLECULES
HYDROPHILIC: polar molec interacts w/ water thru weak attract
Nonpolar molec tend to interact w/ other nonpolar molec
HYDROCARBON MOLECULES: are nonpolar; aggregate together away from polar molec.
HYDRPHOBIC: water hating; nonpolar
HYDROPHOBIC INTERACTIONS: interaction btw hydrophobic molec
VAN DER WAALS FORCES INVOLVE CONTACTS BTW ATOMS
VAN DER WAALS FORCES: occur when atoms of 2 molec r in close prox; weak +&- attractions
result in random variations in e- distribu in one molec = create opposite charge in adjacent molec
important when hydrophobic regions of diff molec such as an enzyme and substrate come together
 important when hydrophobic regions of diff molec such as an enzyme and substrate come together

SECTION 2.3 HOW DO ATOMS CHANGE PARTNERS IN CHEMICAL RXNS? PG. 79

CHEMICAL REACTION: occurs when moving atoms collide with sufficient E to combine/ to change their
bonding partners.
Matter is neither creater nor destroyed
REACTANTS: molecules that interact
PRODUCTS: the resulting molec of rxn
ENERGY: capacity to do work; CHEM: capacity to change
changes in the form of energy asso w/ chem rxn
o Potential Chem E: E stored in bonds btw atoms/molec

SECTION 2.4 WHAT MAKES WATER SO IMP FOR LIFE? PG. 80

WATER HAS UNIQUE STRUCTURE AND SPECIAL PROPERTIES
WATER:
polar form hydrogen bonds 4 pairs e- in VS O repel= tetra
solid less dense (ice floating exp by tetra shape) universal solvent
store heat melting freezing point formation of H2O droplets

1. Ice floats: as solid held by hydrogen bonds; bonded to 4 others;

crystalline struct; farther away than in liquid = less dense
ice forms on top of lake = lake orgs live! And insulates
2. Melting, Freezing, and Heat Capacity:
ice requires lot of E to melt (need to break H bonds)
freezing releases E
water helps minimize variations in atmos temp across planet
o because of high heat capacity > high specific heat
o SPECIFIC HEAT: amount of heat E needed to raise temp of 1 gram of substance 1C
o Heat of Vaporization: lot of heat req to change H2O from liquid to gaseous state
(evaporation)
Evaporation cools environment because heat is absorbed by water for it to change
form ex. sweat
3. Cohesion and Surface Tension: Pg. 81
liquid H2O indiv part move about; H bonds form & break cont
COHESION: capacity of water molec to resist coming apart from one another when placed under
tension (ex. water in roots moving)
o Water evap of leaves and water from roots come up to leaves
Surface tension of exposed water (fly walking on water; slightly overfull cup)
4. The reactions of life take place in aqueous solutions:
SOLUTION: produced when substance (SOLUTE) dissolved in liquid (SOLVENT)
imp molec in biosys polar so soluble in H2O
o Qualitative analyses: identify process: prod, react, steps
o Quantitative analyses: measure []s, mole, Avogadros #, etc
MOLE: amount of substance (grams)
AVOGADROS NUMBER: 6.022x10^23 = # of molec of substance in a single mole

5. Aqueous solutions may be acidic or basic: Pg. 82
ACIDS: release H+ ions in solution: HCl>H+ + Cl-
COOH (acidic) because: COOH> COO- + H+
Strong Acids: completely disassociate in water; no acid remains
BASES: accept H+ ions in solu
Strong Base: completely disassociates in H2O
Ammonia: NH3
Ammonium: NH4+

REVERSIBLE REACTION: rxn that can proceed in either direction
Water is weak acid and base: tendency to ionize into OH- and H+
rxn somewat reversible
can measure acidity by measuring [] of H+ ions
pure H2O has [10^-7M]
pH: -log(10^-#); pure water pH: 7
BUFFERS: mixture of weak acid and corresponding base or weak base and coressp acid

ex. ; bicarbonate ion > carbonic acid
o present in blood system
 o present in blood system
minimizes effect of added acid or base on pH

LAW OF MASS ACTION: imp chem principle of reversible rxns

adding a reactant on one side of reversible sys drives rxn in direction that uses up that comp.
too much acid in digestive system (hydrochloric acid) just add salt like NaHCO3 to act as a Buffer

CH 3. and CH. 4.1 12/28/14 7:43 PM
SECTION 3.1 WHAT KINDS OF MOLECULES CHARACTERIZE LIVING THINGS? PG. 88
POLYMERS: constructed by covalent bonding of smaller molec monomers
MONOMERS: smaller units that covalent bond to form large molec
MACROMOLECULES: polymers w/ molec weights exceeding 1,000
proteins: amino acids - Carbs: monosac
Nucleic Acid: nucleotides - lipids (noncovalent bonding)
FUNCTIONAL GROUPS GIVE SPECIFIC PROPERTIES TO BIOLOGICAL MOLECULES
FUNCTIONAL GROUPS: occur frequently in bio molec; has specific chem properties, and when attached to
larger molec, confers those prop to it
PROPERTIES:
1. Polarity: C-O, N-H, P-O bonds most polar
2. Hydrophobic or charged (ionic)
ISOMERS HAVE DIFFERENT ARRANGEMENTS OF THE SAME ATOMS PG. 89
ISOMERS: molec that have the same chem formula but arranged diff
STRUCTUREAL ISOMERS: diff in how atoms r joined together
CIS-TRANS ISOMERS: involved double bond btw carbon atms
cis: groups/atoms bonded to C at same side
trans: groups/atoms bonded to C at oppo sides
OPTICAL ISOMERS: when a C atoms has 4 diff atoms or groups of atoms attached to it
allows for two diff ways of making attachments (mirror image)
C is called asymmetric carbon
THE STRUCTURES OF MACROMOLECULES REFLECT THEIR FUNCTIONS
proteins in apple tree and human body prob have same funct
reflects biochemistry unity
functions of 4 biochem molec related to their 3-D shapes and to seq and chem properties of their monomers.
Some are compact = water-soluable and capable of intimate ineractions w/ other molec
Proteins and Carbs = long, fibrous struct that provide strength and rigidity to cells and tissues
MOST MARCROMOLECULES ARE FORMED BY CONDENSATION AND BROKEN DOWN BY
HYDROLYSIS PG. 90
CONDENSATION REACTIONS: dehydration synthesis, how polymers are formed through loss of water
result in the formation of covalent bonds btw monomers
needs water and E
HYDROLYSIS REACTIONS: breakdown of polymers and absorb of water
water reacts w/ covalent bonds that link monomers together and splits into H+ and OH-

SECTION 3.2 WHAT ARE THE CHEMICAL STRUCTURES AND FUNCTIONS OF PROTEINS? PG. 90
PROTEINS: polymers made up of 20 amino acids (diff proportions&sequences)
Ex. small proteins (insulin) large (muscle protein)
POLYPEPTIDE CHAINS: branched (linear) polymers of covalently linked amino acids.
AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS PG. 91
AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS PG. 91
AMINO ACID: has Carboxyl and Amino funct group, alpha Carbon attached to a H, and side chain
alpha C is asymmetrical cuze bonded to 4 diff atoms / groups of atoms
o therefore AMINO ACIDS can exist as OPTICAL ISOMERS called D-amino aicds or L-
amino acids (right D and left L)
in pH 7: Carboxyl and Amino groups are ionized:
o

Amino acids are acids and bases

SPECIAL CASES:
o Cysteine: has SH group react w/ another cysteine to form a covalent bond (disulfide bridge)
o Glycine: has single H atom, small enough to fit into tight corners in interior protein molec
o Proline: modified amino group that lacks H and forms covalent bond w/ hydrocarbon side
chain = ring structure
Limits both H bonding ability and ability to rotate around alpha Carbon
Found where a protein bends or loops
SIDE CHAIN (R GROUP): group of elements or groups that is diff for every amino acid
PEPTIDE LINKAGES FORM THE BACKBONE OF A PROTEIN
PEPTIDE LINKAGE: carboxyl groups on 1 amino rxts w/ amino group of another (thru condensation rxn)
C-N link that form thru condensation: are not free to rotate fully = limits folding of polypeptide chain.
O double bonded to C carries slight neg charge wheras H bound to nitrogen founds slight pos charge
o Asymmetry of amino acid leads to formation of bond btw C-N

THE PRIMARY STRUCTURE OF A PROTEIN IS ITS AMINO ACID SEQUENCE PG. 93

PRIMARY STRUCTURE: backbone of polypeptide chain consists of repeating seq N-C-C-N-C-C
initial seq determines final structure shape
THE SECONDARY STRUCTURE OF A PROTEIN REQUIRES HYDROGEN BONDING
SECONDARY STRUCTURE: regular, repeated spatial patterns in diff regions of polypeptide chain
ALPHA HELIX: right handed coil that turns in same direction as standard wood screw
R groups extend outward from polypep backbone of helix
Coiling = H bonds that form btw + partial H from N-H and partial O from C=O, pattern stabilizes
coil
BETA (PLEATED) SHEET: formed from 2 or more polypep chains that are almost completely extended and
aligned
stabilized by H bonds btw N-H and C=O groups of two diff amino acids
o can form btw separate polypep chains or btw diff regions of single polypeptide chain
THE TERTIARY STRUCTURE OF A PROTEIN IS FORMED BY BENDING AND FOLDING PG. 94
TERTIARY STRUCTURE: polypep chain bent @ specific sites and folded back and forth
definition 3-D shape w/ buried interior as well as surface thats exposed
hydrophilic funct groups on outside to rxt w/ other molec
interact btw diff R groups and btw R groups and environ deter tertiary struct
o covalent disul bridges btw specific cysteine side chains hold folded polypep in place
o H bonds btw side chains also stabilize fold in proteins
o Hydrophobic side chains aggregate together in the interior
Interactions stabilized by van der Waals forces
o Ionic attractions form btw positively and negatively charged side chains form salt bridges btw
amino acids (can be near surface or inside)
Occur btw positively and negatively charged ions

