AP Biology Semester One Study
Guide
How to use this study guide:
-->Use this study guide early and often. DO NOT cram a day or two
before the test. Study about 45 minutes at a time and take frequent
breaks. Make this study guide your own! Add colors, images,
analogies, links to animations, practice questions, etc. to make it a
more personalized and interactive tool for yourself. Do NOT simply
read this document over and over again. Address it in small parts
and “quiz” yourself as you go along to make sure it’s really sinking
in. Follow up on any parts on this document that are confusing to
you. Go back to the textbook, powerpoints, animations, a fellow
student, your teacher, etc. to seek further explanation. Lastly, the
answer to the question, “Do we have to know ___?” is yes! Anything
on this study guide is fair game.
Unit 1- Biochemistry: The Chemistry of Life (Ch. 2-3)
What to Know...
Characteristics of Life:
Living things are made up of cells
Living things reproduce
Living things are based on a universal genetic code
Living things grow and develop
Living things obtain and use energy/materials
Living things respond to their environment
Living things maintain homeostasis
Living things as a group evolve over time
Hydrocarbons/organic molecules:
○ Hydrocarbons are organic molecules that consist of only
Hydrogen and Carbon
○ Fats have long hydrocarbon tails
○ Hydrocarbon molecules are mnonpolar and hydrophobic
○ They store a large amount of energy
Properties of water:
○ Cohesive behavior – the ability for same molecules to
stick to each other
○ Ability to moderate temperature – high specific heat
capacity
○ Expansive freezing – ice floats, densest at 4°C
○ Versatility as a solvent – due to its polarity
Polarity: when one part of the molecule has a stronger
electronegativity than the another and as a result has more
time with the electrons. This gives it a slightly negative
charge; while the other pole is slightly positive (Ex: water is a
polar molecule)
Solutions- homogeneous mixtures of solutes dissolved in
solvents.
○ Solute is the thing being dissolved into the solvent (ex: in a
salt solution, salt is the solute and water the solvent)
○ Hydrophobic molecules do not mix with water, hydrophilic
molecules do
*Molarity is a way to measure concentration of a solution. It is
the number of moles of solute per liter of solvent
pH Scale:
○ Acids are substances that increase the concentration of H+ in
a solution
○ Bases are substances that increase the concentration of OHin a solution
○ pH scale refers to the measure of H- concentrations
(logarithmic, -log of ten)
pH= -log [H+ ion]
○ Buffers keep the solution at relatively the same pH; work by
accepting and releasing hydroxyl groups or hydrogen ions; See
blood bicarbonate buffer system as an example
Carbon Bonding:
○ Little tendency to lose/gain electrons (low
electronegativity)
○ Tendency to form covalent bonds (maximum of 4)
○ Molecules with double bonded carbons are flat
○ Most frequent partners in bonding: oxygen, nitrogen,
and hydrogen
Dehydration synthesis/hydrolysis:
○ Dehydration Synthesis refers to the making of a polymer by
taking out a water molecule and combining the 2+ monomers
(usually used to store energy)
○ Hydrolysis (decomposition) refers to the adding of a water
molecule and breaking apart a polymer to form monomers
(when in need of energy)
○ Anabolism or constructive metabolism is the synthesis of
complex molecules from simpler ones together with the
storage of energy; aka. Dehydration Synthesis
○ Catabolism or destructive metabolism is the break down of
large molecules into simpler ones which releases energy; aka.
Hydrolysis
Monomers/Polymers and their components:
○ Monomer is the term for small building blocks of polymers
(they may serve other purposes then to build polymers, like
glucose is a monomer)
○ Polymer is the term referred to the long chain of monomers
that are relatively the same
○ Enzymes usually construct/decompose polymers
into/from monomers
Carbohydrates:
○ End in -ose
○ Composed of Carbon, Hydrogen, and Oxygen in a 1:2:1
ratio
○ Monomer = Monosaccharide (ex. = glucose, fructose,
galactose), simple sugars
○ Polymer = Polysaccharide (ex. = starch, glycogen,
cellulose)
○ Carbohydrates are used for quick energy
○ Disaccharides are two monomers of carbs bonded together =
C12H22O11 (missing an H2O from Dehydration synthesis), ex =
maltose, lactose, sucrose
○ Glycogen is a polysaccharide that forms glucose in hydrolysis
(a glucose chain)
○ Cellulose is a polysaccharide found in plant cell walls
containing glucose monomers; is insoluble
○ Chitin is a fibrous substance consisting of polysaccharides
that are main components in cell walls of fungi
Lipids:
○ Composed of Carbon, Hydrogen, and Oxygen not in the
above ratio
○ Made of glycerol (an alcohol) and 3 fatty acids (hydrocarbon
chain + Carboxyl group)
○ Used for energy, insulation, cushioning
○ Types: Oils, waxes and steroids (cholesterol, sex
hormones)
○ Saturated fats from animals, solid at room temp., no
double bonded carbons
○ Unsaturated fats from plants, liquid at room temp., have
double bonded carbons
○ Phospholipids are lipids that have a phosphate group in its
molecule, make up phospholipid bilayer of cell membranes
○ Steroids are molecules with four rings of carbon (include
hormones)
Proteins:
○ Consist of carbon, hydrogen, oxygen, and nitrogen,
(sometimes sulfur)
○ Monomer: amino acids
○ Polymer: polypeptide
○ Produced in ribosomes ( protein factories in cells)
○ Made of polypeptides made of amino acids (monomers),
there are 20 R Groups
○ *Shape of protein depends on R Group interactions
○ Functions – Defense (antibodies), transport (hemoglobin,
membrane proteins), structure (muscle), enzymes (always end
in –ase and enzymes can be denatured), regulation (hormones)
*Review types of bonds/attractions (H-bonds, disulfide
bridges, ionic bonds, Van der Waals forces) that can exist
between R-groups.
○ Peptide bonds are the bonds that form between amino acids
to form a polypeptide
○ Four levels of protein structure:
○ Primary structure = unique sequence of amino
acids, single chain
○ Secondary structure = consists of folds/coils in
polypeptide chains (Alpha helix, or beta-pleated sheet); made
possible by R-group interactions
○ Tertiary structure = interactions between
secondary structures; determined by interactions between side
chains (R groups)
○ Quaternary structure = results when a protein
consists of multiple polypeptide chains; many tertiary
structures interacting.
○ Denaturation = when a polypeptide chain in a protein is
changed from its original shape; bonds are disrupted
Nucleic Acids:
○ Composed of carbon, hydrogen, oxygen, nitrogen,
phosphorus
○ Monomers = nucleotides (monomers w/ 5 carbon sugar,
nitrogen base, phosphate groups)
○ Polymers = DNA or RNA
○ Functions = High energy storage (ATP is a molecule); storage
and transmission of hereditary info (DNA and RNA)
Six functional groups that are most important in biochemistry
are:
 The hydroxyl group: (-OH) a hydrogen atom is
bonded into an oxygen atom which is bonded to the
carbon skeleton of the organic molecule, organic
molecules containing the hydroxyl group are
alcohols, their specific names usually end in –ol, the
hydroxyl group is polar, water molecules are
attracted to hydroxyl groups, which helps dissolve
organic compounds containing this group
 The carbonyl group: (-C=O)carbon atom joined to
oxygen atom by a double bond
 The carboxyl group: (HO-C=O) entire assembly of a
carbonyl group bonded to a hydroxyl group,
compounds with carboxyl are considered carboxylic
acids or organic acids, this group is a form of
hydrogen ions, thus making it acidic
 The amino group: (H-N-H) one nitrogen atom
bonded to two hydrogen atoms and to the carbon
skeleton
 The sulfhdryl group: (H-S-)sulfur atom bonded to
hydrogen atom, organic compounds with group
called thiols, these help stabilize the structure of a
protein; this group also is responsible for disulfide
bridges
 The phosphate group: (O-P-O34-) one function of this
group is to transport energy between organic
molecules (Ex: ATP)