- since secondary and tertiary struct derives from primary struct, if protein slowly heated only weak interactions
disrupted and second and terit struct break down = Denatured
- in some cases, protein can return to normal but it depends on amount is was heated
THE QUATERNARY STRUCTURE OF A PROTEIN CONSISTS OF SUBUNITS PG. 96
QUATENARY STRUCTURE: many funct proteins contain 2 or more polypep chains (subunits) each folded into
its own unique tertiary struct; when they join together = quaternary structure
example of hemoglobin look up! Pg. 96
SHAPE AND SURFACE CHEMISTRY CONTRIBUTE TO PROTEIN FUNCTION
SHAPE: when things bind to protein, protein adjusts its shape a little bit = induced fit
CHEMISTRY: exposed R groups on surface of a protein permit chm interactions w/ other substances
 CHEMISTRY: exposed R groups on surface of a protein permit chm interactions w/ other substances
ionic, hydrophobic, or hydrogen bonding
ENVRIONMENTAL CONDITIONS AFFECT PROTEIN STRUCTURE PG. 98
Increase in Temp: more rapid molec movements, break H bonds and hdyropho interactions
change in pH change patter of ionizations of exposed carboxyl and amino groups in R groups of amino acids
high concentrations of polar substances can disrupt H bonding thats crucial to protein struct
nonpolar sub may also disrupt where hydrophobic interactions are essential to maintain the structure
PROTEIN SHAPES CAN CHANGE
shapes of proteins change if they undergo covalent modifications
proteins interact w/ other molec and may form weak interactions
proteins undergo convalent modifications: after its made it can be modified by covalent bonding of a
chem group to side chain or 1 or more of its amino acids = change shape and funct of protein
MOLECULAR CHAPERONES HELP SHAPE PROTEINS PG. 99
CHAPERONES: special proteins that help protect the 3-D struct of other proteins
has cage like structure that pulls in polypep and causes it to fold into correct shape and then releases it
NEEDED FOR TWO REASONS:
1. just after protein is made: before it even folded, other things can react w/ it and change shape and funct
2. following denaturation: before it can refold it may present a surface that binds to wrong molec

SECTION 3.3 WHAT ARE THE CHEMICAL STRUCTURES AND FUNCTIONS OF

CARBOHYDRATES? PG. 99
CARBOHYDRATES: make up large groups of molec that all have similar atomic compositions but differ in size,
chec properties, and bio functs
CnH2nOn
o Carbs r source of E
o Used to transport stored E w/in complex orgs
o Serve as carbon skeletons that can be rearranged to form new molec
MONOSACCHARIDES: ex. glucose monomers
DISACCHARIDES: consist of two monomers ex. sucrose glucose and fructose
OLIGOSACCHARIDES: made up of several 3-20 monosaccharides
POLYSACCHARIDES: polymers made up of hundreds or thousands of monosaccharides ex. starch, glycogen,
and cellulose
MONOSACCHARIDES ARE SIMPLE SUGARS PG. 100
GLUCOSE: monosaccharide, blood sugar, used to transp E in humans
Exists in chains and ring forms; ring dominates; alpha and beta ring
Some monosaccs are structural isomers
PENTOSES: are 5-C sugars; two pentoses imp to bio life
Deoxyribose and ribose sugar not isomers but one is missing an O
HEXOSES: group of structural isomers w/ formular C6H12O6 (glucose, fructose, mannose, and galactose
GLYCOSIDIC LINKAGES BOND MONOSACCHARIDES PG. 101
GLYCOSIDIC LINKAGES: condensation rxns that bond monosaccs together
Oligosaccs have additional funct groups that give them special prop
Found covalently bonded to proteins and lipids on outer cell surface (diff human blood groups get
specifities from oligosac chains)
POLYSACCHARIDES STORE ENERGY AND PROVIDE STRUCTURAL MATERIALS
Polysacs are not necessarily linear chains of monomers
STARCHES: comprise a family of gaint molecules of broadly similar struct
Ex. starches but diff starches can be distinguished by the amount of branching that occurs at carbons 1
and 6
Starch is principal E storage comp of plants; readily binds water; when no water, H bonds form btw
unbranched polysac chains
GLYCOGEN: is a water-insoluble, highly branched polymer of glucose
Used to sotre glucose in liver and muscles and E storage comp.
CELLULOSE: most abundant organic compound on Earth; posacc of glucose
Its monosacc are connected by beta rather that by alpha glycosidic linkates
Great structural material (than glycogen); can w/ harsh environ
CHEMICALLY MODIFIED CARBOHYDRATES CONTAIN ADDITIONAL FUNCTIONAL GROUPS PG.
103
some carbs are chemically modified by oxidation-reduction rxns or by addition of funct groups (ex. phosphate,
amino, N-acetyl groups)
When amino group substitues for OH group amino sugars (ex. glucosamine)
SECTION 3.4 WHAT ARE THE CHEMICAL STRUCTURES AND FUNCTIONS OF LIPIDS PG. 104
LIPIDS: hydrocarbons that are insoluable in water (many nonpolar covalent onds)
Fats and oils store E
Phospholipids play imp structural roles in cell membranes
Carotenoids and chlorophylls help plants capture light E
Steroids and modified fatty acids play regulatory roles as hormones and vitamins
 Steroids and modified fatty acids play regulatory roles as hormones and vitamins
Fat in animal bodies serves as thermal insulation
Lipid coating around nerves provides electrical insulation
Oil or wax on the usrfaces of skin, fur, feathers, and leaves repels water and prevents excessive
evaporation of water from terrestrial animals and plants
FATS AND OILS ARE TRIGLYCERIDES
TRIGLYCERIDES: simple lipids (fats and oils)
FATS: triglycerides that are solid @ room temp (20C)
OILS: triglycerides that are liquid @ room temp (20C)
GLYCEROL: small molecule w/ three hydroxyl (-OH) groups (thus its an alcohol)
FATTY ACIDS: long nonpolar hydrocarbon chain and an acidic polar carboxyl group (-COOH)
ESTER LINKAGE: carboxyl group of fatty acid bonds w/ hydroxyl group of glycerol = covalent bond & release
of water
SATURATED FATTY ACIDS: all bonds btw carbon atoms in hydrocarbon are single bonds; usually solid @
room temp
Can be packed tightly
UNSATURATED FATTY ACIDS: the hydrocarbon chain contains one or more double bonds; are liquid @ room
temp
Causes kinks in the chain and doesnt let it pack tightly
Kinks affect fluidity and melting points of lipids
PHOSPHOLIPIDS FORM BIOLOGICAL MEMBRANES PG. 105
AMPHIPATHIC: when a mole has two opposing chemical properties
Ex. fatty acids has polar head (COOH ionizes to COO-) and hydrophobic tail
When fatty acids are bonded to glycerol, carboxyl groups r incorp into ester bonds and result in
triglyceride thats hydrophobic
PHOSPHOLIPIDS: contain fatty acids bound to glycerol by ester linkages but one of several phosphate-
containing compounds replaces one of the fatty acids, giving phospholipids amphipathic properties
BILAYER: a sheet two molecules thick w/ water excluded from the core
PHOSPHOLIPID BILAYER: what membrane in biological organisms are
SOME LIPIDS HAVE ROLES IN ENERGY CONVERSION, REGULATION, AND PROTECTION
CAROTENOIDS: responsible for colors of carrots, tomatoes, pumpkins, egg yoks, and butter
STEROIDS: fam of organic comp, multiple rings, linked thru shared carbons
Ex. cholesterol impo constituent of membranes (maintains solidity)
VITAMINS: small molec that arent synthesized by human body or synthe in inadequate amounts and so must be
acquired from the diet
Vitamin A from green and yellow vegetables, Vitamin D, E, and K are also lipids
WAXES: repel water and keep hair and feathers pliable; also on leave slows evaporation of water and excludes
pathogens; hydrophobic and plastic (malleable @ room temp)
birds and mammals secrete waxy coating onto their hair/feathers;

CHAPTER 4
SECTION 4.1 WHAT ARE THE CHEMICAL STRUCTURES AND FUNCTIONS OF NUCLEIC ACIDS?
PG. 111
NUCLEIC ACIDS: polymers specialized for the storage, transmission, and use of genetic info
DNA: macromolecule that encodes hereditary info and passes it from generation to generation
RNA: info from DNA is translated into RNA to make amino acids
NUCLEOTIDES ARE THE BUILDING BLOCKS OF NUCLEIC ACIDS
NUCLEOTIDE: consists of three components: nitrogen base, pentose sugar, and one to three phosphate groups
NUCLEOSIDES: molec consisting of a pentose sugar and a nitrogenous base (BUT NO Phosphate group)
nucleic acid = nucleoside monophosphates
PYRIMIDINE: six-membrane single-ring structure
PURINE: fused double-ring structure (the girls are pureines)
DEXOYRIBOSE: differs from ribose(absence of one O)
PHOSPHODIESTER LINKAGE: when pentose sugar in last nuc bonds to phosphate in another group
phosphate on the new nucleotide is attached to 5-carbon atom of its sugar (linkage occurs btw it and
the 3-carbon on the last sugar of existing chain)
nucleic acids grow in 5-to-3 direction
oligonucleotides: relatively short, w/ about 20 nucleotide monomers; include RNA molecules that
funct as primers to begin duplication of DNA
BASE PAIRING OCCURS IN BOTH DNA AND RNA PG. 111
adenine, cytosine, guanine, and (thymine DNA only) (uracil RNA only)
COMPLEMENTARY BASE PAIRING: A-T(U), G-C; G-C 3 H-bonds
RNA: single-stranded, base pairing occus btw diff regions of molecule; complementary H-bonding determins 3-D
shapesof some RNA molec.
DNA: double-stranded, consists of two separate polynucleotide strans of same length held together by H bonds
btw base pairs; DNA consistent
DOUBLE HELIX: two polynucleotide strands form a ladder that twists;
 DOUBLE HELIX: two polynucleotide strands form a ladder that twists;
sugar phosphate groups form sides of the ladder and the bases w/ their H bonds form rungs on
inside
DNA CARRIES INFORMATION AND IS EXPRESSED THROUGH RNA PG. 113
DNA REPLICATION: DONE BY POLYMERIZATION USING AN EXISTING STRAND AS A BASE-
PAIRING TEMPLATE
TRANSCRIPTION: DNA sequences can be copied into RNA;
TRANSLATION: nucleotide sequence in RNA can be used to specify seq of amino acids in polypeptide chain
GENE EXPRESSION: process of transcription and translation
DNA: transcripted from 5-3
GENOME: complete set of DNA in a living organism
GENES: sequences of DNA that are transcribed into RNA
THE DNA BASE SEQUENCE REVEALS EVOLUTIONARY RELATIONSHIPS PG. 114
closely related species have more in common in their DNA
DNA sequencing revealed close rela btw unexpected species
NUCLEOTIDES HAVE OTHER IMPORTANT ROLES
ATP (modified nucleotide) acts as E tranducer in biochem rxns
GTP (guanosine triphosphate) E source, esp in protein synthesis
transfers info from environ to cells
cAMP (cyclic adenosine monophosphate) special nuc w/ additional bond btw sugar and phosphate (essential for
actions of hormones and transmission of info by nervous system)
play role as carriers in synthesis and breakdown of carbs and lipids

CH. 8 pg. 192 12/28/14 7:43 PM
CH. 8
**How did Detergents arise?
- Otto Rohm came up with the idea of using digestive enzymes to remove stains; STAIN: nonpolar stuff stuck to
nonpolar stuff
IDEA: make stains soluble > enzymes hydrolyzed nonpolar stains
PROBLEMS: grow enzymes in large doses, use diff enzymes to break down diff things
o Lipases for lipids, amylases for starch
WHAT PHYSICAL PRINCIPLES UNDERLIE BIOLOGICAL ENERGY TRANSFORMATIONS? PG. 193
CHEMICAL REACTION: occurs when atoms have sufficient E to combine/change bonding partners
REACTANTS: molec/comp that r present in beginning of rxn
PRODUCTS: molec/com thats result of rxn
METABOLISM: sum total of all chem rxn occurring in bio sys @ given time
o Metabolic rxn involvs E changes
o Energy is capacity to do work or capacity for change
THERE ARE TWO BASIC TYPES OF ENERGY
POTENTIAL E: E of state or position (stored E); ex. in bonds
KINETIC E: E of movement; does work, makes things change; ex. heat
E can be converted
ex. reading book: Light E> Chem E in eye> electrical E in brain> Kinetic E muscle turning pg
THERE ARE TWO BASIC TYPES OF METABOLISM
ANABOLIC RXNS: link simple molec to form more complex molec; builds
require E input; E captured in chem bonds; ex. synthesis
o captured E stored as potential E
CATABOLIC RXNS: break down complex molec into simpler ones;
release E stored in bonds; ex. hydrolysis
two types of rxns linked; E relased in cata used for ana rxn
LAWS OF THERMODYNAMICS: derived from studies of fund physical prop of E and how it interacts w/
matter; applied to living systems
THE FIRST LAW OF THERMODYNAMICS: ENERGY IS NEITHER CREATED NOR DESTROYED PG.
194
First law: in any E conversion, E is neither created nor destroyed
total E before and after rxn same;
ex. potential E in carbs and lipids > potential E in ATP > kinetic E to do work (mucle
contraction/protein synthesis)
THE SECOND LAW OF THERMODYNAMICS: DISORDER TENDS TO INCREASE
Second law: when E is converted, some E becomes unavailable to do work; released E associated w/ disorder
= process not 100% efficient
disorder = randomness due to thermal motion of part (E so dispersed, its unstable)
ENTROPY (S): measure of disorder in a system (living thing, cell, etc)
takes E to impose order in system; applies to all rxns not just bio ones
ENTHALPY (H): total E in system
FREE E (G): usable E that can do work
1. TOTAL E = USABLE E + UNUSABLE E = ENTHALPY + UNUSABLE E
2. UNUSABLE E = ENTROPY(S) ABSOULTE TEMP(T)
3. H = G + TS
we cannot measure G, H, S absolutely but can measure change in each @ constant temp
4. change in free E:
5. at constant temp:
G < 0 = free E relased; G >0 = free E consumed

prod more disorder than react; ex. protein hydrolysis amino acids move more freely than proteins do
nd
2 law applied to bio systems:
10 kg of bio matter needed to produced 1 kg of human tissue = so much E lost to entropy
also, it takes a lot of E for our metabolic activities which upholds our order
o see the 2 components of 2nd law r upheld in our bodies
CHEMICAL RXNS RELEASE OR CONSUME E PG. 195
EXERGONIC RXNS: rxns that release free E (-G) ex. catabolic
ENDERGONIC RXNS: rxns that absorb free E (G); ex. anabolic
as A>B in rxn, it can go back as well; [A or B] favors the direction of the rxn
CHEMICAL EQUILIBRIUM: balance btw forward and revers rxn at certain [] of A and B @ which G = 0
CHEMICAL EQUILIBRIUM AND FREE ENERGY ARE RELATED PG. 196
All rxns have equi point; not always completed
G for all rxn related to point of equi
if Equi point farther toward completion, more free E released
G also depends on: [] of react and prod, temp, pressure, pH of solution
standard lab condition = 25C, 1 atm, 1M concentration of solutes, pH 7
large + G = rxn hardly proceeds to right (A>B)
makes sense, it means, its an anabolic rxn that takes a LOT of E
if [B] large then, rxn flow to left and equi point when B almost gone
G near 0 = free E of react and prod almost same
SECTION 8.2 WHAT IS THE ROLE OF ATP IN BIOCHEMICAL ENERGETICS? PG. 197
USES OF ATP
1. ATP needed to capture and transfer E; free E released by exergonic rxn changed ADP + inorganic phosphate
(HPO4 2-) into ATP
to release E, ATP is hydrolyzed
 to release E, ATP is hydrolyzed
2. ATP can be converted into a building block for nucleic acids
ATP releases large E when hydrolyzed
ATP can phosphorylate (donate P groups to) diff molec, which then gain E that was stored in ATP
ATP HYDROLYSIS RELEASES ENERGY
ATP: nitrogenous base adenine bonded to ribose attached to 3 P groups

exergonic rxn; G in stand lab cond = -7.3 kcal/mol = -30kJ/mol
in cellular cond G can be -14 kcal/mol
both correct but in diff cond
ATP can be hydrolyzed into: ADP & P group, adenosine monophosphate (AMP) & a pyrophosphate ion (P2O7 4-)
P groups charge so takes a lot of E to create the bond in ATP
This bond P~O bond (phosphoric acid anhydride bond) high E
o Higher E than in OH bond result of hydrolysis
BIOLMINESCENCE PG. 198
BIOLUMINESCENCE: production of light by living org; endergonic rxn driven by ATP hydro

ATP COUPLES EXERGONIC AND ENDERGONIC RXNS

for Euk and Prok, Cellular Resp (exergonic) > E released > ATP formed > fuel for ender rxn = metabolism
overall G for coupled rxns is neg (exergonic which is y they r still occurring)
ex. glucose 6-phosphate synthesized (1st step in catabolism of glucose)

avg person produces 40 kg of ATP per day!

SUMMARY
8.1
st
1. 1 TLaw: E neither created or destroyed
nd
2. 2 TLaw: for any E conversion, Entropy increases (randomness inc or disorder)
3. Exergonic (G -); all forms of E can be converted
4. Metabolism is the total of all rxns happenin in bod @ given time
5. Enthalpy = total E in system (H); G = free E; S = Entropy
6. UNUSABLE E = ENTROPY(S) ABSOULTE TEMP(T)
7. H = G + TS
8.2
1. ATP stores E in P~O (phosphoric acid anhydride bond )
2. Exergonic rxn (ATP > ADP + Pi) used to power Endergonic Rxn (catabolism of glucose or protein synthesis or
transport etc)

Ch. 9 pg. 213 12/28/14 7:43 PM
SECTION 9.1 HOW DOES GLUCOSE OXIDATION RELEASE CHEMICAL ENERGY? PG. 214
E released when ATP broken (exer) and fuels ener rxns
st
glucose fuel for most animals, also fats and proteins can be used but must 1 be converted to glucose
some prokaryotes (bacteria and archaea) get E from metal ions, hydrogen sulfide, and ammonia
* thru oxidation E obtained from glucose
1. Complex chem transformation occurs in series of separate rxns that form metabolic pathway
2. Each rxn catalyzed by specific enzyme
3. Many metab pathways r similar in all orgs from bacteria to humans
3. Many metab pathways r similar in all orgs from bacteria to humans
4. In euk, many metab pathways are compartmentalized, certain rxns occurring inside specific organelles
5. Some key enzymes in each metab pathway can be inhibited or activated to alter rate of pathway
CELLS TRAP FREE ENERGY WHILE METABOLIZING GLUCOSE
if glucose burned, rxts w/ O2 = CO2 + H2O + E(heat) (oxidation-reduction rxn);
glucose loses electrons; oxygen gains (reduced)
released E stored in P-O bond of ATP
standard free E change results from complete conversion of glucose

GLYCOLYSIS: begins glucose catabolism; converted to two molec of 3-C product Pyruvate and little E released
PYRUVATE: 3-C product released in 1st step of glycolysis
ANAEROBIC: metabolic process that doesnt require O2 to occur; small E production
CELLULAR RESPIRATION: uses O2 from environ; pyruvate converted to 3 CO2 molec by pyruvate oxidation,
citric acid cycle, and electron transport system
AEROBIC: uses O2 to run metabolic pathways
FERMENTATION: anaerobic; converts Pyruvic acid into lactic acid or ethyl alcohol; small E production
REDOX REACTIONS TRANSFER ELECTRONS AND ENERGY PG. 215
OXIDATION-REDUCTION RXN: 1 substance transfers e- to another sub
REDUCTION: gain of 1 or more e- by an atom, ion, or molec
OXIDATION: loss of 1 or more e-
ex. glucose = reducing agent (e- donor); O2 oxi agent (e- acceptor)
transfer of e- associated w/ transfer of H ions (H = H+ + e-)
when molec looses H atoms it becomes oxidized
more oxideized a carbon atom is, the less its stored free energy
THE COENZYME NAD+ IS A KEY ELECTRON CARRIER IN REDOX RXS
coenzymes, small molec that assist in enzyme-catalyzed rxs
ADP acts as a coenzyme as it packs E into ATP
NAD+ coenzyme that are as an e- carrier in redox rxns