Be Able To...
Identify/ Recognize the four types of biomolecules
Identify/Recognize a monomer or polymer
Identify/Recognize the functional groups listed
Identify/Recognize a dehydration synthesis or hydrolysis
reaction



Describe the structure of a protein *levels
Calculate pH of a solution given either [H+] or [OH-]
Predict how buffer systems react to certain conditions
Unit 2- Cell Biology and Membrane Transport (Ch. 45)
What To Know...
Unicellular: Made of one cell.
Multicellular: Made of many cells.
Different Cell Types:
 Eukaryote: A type of cell with a membrane/enclosed
nucleus and membrane/enclosed organelles, present in
protists, plants, fungi, and animals.
 Prokaryote: A type of cell lacking a membrane/enclosed
nucleus and membrane/enclosed organelles; found only
in the domains of bacteria and archaea.
Parts of Cell
 Organelle: one of several formed bodies with specialized
functions, suspended in the cytoplasm of eukaryotic
cells.
 The eukaryotic cell’s genetic instructions are housed in
the nucleus and carried out by the ribosomes (protein
factories)
 The endomembrane system regulates protein traffic and
performs metabolic functions in the cells;
o Endomembrane system: the collection of
membranes inside and around a eukaryotic cell,
related either through direct physical contact or by
the transfer of membranous vesicles.
o Endoplasmic reticulum: extensive network of
membranes (smooth and rough)
o Golgi Apparatus: consists of flat membranous sacs,
receives, sorts, and ships proteins; is particularly
extensive in cells that specialize in secretion
o Lysosomes- digestive compartments; contain
digestive/hydrolytic enyzmes
o Vacuoles- membrane-bound, maintenance
compartments
 Mitochondria and chloroplasts change energy from one
form to another
o mitochondria- membrane-bound organelles; sites of
cellular respiration
o
o

chloroplasts- membrane-bound organelles; sites of
photosynthesis
ALL EUKARYOTES have mitochondria
The cytoskeleton is a network of protein fibers
(microtubules and microfilaments) that organize
structures and activities in a cell
Structure of the Cell Membrane
 Fluid-mosaic model: The currently accepted model of cell
membrane structure, which envisions the membrane as a
mosaic of individually inserted protein molecules drifting
laterally in a fluid bilayer of phospholipids.
 Amphipathic molecule: A molecule that has both
hydrophilic region and a hydrophobic region.
 Phospholipids: molecules that have a polar, hydrophilic
head and a non polar, hydrophobic tail.
 Hydrophilic: Having an affinity for water “water loving”
 Hydrophobic: Having an aversion for water;
 Integral Protein: typically trans-membrane proteins with
hydrophobic regions that completely span the
hydrophobic region of the membrane.
 Peripheral Protein: Protein appendages loosely bound to
the surface of the membrane and not imbedded in the
lipid bilayer.
 Cholesterol: A steroid that forms an essential component
of the cell membrane and acts as a precursor molecule for
synthesis of other biological important steroids.
Transport Through the Membrane
 Transport Proteins: A Transmembrane protein that helps a
certain substance or class of closely related substance to
cross the membrane.
 Concentration Gradient: the difference in concentrations
of a chemical substance; cells often maintain
concentration gradients of ions across their membranes.
When a gradient exists, the ions or other chemical
substances involved tend to move from where they are
more concentrated to where they are less concentrated.
 Hypertonic: useful in comparing two solutions, referring
to the one with greater solute concentration.
 Hypotonic: useful in comparing two solutions, referring to
the one with lower solute concentration.
 Isotonic: Two solutions with equal solute concentrations
Osmoregulation: The control of water balance in
organisms living in hypertonic, hypotonic, or terrestrial
environments.
 Water Potential: quantifies the tendency of water to move
from one area to another due to solute concentration and
water pressure. Water potential equation= Ψ = Ψp +
Ψs (You will be given this equation, do not memorize)
Ψp = pressure potential
Ψs = solute potential
The water potential will be equal to the solute potential of a
solution in an open
container, since the pressure potential of the solution in an
open container is
zero.
the Solute Potential of the Solution
Ψs = – iCRT
i = ionization constant (For sucrose this is 1.0 because sucrose
does not
ionize in water.)
C = molar concentration
R = pressure constant (R = 0.0831 liter bars/mole K)
T = temperature in Kelvin (273 + ºC)




Turgid: Firm. Walled cells become turgid as a result of the
entry of water from a hypotonic environment.
Plasmolysis: A phenomenon in walled cells, in which the
cytoplasm shrivels and the plasma membrane pulls away
from the cell wall when the cell loses water to a
hypertonic environment.
Cytolysis: Cell bursts due to too much water entering
Passive Transport Vs. Active Transport
Passive transport: the movement of molecules through a
membrane from high to low conc.; NO ENERGY required
 Osmosis: the diffusion of water across a selectively
permeable protein. (Hi--> Lo) Aquaporins: A transport
protein in the plasma membrane in a plant or animal cell
that specifically facilitates the diffusion of water across a
membrane (osmosis).
 Simple Diffusion: the spontaneous tendency of a
substance to move down its concentration gradient to a
more concentrated to a less concentrated area. (Hi-->
Lo)