Reduction rxn: NAD+ + H+ + 2e- > NADH

 Reduction rxn: NAD+ + H+ + 2e- > NADH
Oxidizing rxn: NADH + H+ + O2 > NAD+ + H2O (highly exergonic)
NADH larger carrier of free energy (more than ATP)
FAD also electron carrier
AN OVERVIEW: HARVESTING ENERGY FROM GLUCOSE PG. 216
euks and proks can harvest E from glucose by combining diff combinations
Aerobic cond: O2 is final e- acceptor, 4 pathways operate
glycolysis > pyruvate oxidation > citric acid cycle (krebs)> electron transport(ATP
synthesis/respiratory chain)
in euks and many proks: pyruvate oxi, citric acid cyc, and resp chain dont funct in anaerobic conds
usually pyruvate from glycolysis metab by fermentation or rarely thru the respiratory chain

SECTION 9.2 WHAT ARE THE AEROBIC PATHWAYS OF GLUCOSE CATABOLISM? PG. 217
Aerobic: glycose > 2 3-C pyruvate (py oxi and citric acid cyc) NAD+ (reduct of e- carrier) <~> (CO2) and
NADH(resp chain) > ATP
In resp chain, redox rxn = oxidative phosphorylation of ADP by ATP synthase
IN GLYCOLYSIS, GLUCOSE IS PARTIALLY OXIDIZED AND SOME ENERGY IS RELASED
in Cytosol; 10 enzyme-catalyzed rxns
INVEST: 2 ATP
DURING: covalent bonds btw C and H atoms oxidized and releases E
PRODUCT: 2 pyruvate (acid), 4 ATP, and 2 NADH(reduced); (net: 2 ATP)
Glucose > 2 3-C sugar > oxidized into Pyruvate
G-3-P is oxidized
PYRUVATE OXIDATION LNKS GLYCOLYSIS AND THE CITRIC ACID CYCLE PG. 218
pyruvate transported into mitochondrial matrix
Oxidation of pyruvate to a 2-C acetate molecule and CO2
Binds to coenzyme A to make:
ACETYL COENZYME A (ACETYL COA): 2-C acetate bound to CoeA
CoA is used in other rxns as a carrier of acetyl group (H3CC=)
Main role donate its acetyl group to 4-C oxaloacetate = 6-C citrate
o Initiates citric acid cycle
FORMATION of ACETYL COA: exergonic
Links glycolysis and further oxidative rxns
catalyzed by pyruvate dehydrogenase complex
THE CITRIC ACID CYCLE COMPLETES THE OXIDATION OF GLUCOSE TO CO2
Acetyl CoA starting point citric acid cycle;
TOTAL: 8 rxns to oxidzie 2-C acetyl group to 2 CO2
REACTANTS: oxaloacetate and Acetyl CoA = citrate, water
Free energy: captured by GDP and NAD+ and FAD
PRODUCT (of 1 pyruvate): 3 NADH, 1 FADH2, 1 GTP (changes into ATP and GDP)
oxaloacetate regenerated at last step
for 1 glucose > 2 pyruvate = 2 turns of cycle
GLUCOSE OXIDATION (glycolysis to citric acid cycle):
- 6 CO2, 10 NADH, 2 FADH2, 4 ATP
PYRUVATE OXIDATION AND THE CITRIC ACID CYCLE ARE REGULATED BY THE
CONCENTRATIONS OF STARTING MATERIALS PG. 219
if present O2 takes electrons released by oxidation of NADH and FADH2 and is reduced to H2O
O2 necessary for pyruvate oxidation and citric acid cycle to continue
- electrons not directly passed to O2

SECTION 9.3 HOW DOES OXIDATION PHOSPHORYLATION FORM ATP?

OXIDATION PHOSPHORYLATION: process of ATP synthesis resulting from reoxi of electron carriers in
presence of O2
RESPIRATORY CHAIN: electrons from NADH and FADH2 pass thru this; its a series of membrane-associated
electron carriers
flow of e- thrus this pathway = active transport of protons out of mitochondrial matrix and across inner
mitochondrial membrane
creates proton [] gradient
ATP SYNTHASE: channel protein that synthesis ATP by physically changing; it uses the proton gradient across
the membrane to be powered
Chemiosmosis: use of proton gradient to get work done
since protons cant travel across membrane, the ATP synthase is the only way for them to cross to
reach equilibrium
* Why cant NADH be oxidized and harvested directly?
Too explosive and no efficient way to harvest the E like that
o No single rxn is soo endergonic that it can use it all up
THE RESPIRATORY CHAIN TRANSFERS ELCTRONS AND PROTONS AND RELEASES ENERGY PG.
220

PROTON DIFFUSION IS OCUPLED TO ATP SYNTHESIS PG. 221

PROTON-MOTIVE FORCE: uses H+ concentration across membrane as an E source
CHEMIOSMOSIS: coupling proton motive force wi atp synthesis
- THE CHEMIOSMOTIC MECHANISM FOR ATP SYNTHESIS
- EXPERIMENTAL DEMOSTRATION OF CHEMIOSMOSIS
- HOW ATP SYNTHASE WORKS: A MOLECULAR MOTOR
- ELECTRON TRANSPORT CAN BE TOXIC
SOME MICROORGANISMS USE NON-O2 ELECTRON ACCEPTORS PG. 224
ANAEROBIC RESPIRATION:

SECTION 9.4 HOW IS ENERGY HARVESTED FROM GLUCOSE IN THE ABSENCE OF OXYGEN? PG.
225
Fermentation also occurs in cytoplasm
All rely on regenerating NAD+s so that glycolysis can continue
LACTIC ACID FERMENTATION: pyruvate serves as electron acceptor and end product is lactate
In microorganism and complex organisms (plants and vertebrates)
When not enough O2 break down glycogen
Build up of H+ = cell becomes more acidic
Lactate dehydrogenase works both ways can change lactate in to pyruvate > CO2 in aerobic resp
ALCOHOLIC FERMENTATION: in yeast cells and some plant cells (in anaerobic cond); process req two
enzymes, pyruvate decarboxylase and alcohol dehydrogenase (metab pyruvate to ethanol)
Reversible; final product = ETHANOL
Recycles NAD+ to cont glycolysis
Very little E released and so orgs are small and grow slowly
CELLULAR RESPIRATION YEILDS MUCH MORE ENERGY THAN FERMENTAION PG. 226
Net E from gly&ferm: 2 ATP
Fermentation only partially oxidizes glucose > end products of fermentation have more E than wat
was harvested
Cellular resp yields 32 ATP
THE YIELD OF ATP IS REDUCED BY THE IMPERMEABILITY OF MITOCHONDRIA TO NADH
toll of 1 ATP must be paid for each NADH molec thats produced in glycolysis and must be shuttled into mitoc
matrix (so the net yield is 30 ATP)
NADH shuttle systems: trans e- cap by glycolysis onto substrates that r capable of movement across mitoc
membrane
 membrane
SECTION 9.5 HOW ARE METABOLIC PATHWAYS INTERRELATED AND REGULATED? PG. 227
CATABOLISM AND ANABOLISM ARE LINKED
- CATABOLIC INTERCONVERSIONS
- ANABOLIC INTERCONVERSIONS
GLYCONEOGENSIS:
CATABOLISM AND ANABOLISM ARE INTEGRATED PG. 228

METABOLIC PATHWAYS ARE REGULATED SYSTEMS PG. 229

CH. 10 Photosynthesis 12/28/14 7:43 PM
Photosynthesis two parts:
Occur in Chloroplast:
- Light rxns: convert light E into Chemical E as ATP and reduced e- carrier NADPH (acts as reducing agent in
photosynthesis)
- Light-independent (carbon fixation/dark) rxns: dont use light but use ATP and NADPH made by light rxns and
CO2 to make carbs
- O2 produced in photosynthesis comes from H2O NOT CO2
Photochemistry:
light is:
1- electromagnetic radiation: propagated in waves, E is inversely proportional to Wavelength (shorter wave =
greater E)
2- Photon: have no mass but acts like a particle
- photos are absorbed by molec to harvest their E for bio processes
* receptors only absorb specific wavelengths
* Photon maybe: reflected (scattered), transmitted (pass thru), or absorbed (E added) by molecule
when E absorbed, moles e- gets exicted = unstable
goes from ground state to excited state
o of ground state and excited state = E of photon
Photobiology:
Pigments: molec that absorb wavelengths in visible spectrum
o Ex. Chlorophyll absorbs blue and red light, rest scattered (green)
Absorption spectrum: result of plotting light absorbed by purified pigment against wavelength for
that pigment
Action Spectrum: plot of rate of photosynthesis carried out by org against wavelength of light to
which its exposed.
o Can be determined by:
o 1. Org in closed container
o 2. exposure to specific wavelength light for period of time
o 3. measure rate of photosyn by amount of O2 released
o 4. repeat w/ diff wavelength light
LIGHT-DEPENDENT REACTIONS:
- in thylakoid membrane
- Chlorophyll a = major pigment
complex ring structure w/ magnesium at center (e- donor)
long hydrocarbon tail anchors I to proteins w/in large multi-protein complex called photosystem
light-harvesting complexes (antenna systems): when chlorophylls a,b,c or carotenoids/phycobilins are arranged
into 1 system to harvest light
Reaction center: has multiple light-harvest complexes
PROCESS: light E >light-harvest center->rxn center(where chlorophyll a participates in redox rxns) = light
E -> chem E
- Accessory pigments: ex. chlorophyll a and other pigment that absorb light; diff orgs have diff combinations of
accessory pigments

HOW PHOTOSYSTEMS WORK: pg. 239

- they are in THYLAKOID MEMBRANE of Choloplasts
1. Pigment absorbs E and starts to rapidly head back to ground state
2. E released by this pigment is absorbed by adjacent pigments
3. occurs till u get to chlorophyll a (Chl) molec at REACTION CENTER
4. Chl becomes exicted (chl*)
5. ^THIS IS WHEN Light E CONVERTED TO Chem E
6. exicted enough to give up an e- to chemical acceptor
Chl* + acceptor > Chl+ + acceptor-
7. Chlorophyll oxidized and acceptor mole is reduced

REDUCTION LEADS TO ATP AND NADPH formation: pg. 239

- e- passed down from 1 carrier to another in E downhill series of redox rxns
- Thylakoid membrane has similar ETC like respiratory chain in mitochondria
- ATP formed thru chemiosmosis
- Final e- acceptor = NADPH
- NON-CYCLIC ELETRON TRANSPORT: uses E from light to generate NADPH and ATP. Uses two
photosystems:
Photosys 1: has P700 chlorophylls at rxn center; best absorbs light at 700 nm and passes excited e-
(thru intermediate molec) to NADP+ > NADPH
Photosys 2: P680 chlorophylls at its rxn center, oxidizes water molec and passes its energized e- thru
series of carriers to produce ATP

1. Photosystem 2:
After excited chlorophyll in rxn center gives up e- it grabs another one from water by splitting the H-O-H
bonds
energetic e- passed thru series of membrane-bounds to a final acceptor @ lower E level
2. Photosystem 1: pg. 240
 2. Photosystem 1: pg. 240
exicted e- from Chl* reduces acceptor;
grabs e- for itself BUT from last carrier in ETC
^ links the two photosystems together
pass thru and reduces NADP+ > NADPH

Cyclic Electron Transport: only uses photosystem 1 and the ET system to produce ATP but no NADPH
cyclic beause e- passed from excited chlorophyll and recycles back to same chlorophyll
Photophosphorylation: similar to chemiosmosis; in chloroplastwhen ETC is coupled to transport of protons
across thylakoid membrane
lumen becomes acidic w/ respect to the stroma
charged across thylakoid membrane
then pass back across ATP synthases

10.3 pg. 241

enzymes that catalyze CO2 fixations dissolved in stroma of cholop (where rxns occur)
they use E in ATP and NADPHA to reduce CO2 to carbs
CO2 fixations almost only occurs in the light
Calvin Cycle: CO2 attaches to 5-C molec (RuBP), broken down, product 2 3-C product (G3P) formed, and RuBP
regenerated
catalyzed by Rubisco enzyme - most abundant protein in the world
GO bACK AND READ PG. 243
LIGHT STIMULATES CALVIN CYCLE pg. 244
light-induced pH changes in stroma (when protons pumped into thylakoid lumen) activate Calvin cycle enzymes
(ex. when pH increases to 7,8, rubisco is activated)
light-induced ET reduces disulfide bridges in 4 Calvin cycle enzymes and activates them
Pentose Pathway: parallel 2 glycolysis; oxidizes glucose; produces pentose

CH. 5.1-5.3 Organelles 12/28/14 7:43 PM
5.1 pg.
Cell Theory: 1. Cells r fundamental units of life 2. All living orgs are compo of cells 3. All cells come
Surface are to volume ratio: surface area doesnt increase at the same rate as volume, very important because it
affects organisms survival
chemical activity carried out by cell proportional to volume; but surface area of the cell determines
amount of substances that can enter into cell
Plasma Membrane: very thin structure forms the outer surface of every cell; lipid bilayer w/ proteins embedded
into membrane and other molec
selectively permeable barrier
allows cell to maintain a more or less constant internal environment
Prokaryotes: no organelles, or nucleus but have plasma membrane
Eukaryotes: has membrane bound organelles (protists, plants, fungi, and animals)
Nucleus: most of cells DNA is located and where gene expression begins, division of labor

5.2 pg. 130

Nucleoid: region where DNA is located
Cytoplasm: enclosed in plasma membrane, liquid component (cytosol) and insoluble filaments and particles
Cytosol: mostly water and dissolved ions, small mole and soluble macromolecules
Ribosomes: complexes of RNA makes proteins from RNA
FEATURES IN SOME PROKARYOTES: pg. 131
Cell Wall: outside plasma membrane, structure, rigidity, shape,
in bacteria contains peptidoglycan
or Outer membrane encloses peptidoglycan layer not a major barrier to movement of molecules
across it
or Capsule slimy layer of polysaccharides; protect bacteria from attack by white blood cell or from
drying out
Internal Membrane: bacteria, contains molec needed for photosynthesis
Flagella: appendages, complex motor protein spins on its axis and moves the cell; anchored to plasma membrane
and to outer membrane of cell wall
Pili: made of protein that project from surfaces of some types of bacterial cells; help with adherence or conjugation
(sex) pili help two bact exchange genetic info
Cytoskeleton: collective name for protein filaments that play roles in cell division/maintain shape of cells in
both eukaryotes and prokaryotes

5.3 Pg. 132 Features of Eukaryotic Cells

compartmentalization key to eukaryotic cell funct; each organelle has own role, specialized
 compartmentalization key to eukaryotic cell funct; each organelle has own role, specialized
Ribosomes: has 2 diff-sized subunits; makes proteins contains more than 50 diff protein molec all non-
covalently bound to ribosomal RNA
found in Endoplasmic Reticulum or Cytoplasm
Nucleus: beginning of gene expression (turned on and off), where most DNA is
Nucleolus: where ribosomes begin to be assembled from RNA and proteins
Nuclear Envelope: integrated structure comprised of 2 membranes; separates genetic info from
cytoplasm and what goes in and out the nucleus
Pg. 136
Chromatin: DNA is combined w/ proteins (histones) to make fibrous complex
Chromosomes: long, thin threads that chromatic occurs in
prior to cell this chromatin becomes tightly compacted and condensed
Endomembrane system: interconnected system of membrane-enclosed compartments that are sometimes
flattened into sheets and sometimes have other characteristic shapes
includes: plasma membrane, nuclear envelope, ER, golgi apparatus, lysosomes (come from Golgi),
vesicles
membrane components can shift from one organelle to another (so all membranes related functionally)
Endoplasmic Reticulum:
inside called lumen, has surface area greater than plasma membrane (very folded)
RER: receives newly synthesized proteins into its lumen; transports these proteins to other locations of
the cell; saclike
o Proteins can be chemically altered to alter functions and tag for delivery to specific places;
o Formation of disulfide-bridges, tertiary structure folding
o membrane-bound proteins
Vesicle pops off with them
SER: more tubular;
o proteins from RER can be chemically modified here; make them more water soluble and polar
o Site for glycogen degradation
o Lipids and steroids are synthesized
o Stores calcium ions, released to trigger cell responses
Golgi Apparatus: has flattened sacs (cisternae) piled up and small membrane-enclosed vesicles
receives protein-containing vesicles from RER
modifies, concentrates, packages, and sorts proteins before they are sent to their cellular or
extracellular destinations
adds carbs to proteins and modifies other carbs that were attached to proteins in RER
where some polysaccharides from plant cell wall are synthesized
o three parts cis (close to RER), trans (opposite), medial region
o cis: protein containing vesicles from RER fuse here; release cargo
o medial: transport proteins, modified
o trans: vesicles bud off from here
Lysosomes:
primary lysosomes come from Golgi apparatus (contain digestive enzymes) where proteins, polysacc,
nucleic acids and lipids are hydrolyzed into monomers
single membrane; breaks down food, other cells, foreign objects
o Phagocytosis: materials enter cell; pocket forms in plasma membrane and deepens and
encloses material from outside
o Secondary lysosomes: occurs when phagosome fuses w/ primary lysosomes (digestion
occurs in this)
Pg. 138
Autophagy: programmed destruction of cell components and lysosomes are where cell breaks down its own
materials
if phagocytosis doesnt occur ex. Tay-Sachs disease
pg. 139
Mitochondria: primary function is to harvest chem energy
where cellular respiration occurs; has own DNA (moms side)
outer membrane smooth, lets everything in
inner membrane more controlling, has high SA-V ratio
Plastids: one class of organelles; autonomously
mitoc,
chloroplasts: contains green pigment chlorophyll; photosynth
o thylakoids: individual sac; stacked up = granum
o its membrane
Peroxisomes: organelles that accumulate toxic peroxides (ex. hydrogen peroxide H2O2 byproduct of some rxns);
single membrane
disease ex. Zellweger; cell gets too acidic dies
Glyoxysomes: similar to peroxisomes but only in plants
where stored lipids are converted into carbs for transport
 where stored lipids are converted into carbs for transport
Vacuoles: particularly in plants, fungi, and protists
storage; structure (keep cell rigid); reproduction (have pigments that are visual cues to attract animals
that assist in pollination), digestion (have enzymes that hydrolyze stored proteins into monomers)
contractile ones get rid of excess water that rushes into cell
pg. 142
Cytoskeleton: supports cell and maintains shape; holds organelles and other particles in position, moves organelles
and other part around cell cytoplasm, interacts w/ extracellular structures (helps anchor cell in place)
Microfilaments: exist as single filaments in bundles, or in networks
o Help entire cell/ parts move, determine and stabilize shape
o Assembled from monomers of action (esp in animals)
o Actin filaments in muscle: myosin and interactions of these two proteins account for
contraction of muscles
intermediate filaments: many diff kinds specific to few cell types; share general structure (ex. proteins that make
up hair and nails)
Tough, ropelike protein assemblages, more permanent than microtubules or microfilaments
o Anchor cell structures
o Resist tension
Microtubules: long, hollow, unbranched cylinders
form rigid internal skeleton
acts as framework along which motor proteins can move structures
Tubulin: microtub that are assembled from dimers of protein tubulin (made of two monomers)
Motor Proteins: specialized molec that use cellular E to change their shapes and move; bind to and
move along microtubules

Cilia: occur by hundreds on individuals cells; move stiffly to either propel or move fluid over a stationary cell
9+2 array of microtubules; 9 pairs
Flagella: longer than cilia; occur singly or in pairs can push or pull a cell thru aqueous environment
** movement of cilia and flagella results from sliding of microtubule doublets sliding past one another; driven by
motor protein dynein

- Kinesin: carry protein-laden vesicles (walking proteins)


CH. 6 12/28/14 7:43 PM
6.1 pg. 154
Fluid Mosaic Model: made up of many discrete components and move freely
these membranes receive signals, move things in and out of cell, specialized for certain functions
carbs located outside of cell and interact w/ external environ; act as id tags
Lipid bilayer: polar heads, hydrophobic tails, phospholipids *usually
Saturated chain = tight packing all C bonded to max # of H
Inner and out halves of bilayer have very diff phospholipids
Cholesterol helps pack membrane tightly
Peripheral Membrane Proteins: lack exposed hydrophobic groups and are not embedded in bilayer
has charged regions that react w/ polar heads of PL bilayer
Integral Membrane Proteins: least partly embedded in PL bilayer
have both H2O phylic/phobic regions
Transmembrane Protein: all the way thru PL bilayer,
have Transmembrane domains: extend thru bilayer
also has domains on inner and outer side of w/ specific functs
pg. 157 Plasma membrane carbs r recog sites
they may be covalently bonded to lipids or to proteins
Glycolipid: consists of carb covalently bonded to lipid; serve as recog signal for interactions btw cells
Glycoprotein: one/more short carb chains to protein (carbs = oligosaccharides); function in cell recog
and adhesion
6.2 pg. 158
Both cell recog and adhesion require plasma membrane
involve proteins and carbs at cell surface (proteoglycans)
Adhesion:
can be carbs interacting w/ one another
carbs interact w/ membrane protein on another cell
or two proteins interacting
homotypic: same molec sticks out of both cells and exposed surfaces bind together
heterotypic: binding btw diff molec on diff cells
Cell Junctions: specialized structures, where cells connect to adjacent cells
Tight Junctions: prevent substances from moving thru space btw cells (ex. cell in bladder so urine
doesnt leak out)
o Maintain distinct faces of cell w/in tissue by restricting migration of membrane proteins over
cell surface
Desmosomes: hold neighboring cells firmly together (like welds/rivets); materials in extracellular
matrix sill move
Gap Junction: channels that run btw membrane pores in adj cells, allwing substances to pass btw cels
(ex. in Heart, allow for rapid spread of electric current)