Facilitated Diffusion: The spontaneous passage of
molecules and ions, bound to specific carrier proteins,
across the biological membrane down their concentration
gradient (Hi→ lo)
Active Transport: the movement of a substance across a
biological membrane against its concentration or
electrochemical gradient with the help of energy input and
specific transport proteins. (Lo--> Hi)
 Phagocytosis: A type of endocytosis involving large
particulate substances.
Extracellular Components
 Cilia: Tiny hair-like structures; aid in a cell’s movement
 Flagellum: A long cellular appendage specialized for
locomotion. The flagella of prokaryotes and eukaryotes
differ in both structure and function.
 Pseudopodia: A cellular extension of amoeboid cells used
in moving and feeding
 Extracellular Matrix: the substance in which animal tissue
cells are embedded consisting of protein and
polysaccharides.
o Collagen: A glycoprotein in the extra cellular matrix
of animal cells that forms strong fibers, found
extensively in connective tissue and bone; the most
abundant protein in the animal kingdom.
o Proteoglycans: A glycoprotein in the extra cellular
matrix of animal cells, rich in carbohydrates.
o Integrins: surface receptor proteins that are built
into the plasma membrane
o Fibronectins: an ECM glyoprotein that attaches the
ECM to integrins
o Plasmodesmata: membrane-lined channels that span
the cell walls of two neighboring PLANT cells
o Desmosomes: a type of cell junction that fastens
cells together into strong sheets
o Gap Junction: a type of cell junction; a cytoplasmic
channel that connects neighboring cells; similar to
plasmodesmata of plant cells

Be able to...
Identify/Recognize a prokaryotic, eukaryotic, plant,
animal, or bacterial cell




Explain how proteins are made, processed and shipped
out of a cell
Explain how substances are transported across a
membrane either passively or actively
Identify the hypo/hypertonic solutions in a given
scenario; predict how substances will move
Calculate water potential from given values using water
potential equations
Unit 3- Cellular Energetics: Photosynthesis and
Respiration (Ch. 6-8)
What To Know…










Catabolic pathways: a series of degradative processes
(break down)
Anabolic pathways: a series of processes that build
complicated molecules from smaller ones
Bioenergetics: the study of how energy flows through
living organisms
Kinetic energy: energy associated with the relative motion
of objects (ex: thermal energy)
Potential energy: energy that is not kinetic energy that
matter possesses because of its location or structure (ex:
chemical energy)
Free Energy- the portion of a system’s energy that can
perform work when temperature and pressure are
uniform.
First Law of Thermodynamics- energy can be transferred
or transformed but never created or destroyed.
Second Law of Thermodynamics- every energy transfer or
transformation increases the entropy of the universe.
In order for a process to be “spontaneous” it must
increase the entropy, or disorder, of the universe.
Change in free energy can be calculated with Gibbs Free
Energy Equation:






If change in free energy is negative, then reaction is
exergonic
If change in free energy is positive, then reaction is
endergonic
ATP is the main energy molecule in a cell. It is a nucleic
acid consisting of ribose, adenine, and 3 phosphate
groups.
The hydrolysis reaction of ATP is exergonic and
immediately releases energy that can power cellular
processes.
Energy coupling- the use of an exergonic process to
power an endergonic one.
Roles of enzymes in biochemical reactions:
○ Enzymes’ names end in -ase
○ An enzyme is a catalytic protein
○ Activation energy is the energy that must be overcome
for a product(s) to undergo a chemical reaction
○ Enzymes speed up a chemical reaction by lowering the
activation energy barrier by stressing the chemical bonds of
the substrates (reactants in an enzymatic chemical reaction),
and/or creating an ideal environment (pH, salinity, temp.) for
the reaction
○ Only speed up reactions that would occur eventually
○ Very substrate specific (usually only 1 substrate fits into
the active site of 1 enzyme)
○ *Enzymes have optimal temps. and pH’s for reactions
○ *Inhibitors interact with enzyme in some way,
decreasing its effectiveness,
-->Non competitive inhibitors bond in places other
than active site (allosteric sites), competitive inhibitors
compete for the active site so that no other substrate can
bond there
○ *Allosteric regulation is the term for when a molecule
bonds to another site other than the active site (non
competitive inhibitors are examples) and can either inhibit or
stimulate enzymatic chemical reactions


Exergonic reaction- releases energy
Endergonic reaction- absorbs energy
○ Metabolism is the totality of an organism’s chemical
reactions