Cell membranes adhere to extracellular matrix

imp in maintaining integrity of a tissue
Integrin: transmembrane protein often mediates attachment of epithelial cells to extracellular matrix
o Bind to protein in extracellular matrix and to actin filaments inside cells
Binding in non-covalent and reversible
6.3 pg. 161
Selective Permeability: allows membrane to deter what substances enter or leave cell/organelle
Passive transport: dont req input of chem E
 Passive transport: dont req input of chem E
Active transport: req input of chem E
Passive transport depends on concentration gradient: [] of substances inside and out membrane
1. Simple diffusion thru PL bilayer
2. Facilitated diffusion vis channel/carrier proteins
Diffusion: process of random movement toward a state of equilibrium
movement of each particle random but net movement is directional towards less []ed side
smaller molec diffuse faster
higher temp = faster diffusion
greater [] gradient = faster diffusion
in smaller celler, diffusion is a great mechanism, larger = less impact
diffusion of part can be affected by properties of membranes (permeability)
Simple diffusion: small molec pass thru PL bilayer of memb
molec is hydrophobe, soluable in lipids
electrically charged (amino acids, sugars, ions) dont pass easy
Osmosis: diffusion of water across membranes; passive
Hypertonic: higher solute [] than other solution
Isotonic: solutions have = []s
Hypotonic: has lower [] than other solu
Turgor pressure: pressure w/in cell against cell wall in plants; keeps plants upright and attached to each other
Facilitated Diffusion: has two forms
Channel proteins: integral membrane proteins, form channels across membrane
Carrier proteins: bind substances and speed up their diffusion thru PL bil
Ion channels: channel proteins; helps with movement of ions across membrane, particular to specific ions
gated channel: opened or closed to ion passage; opens when stimulus causes a change in 3-D shape of
channel
ligand: chemical that binds to gated channel and stimulates it to open
Aquaporin: protein channel that allows water to cross PL bilayer
Carrier Proteins: transport polar molecules such as sugars/amino acids
in simple diffusion rate depends on [] across membrane
in carrier-mediated transport, it gets to a point where diffusion rate becomes constant (saturated)
6.4 pg. 166 ACTIVE TRANSPORT

Uniporter: moves single substance in one direction (ex. calcium binding protein)
Coupled Transporters: move two substances at once
Symporter: moves two substances in same direction
Antiporter: moves two substances in opposite direction (one into cell or organelle and other out of
cell/organelle)
Primary active transport: involves direct hydrolysis of ATP (provides E required for transport)
Secondary active transport: doesnt use ATP directly (E supplied by ion [] gradient estab by primary active
transport)
Sodium-potassium (Na+-K+) pump: found in all animal cells; pumps Na+ out of cell and K+ into cell (against
concentration gradient)
integral membrane glycoprotein
Both symporters and anitporters are used for secondary active transport
 6.5 pg. 168 how do large molecules enter and leave the cell?
primarily by endocytosis and exocytosis
Endocytosis: group of processes that bring small and large molec, and even small cells into eukaryotic cells
In all three process PL membrane invaginates, forms small pockets, becomes vesicle and separates
from PL membrane
o Phagocytosis: engulfs large particles/cells; used for feeding or engulf foreign materials to
break them down; non-specific
Good vacuole or phagosome fuses w/ lysosomes
o Pinocytosis: smaller vesicles form, brings in fluids; nonspecific
o Receptor-mediated endocytosis: molec at cell surface recognize and trigger uptake of
specific materials (ex. below); specific

Receptor-mediated endocytosis: how it works pg. 169

used by animal cells to captures specific macromol from cells envir.
Receptor Proteins: proteins that bind to specific molec w/in cell/external envir
o Receptor protein binds to specific molec
o Coated pit invaginates > coated vesicle around macromolec
o Clathrin molec strengthen and stabilize vesicle
o Carried into cytoplasm > clathrin coat shed
o Fuse w/ lysosome > digested thru hydrolysis
o Products released into cytoplasm
this is how cholesterol taken up by mammalian cells
made and packaged in liver, circulated in bloodstream, binds to ligand, etc
Exocytosis: materials packaged and secreted from cell

Ch. 11 CELL CYCLE 12/28/14 7:43 PM
11.1 pg. 254 how do prokaryotic and eukaryotic cell divide?
Reproductive signal: initiates cell and may originate from either inside or outside cell
Replication: of DNA must occur so new cells have genetic info
Segregation: cell must distribute replicated DNA to each new cell
Cytokinesis: when 2 new cells separate
PROKARYOTES:
Binary fission: cell grows in size, replicates dna, separates cytoplasm and DNA into two new cells
reproductive signals: environ conditions, nutrient []
Chromosome: consists of long, thin DNA molec w/ proteins attached to it
Most prokaryotes have one main chromosome
Two regions of prokaryotic chromo play functional role in cell reprod
 Two regions of prokaryotic chromo play functional role in cell reprod
o Ori: site where replication of circular chromo starts
o Ter: site where replication ends
Chromo rep occurs as DNA threaded thru replication complex
Replication starts at center and moves to oppo ends
Cytokinesis: right after rep complete; plasma mem pinches, etc
EUKARYOTES:
reproductive signal: independent of environ; but on the function of the entire organism
Replication: more intricate because there are more chromosomes
Segregation: new replicated chromosomes are closely associated w/ each other (sister chromatids) and Mitosis
segregates them into 2 new nuclei
Meiosis: nuclear occurs involved w/ sexual reprod; 4 diff cell
11.2 How is Eukaryotic Cell Division Controlled? Pg. 256
Cell Cycle: period from 1 to another; mitosis, cytokinesis, interphase
Interphase: cell nucleus visible and typical cell functions occur (DNA replication)
o G1 Phase: each chromosome single, unreplicated w/ proteins
Non usually in G0 resting state; needs to be prompted to exit this state
o G1-to-S transition: commitment made to DNA rep
o S Phase: DNA replication occurs; two sister chromatids occur
o G2 Phase: cell makes prep for mitosis (makes centrioles, etc)
Pg. 257
Cyclin-Dependent Kinases (Cdks): affects progress of cell cycle
it catalyzes transfer of Phosphate group from ATP to target protein = Phosphorylation
Cyclin: binds to Cdk and activates them
Cell cycle checkpoints: activity Cdks
o G1 checkpoint (R): cell stops while DNA repaired or cell death
o S: Incomplete replication/DNA damage extensive to be fixed
o G2: DNA damage
o M: chromosome unattached to spindle
Growth Factors: external chemical signals that stimulate cell
 Centrosome: made of pair of centrioles from which spindle apparatus comes determines plane of cell
After prophase Kinetochores develop on each sis chromatid so that they can separate in Anaphase
*** Chrmatids share a centromere, chromosomes have their own centromere
 nonkinetochore microtubules change shape of the cell
kinetochore microtubules help the chromosomes move and align
 cleavage furrow: region where proteins pinch in the center of the cell until it separates into two (in animal cells)

MEIOSIS:
synapsis: homologous chromosomes pair by adhering along their lengths
lasts from prophase 1 to metaphase 1
Tetrad: formed when four chromatids of each pair of homologous chromosomes get together
Chiasmata: X-shpaed appearance of the tetrad; reflects exchange of genetic material btw nonsister
chromatids; crossover occurs
Recombinant Chromatids: result of crossover; + genetic diversity
Law of Independent Assortment: when homologous chromosomes separate; random if mom side or dad side of
our gene lines up in center for metaphase 1
if doesnt go right: Nondisjunction = Aneuploidy condition in which one or more chromosomes are
either lacking/present in excess
Trisomic (21 = downsyndrome)
Monosomic (21 = cell death no zygote)
Translocation: piece of chromosome may break away and become attached to another chromosome (if
in 21 = down syndrome)
Law of Segregation: two alleles in a pair will separate into different gametes;

Meiosis 1: Crossing over: responsible for diversity that exists within a species
Crossing over is a process in which genes swap positions on matching chromosomes; new combination of genes
on each chromosome

- During metaphase I, homologous pairs of chromosomes line up on the metaphase plate. This is very different from
mitosis, when sister chromatids line up, completely independent of their homologues.
mitosis, when sister chromatids line up, completely independent of their homologues.

- During anaphase I, homologous pairs are pulled apart, and they move toward the poles of the cell.

- In telophase I, cytokinesis occurs and two new daughter cells are formed. Meiosis I ends with the production of
two haploid daughter cells because the homologous pairs of chromosomes have been separated.

- Meiosis II begins with two haploid cells, each containing too much DNA. Remember that while homologouspairs
of chromosomes were separated in Meiosis I, each homologous chromosome is still connected to its sister
chromatid. The presence of a sister chromatid for each chromosome at the start of Meiosis II means that each cell
contains too much DNA. The events in meiosis II are almost identical to the events of mitosis.
 In Meiosis II (which is essentially like mitosis), the sister chromatids separate from each other. Thus, as the result of
meiosis, four haploid cells are produced. Note that those four cells are not always viable. In humans, male germ cells
will produce four viable sperm cells. However, in the case of females, only one of the four will survive as an egg.
The end result of meiosis is four unique haploid daughter cells. Genetic variability is introduced in various ways
during meiosis:
Crossing over during prophase 1: crossing over introduces novel combinations of traits among offspring.
Segregation of chromosomes into gametes: the maternal and the paternal copy of each chromosome pair will
segregate to different gametes. However, which goes to which cell is a random process. Thus, the possible number
of combinations is astounding: in the case of humans, with 23 chromosomes, it is 223(8,388,608).
When you add that fertilization is also a random process, you can get an idea of the incredible number of
combinations of possible offspring showing up even in one family.

Ch.12.1-12.5 12/28/14 7:43 PM
12.1 pg. 281
Theory of Blending inheritance: blended phenotype of genotype
Theory of Particulate inheritance: each determinant had physically distinct nature; when gametes fused,
determinants stayed intact
Mendel: studied pea plants; to study how genes were passed on
Character: observable physical feature
Trait: particular form of a characteristic
Parental Generation (P): true-breeding plants (1st generation)
First filial generation F1: generation after true breeds
Second filial generation F2: offspring of F1 (self-polli or not)
Monohybrid cross: F1 crossed with F1 (crossing 2 hybrids)
Dominant: more often in F2 generation
Recessive: less often in F2 generation
Genes: hereditary determinants (codes for a particular trait)
Diploid: having 2 copies of each gene
Haploid: state of having one copy of each gene
Alleles: different form of the same gene
homozygous, heterozygous, phenotype, genotype
Dihybrid Cross: cross btw individuals that are identical double heterozygotes
MENDELS TWO LAWS:
***Corresponds to which step in meiosis?
1. Law of segregation: when gametes produced, two copies of a gene separate so that each gamete receives only
one copy
2. Law of independent assortment: alleles of different genes assort independently of one another during gamete
formation (moms or dads which side they get doesnt matter)
12.2: pg. 291
Pleiotropic: single allele can influence more than one phenotype
12.3: pg. 292
(some examples?)Epistasis: to stand upon occurs when phenotypic expression of one gene is affected by another
gene
Inbreeding: matings among close relatives;
Inbreeding Depression: results in offsprings of lower quality than matings between unrelated
individuals
Heterosis: hybrid vigor after crossing inbred lines;
the increase in growth, size, fecundity, function, yield, or other characters in hybrids over those of the parents.
Penetrance: proportion of individuals in a groups with a given genotype that actually show the expected
phenotype
if not everyone exhibits the trait, then allele said to he incompletely penetrant
Expressivity: degree to which a genotype is expressed in an individual
sometimes diff phenotypes can result from same allele
MOST COMPLEX PHENOTYPES ARE DETERMINED BY MULTIPLE GENES AND THE ENVRIONMENT
PG. 294
Quantitative: continuous variation in a trait within a population (height)
controlled by genes and the environment
Quantitative trait loci: genes that together determine complex characters (is this referring to genes interacting
with the environment?)
12.4 pg. 295
* also independent assortment of linked genes?
Linked Genes: Genes on the same chromosome; do not follow Mendels law of independent assortment all the
time
 time
can of course change when crossover occurs in Prophase 1
When crossing over takes places between two linking genes
Recombinant Frequencies: calculated by dividing the number of recombinant progeny by the total number of
progeny
greater if loci further apart
Monoecious: same individual produces both male and female gametes
Dioecious: can only reproduce thru male and female gametes by male and female individuals
Sex Chromosomes: determine sex of the organism
Autosomes: remaining chromosomes
pg. 298
Primary sex determination: SRY gene encodes protein involved in this process
if SRY protein present, then embryo develops sperm-producing testes
if embryo has no Y chromosome, SRY gene is absent and SRY protein is not made
DAX1 gene on X chromosome produces anti-testis factor
Secondary Sex Characteristics: body type, breast, body hair, voice
gonads produce hormones to control the formation of 2nd sex chara
Sex-linked inheritance: inheritance of a gene thats carried on a sex chromosome

13.1-13.5 12/28/14 7:43 PM

13.1 pg. 308
DNA from one type of bacterium genetically transforms another type
ex. R and S strand of the virus; R stand took in DNA from S strand and transformed and became dangerous
Transformation
Viral infections also confirmed that DNA is the genetic material and not Proteins
Griffith = transformation
Hershey/chase = Dna or protein that is genetic info
pg. 311
Transfection: transformation of eukaryotic cells by DNA
Genetic Marker: gene whose presence in the recipient cells confers an observable phenotype.
13.2 pg. 312
Watson and Crick found it to be a double helix from x-ray diffraction (Franklins)
Chemical evidence from base composition shows that they paired AT and GC
Chargaffs Rule: AT and GC
DNA MOLECULE:
Sugar-phosphate backbone on outside
Antiparallel: two strands ran in opposite directions
4 things:
1. DNA is double stranded
2. DNA is a right-handed helix
3. DNA is antiparallel
4. DNA has major and minor grooves in which edges of Nitrogenous bases are exposed
Hydrogen bonds btw bases hold helix together
Van Der Waals forces btw adjacent bases on same strand
5 end: one end of a chain is free 5 Phosphate Group (OPO3-)
3 end: free 3 Hydroxyl Group (OH)
Grooves exist because backbones of two strands are closer together on one side of the double helix (minor groove)
than on other side (major groove)
Exposed outer edges of the base pairs are accessible for additional hydrogen bonding
13.3 Pg. 316
Semiconservative, conservative, and dispersive
Meselson and Stahl proved semiconservative nature of DNA replication
* DNA replicated from 5-3 end; bases added to the 3 side
Formation of phosphodiester linkage (condensation rxn)
Origin of Replication: pre-replication complex binds, proteins recognize specific DNA sequences
within the ori
Replication Forks: fork where the helicase continues to unwind
Helicase: unwinds DNA
Single-strand Binding Proteins: bind to unwound strands to keep them from associating into a double
helix
Primase: lays down RNA primer where DNA polymerase can attach and start laying bases
Primer: short starter RNA strand (could also be DNA)
DNA Polymerase: add nucleotides to 3 end of new strand
RNA Primer: degraded and DNA poly lays down DNA instead
Ligase: connects DNA fragments together and replication complete
Leading Strand: oriented so that it can grow continuously at its 3 end as the fork opens up
 Leading Strand: oriented so that it can grow continuously at its 3 end as the fork opens up
Lagging Strand (Okazaki Fragments): oriented so that as fork opens up, its 3 gets father and farther from the
fork
opposite direction of synthesizing as the replication fork
DNA Poly 3 lays down DNA btw all the RNA primers
Processive: they (DNA poly) catalyzes the formation of many phosphodiester linkages each time they bind to a
DNA molecule
Sliding DNA Clamp: attached to DNA poly and helps many bases to be added each rxn and increases efficiency of
DNA.
Replication complexes seem to be stationary, attached at specific position on nuclear matrix
its DNA that moves thru (slides into replication complex)
Telomeres: repetitive sequences at the ends of chromosomes; they are not fully replicated and are prone to repair
TTAGGG (repeated 2,500 times at each chromosome end)
They bind special proteins that prevent DNA repair system from recognizing chromosome ends as
breaks
Replication of Okazaki frag occurs to RNA primers so when terminal RNA primer removed, DNA
Poly cannot bind to it and therefore, that itty sequence of DNA cannot be replicated
o Cuze theres no 3 end to extend
o After many cell divisions genes near ends of chromosomes lost and cell dies
Telomerase: protein in bone marrow stem cells and gamete producing cell that catalyzes addition of
telomere sequences in these cells
o Expressed a lot in cancer cell (might be reason for their success)
13.4 pg. 324
FIXING ERROR IN REPLICATION:
Proofreading: corrects error in replication (as DNA poly makes them)
Mismatch Repair: scans DNA immediately after its been replicated and corrects any base-pairing mismatches
Excision Repair: removes abnormal bases that have formed because of chemical damage and replaces them wi/
functional bases
When DNA poly recog a mispairing of bases, it removes the improperly intro nucleotide and tries again
After DNA replicated, another set of proteins survey newly replicated molecule and look for mismatches base pairs
When this fails, DNA sequence is altered (ex. colon cancer)
DNA can also be damaged during life of a cell (ex. in G1 phase)
high E radiation from environment/random spontaneous chem rxns all damage DNA
o ex. covalent bond btw adjacent thymine primary cause for cancer = thymine dimer
Excision Repair: repairs damage to existing DNA molecules
13.5 pg. 325
Polymerase Chain Reaction: technique essentially automates replication process by copying short region of DNA
many times
CONTAINS:
sample double-stranded DNA from bio sample (template)
two short artificially synthesized primers complementary to ends of template DNA
four dNTPs (dATP, dTTP, dCTP, dGTP)
DNA polymerase can tolerate high temps w/out becoming degraded
Salts and buffer to maintain near-neutral pH
PROCESS:
1st heat rxn mixtures near boiling point (denatures DNA temp)
Rxn cooled to let primers bind
Warmed to optimum temp for DNA poly to catalyze product of new complementary strands
PRIOR KNOWLEDGE:
of ends of 3 strand (so that they can make the RNA primers)
found DNA poly from orgs in hot springs that withstood high temp

Ch. 14.2-14.6 *finish 14.4 12/28/14 7:43 PM

14.1 pg. 330:
OBSERVATION IN HUMANS LED TO PROPOSAL THAT GENES DETERMINE ENZYMES
study of disease led to discovery that an enzyme was not being produced because of a mutant allele
started by correlating to enzyme but needed more than that
Experiments on bread mold estab genes determine enzymes
Model Organisms: have certain characteristics that make them attaractive experimental subjects (easy
to grow, short generation times, easy to manipulate, produce large number of progeny)
o Ex. pea plants, fruit flies (drosophila), bread mold, and E. Coli
Mutagen: something that damages DNA causing
Mutations: heritable alterations in DNA sequences
One-gene, One-Enzyme Hypothesis: results suggested that mutations have simple effects, and that each mutation
causes defect in only one enzyme in metabolic pathway
been modified: many proteins, enzymes, composed of more than one polypeptide chain (has subunits)
so in many cases each gene encodes for a subunit of a protein w/ quaternary structure
 so in many cases each gene encodes for a subunit of a protein w/ quaternary structure
so one-gene, one-polypeptide relationship
14.2 pg. 332 HOW DOES INFORMATION FLOW FROM GENES TO PROTEINS?
Transcription: info in DNA seq copied to complementary RNA seq
Translation: RNA seq used to create the amino acid seq for polypep
* Francis and Crick suggested that DNA can be used to create protein but not the other way around
Central Dogma: DNA->RNA->Polypeptide
THREE TYPES OF RNA HAVE ROLES IN INFORMATION FLOW FROM DNA TO PROTEIN pg. 333
Messenger RNA: complementary strand of DNA; travels from nucleus to cytoplasm; translated into polypep
Ribosomal RNA: RNA found in ribosome
Ribosome: essentially a protein synthesis factory composed of multiple proteins and several RNA
Transfer RNA: can both bind a specific amino acid and recognize specific sequences of nucleotides in mRNA
Many viruses have RNA rather than DNA as genetic material
Since RNA is single stranded, it is transcript-ed to double stranded DNA, then transcription occurs to produce
multiple copies of the RNA seq
Reverse Transcription: synthesis of DNA from RNA
Retroviruses: orgs that carry out reverse transcription
14.3 HOW IS THE INFO CONTENT IN DNA TRANSCRIBED TO PRODUCE RNA? Pg. 334
RNA synthesis directed by DNA = transcription
REQUIRES:
1. DNA template for complementary base pairing
2. 4 of the RNA bases ATP, GTP, CTP, UTP
3. RNA polymerase enzyme
4. Salts and pH buffer to create appropriate chem environ for RNA poly if in test tube
* Transcription also creates: tRNA and rRNA not just mRNA
These RNAs are encoded for by specific genes
ALL RNAS AND THEIR FUNCTIONS/ROLES:

RNA Polymerases: from both pro and eukaryotes catalyze synthesis of RNA from DNA template (several types in
euk but one in prok)
all share common structure
like DNA poly, RNA poly catalyze addition of nucleotides in a 5-3 direction and are processive (single enzyme-
template binding event results in the polymerization of hundreds of RNA bases
Unlike DNA poly, RNA poly does not require a primer

TRANSCRIPTION (3 STAGES) PG. 334:

1. INITIATION:
b. RNA polymerase binds to special DNA seq = Promoter
i. Each gene usually has one; in pro and viruses, they share one promoter
ii. Control sequences that tell RNA poly: where to start transcription and which strand of
DNA to transcribe
c. Promoter reads in particular direction and orients RNA polymerase to aim it at correct strand to
use as template
d. Initiation site of promoter: where transcription begins
e. Groups of nucleotides lying upstream from initiation site (5 on non-template strand and 3 on
template strand) help RNA poly bind
f. Other proteins help direct polymerase onto promoter Sigma factors and Transcription factors
i. Help determine which specific genes are expressed at part time in cell
ii. Not all promoters are identical; some more effective at transcription initiation than others
2. ELONGATION:
 2. ELONGATION:
a. After RNA polymerase has bound to the promoter
b. RNA poly unwinds the DNA about 10 base pairs at a time and reads template strand in 3 to 5
direction
c. 1st nucleotide in the new RNA forms its 5 end and subsequent nucleotides complementary to DNA
template added to 3 end
d. RNA transcipiton antiparallel to DNA template strand
e. RNA poly uses ribonucleoside triphosphates as substrates, removing 2 P groups from each
substrate molec and using the released E to drive polymerization rxn
f. RNA polymerase do not proofread so more errors (but RNA has short life span and multiple
copies)
3. TERMINATION:
a. Termination: particular base seq that specify end of transcription
b. Mechanism that controls it not well understood but newly formed transcript forms a loop that
causes transcript to fall away from DNA template and RNA polymerase
c. Or helper protein binds to specific seq on transcript and causes RNA to detach from DNA template

THE INFORMATION FOR PROTEIN SYNTHESIS LIESIN THE GENETIC CODE pg. 336:
Genetic code: relates genes (DNA) to mRNA and mRNA to amino acids that make up proteins
Codon: specifies part amino acid; complementary to corresponding triple bases of DNA molec
CHARACTERISTICS OF THE CODE:
more than 20 code words could be written w/ alphabet consisting of only 4 letters
A triplet code was the only one that could explain the 20 amino acid codes being possible and most efficient
Start Codon: only one codon AUG
Stop Codon: has three UAA, UAG, UGA
Genetic Code: redundant but not ambiguous
Its nearly universal: same basic genetic code used by all species on our planet
So it must be ancient (mitoch and cholo are expectations)
So common lang of evolution
14.4 HOW IS EUK DNA TRANSCRIBED AND THE RNA PROCESSED? Pg. 338
Nucleus separates transcription and translation in euk
MANY EUK GENES ARE INTERRUPTED BY NONCODING SEQUENCES
Nucleic Acid Hybridization: two steps:
1. Sample of chromosomal DNA containing gene is denatured to break the H-bonds btw base pairs and
separate 2 strands
2. Single-stranded mRNA (probe) incubated w/ denatured DNA; if it has complementary base pairs,
and separate the 2 strands and probe-target double helix forms by h bonding btw bases and resulting
double-strand is called a hybrid
Pre-mRNA: right after transcription but still has unusable/non-coding parts that need to be excised; hybridized w/
chromosomal DNA
Introns: intervening regions of DNA (that are transcribed by cut out); interrupt but NOT scramble
Exons: expressed sequences in the mRNA that reaches the ribosome and is translated
sometimes, separated groups of exons often encode diff functional regions (domains) in proteins
EUKARYOTIC GENE TRANSCRIPTS ARE PROCESSED BEFORE TRANSLATION
5cap: added to 5 end of the pre-mRNA as its transcribed; 5 cap is chemically modified GTP
protects mRNA from being digested by ribonucleases that break down RNAs
facilitates binding of mRNA to ribosome for translation
poly A tail: added 3 end of pre-mRNA at end of transcription
(AAUAAA) followed by 100-300 adenine bases - after last codon
helps export mRNA from the nucleus and is important for mRNA stability
 helps export mRNA from the nucleus and is important for mRNA stability
RNA Splicing: removes the introns and splices the exons together
as soon as transcription over, Small nuclear ribonucleoprotein particles (snRNPs) bind to ends of
each intron
each snRNP has RNA component
consensus sequences: short stretches of DNA that appear w/ little variation in many diff genes; btw
introns and exons
14.5 HOW IS RNA TRANSLATED INTO PROTEINS? Pg. 341
1. tRNAs must read mRNA codons correctly
2. tRNAs must deliver the amino acids that correspond to each mRNA codon
tRNAS carry specific amino acids and bind to specific codons
tRNAs binds to part amino acids (covalent attachment is at 3 of tRNA)
tRNAs bind to mRNA there is a triplet of bases called anticodon: complementary to mRNA codon
tRNA and mRNA bind together via non-covalent h-bonds
mRNA 5-CGG-3
tRNA 3-GCC-5
tRNAs interact wi/ ribosomes: non-covalent and shape helps tRNA fit
- cell does not make 61 diff species of tRNA
Wobble: cell gets by w/ about 2/3rs of that number of tRNA species because the specificity of the base at 3 end of
the codon (and 5 end of anit-codon) is not so strict
possible because in some cases unusual/modified nucleo bases occur in 5 position of anticodon?
EACH TRNA IS SPECIFICALLY ATTACHED TO AN AMINO ACID
aminoacyl-tRNA synthetases: attach correct amino acid to each tRNA

THE RIBOSOME IS THE WORKBENCH FOR TRANSLATION:

Ribosome: molecular workbench where the task of translation is accomplished
structure lets it hold mRNA and charged tRNAs in correct positions
1 large and 1 small subunit and dozen molec interact noncovalently
On large subunit 3 places where tRNA can bind
1. A (aminoacyl tRNA) site: where the charged tRNA anticodon binds to the mRNA codon: lines up
correct amino acid to growing polypep
2. P (peptidyl tRNA) site: where tRNA adds its amino acid to polypep chain
3. E (exit) site: where tRNA, having given up its amino acid is released and heads back to cytosol to
pick up other amino acid
o h-bonding occurs when right tRNA and mRNA bind
TRANSLATION TAKES PLACE IN THREE STEPS:
1. INITIATION:
Initiation complex: consists of charged tRNA and small ribosomal subunit (both bound to mRNA)
Load mRNA onto ribosome (small ribosomal subunit binds to 5 cap on the mRNA and moves along
the mRNA till it reaches start codon)
mRNA start codon genetic code is AUG
then large subunit of ribosome joins complex
methionine-charged tRNA now lies in P site of ribosome, A site is aligned w/ second mRNA codon
INITIAION FACTORS: are mRNA, 2 ribosomal subunits, and met charged tRNA
2. ELONGATION:
tRNA w/ anticodon of 2nd codon enters A site of large s-unit
it breaks bond btw tRNA and its amino acid in P site
catalyzes formation of peptide bonds btw amino acid and one attached to tRNA in A site
peptidyl transferase activity: because large ribosomal subunit performs these two actions above
Met becomes N terminus of new protein; remains attached to tRNA at A site
o Proves RNA and catalytic RNA evolved before DNA
3. TERMINATION:
When stop codon (UAA, UAG, UGA) reached, elongation cycle ends and translation terminated,
enters A site
They bind to protein release factor (which allows for hydrolysis of bond btw polypep chain and tRNA
in P site)
 in P site)
POLYSOME FORMATION INCREASES THE RATE OF PROTEIN SYNTHESIS: PG. 345
Polyribosoome or polysome: several ribosomes attach to mRNA to produce several polypeptides
14.6 WHAT HAPPENS TO POLYPEPTIDES AFTER TRANSLATION? 346
signal sequences in proteins direct them to their cellular destinations
polypeptide could fold into 3-D shape and perform its cellular role
it may acquire signal sequence (signal peptide) short stretch of amino acids that indicates where in the cell the
polypeptide belongs
protein synthesis always begin on free ribosomes and default location is cytosol
in absence of signal seq, protein remains in same cellular compartment where it was synthesized
if signaled to organelle > once bound, a channel forms in organelle memb
targeted protein moves into org
ex. 20 hydrophobe amino acids in N terminus > directed to RER
MOST PROTEINS ARE MODIFIED AFTER TRANSLATION: pg. 348

TYPES OF MODIFICATIONS AFTER TRANSLATION:

Proteolysis: cutting polypeptide chain, rxn catalyzed by enzymes called proteases
allows fragment to fold into different shapes
Glycosylation: adding sugar to protein; glycoproteins; ex. directs proteins to lysosomes
important for targeting and recognition
Phosphorylation: added phosphate groups
alter the shape of the protein; often expose active site of enzyme or binding site for another protein