Metabolic pathway: a series of chemical reactions in
which a specific molecule is altered resulting in a specific
product
Oxidation: Loss of electrons “lost ox”
Reduction: Gain of electrons “Re Gain”
○ Feedback occurs when an enzymatic reaction occurs and the
product builds up, binds to the enzyme (not in its active site)
and either inhibits OR promotes the reaction. (negative = stops
enzyme activity, positive = stimulates)







Photosynthesis: process by which light energy is
converted to chemical bond energy and carbon from CO2
is fixed into organic compounds.
Autotrophs: “self-feeders”, organisms that produce
organic molecules from CO2 and other inorganic molecules
Heterotrophs: “other-feeders”, Can’t make own food-have
to obtain food from another source, they are consumers of
biosphere.
Stomata: Microscopic pores in leaves where CO2 enters
the leaf and O2 exits; water vapor moves through them as
well
Mesophyll Cell: Type of cell in the interior tissue of the
leaf; contains 30-40 chloroplasts!!! This is where the
majority of photosynthesis occurs.
Pigments are substances that absorb visible light (ex.
chlorophyll)
Accessory Pigments absorb different wavelengths of light
than chlorophyll to supplement total light absorption of
the organism










Light reactions of photosynthesis: In the thylakoids, splits
water (photolysis), releases O2, produces ATP and NADPH
to be used in dark reactions.
Electron carriers- transport energized electrons within the
process of photosynthesis and/or cellular
respiration. Examples include NADH, FADH2, NADPH.
*Chemiosmosis is the diffusion of ions across a
selectively-permeable membrane. More specifically, it
relates to the generation of ATP by the movement of
hydrogen ions across a membrane during cellular
respiration and/or photosynthesis. ATP synthase moves
H+ ions with the concentration gradient, thereby
harnessing energy into molecules of ATP.
ATP synthase is the enzyme that makes ATP by
chemiosmosis. It allows protons to pass through the
membrane using the kinetic energy to phosphorylate ADP
making ATP.
Dark reactions of photosynthesis/ Calvin Cycle/ Lightindependent reactions/carbon fixation- in the stroma,
forms G3P (sugar) from CO2 using ATP and NADPH
Photorespiration: on hot, dry days plants close stomata to
conserve water, which reduces access to CO2 and causes
O2 to build up; O2 is consumed and CO2 released without
producing ATP and sugar.
C4 plants- minimize photorespiration by using PEP
carboxylase to incorporate CO2 into four carbon
compounds in mesophyll cells- compounds go to bundlesheath cells and can release their CO2 there to be used in
Calvin Cycle
CAM Plants- open stomata at night to incorporate CO2 into
organic acids- stomata close during the day, CO2 released
from organic acids and used in Calvin cycle when light is
present, examples: cactus, pineapple (live in dry
environments)
Respiration- process by which biochemical energy
contained in nutrients is converted into ATP to power
cellular processes; two types--aerobic or anaerobic
Glycolysis- A process that breaks down glucose into two
molecules of pyruvate-a three carbon molecule. It’s the
first process in cellular respiration. It yields a small
amount of ATP, (4 ATP produced, but 2 ATP is the net
yield.)






The Citric Acid Cycle, or the Krebs cycle is a series of
enzyme-catalyzed chemical reactions of central
importance in all living cells that use oxygen (aerobic); it
follows glycolysis. In eukaryotes, the citric acid cycle
occurs in the matrix of the mitochondrion. It releases CO2
as a waste product; it produces FADH2, NADH, and ATP.
Oxidative phosphorylation- The final process in aerobic
cellular respiration. It is the production of ATP using
energy derived from the redox reactions of an electron
transport chain. The enzyme ATP synthase moves H+
ions with the concentration gradient to produce molecules
of ATP.
Alcohol fermentation- pyruvate produced in glycolysis is
converted to ethanol, releasing CO2- used by yeast in
brewing/baking/winemaking
Lactic acid fermentation- pyruvate produced in glycolysis
is reduced to NADH forming lactate with no release of
CO2; used by human muscle cells to generate ATP when
O2 is scarce→ causes cramps!
Facultative Anaerobes- Organisms that make ATP by
aerobic respiration if oxygen is present but may switch to
fermentation under anaerobic conditions.
Obligate Aerobe- An organism that requires oxygen for
cellular respiration and cannot live without it.
Be Able To…









Identify an exergonic or endergonic reaction based on the
value of delta G.
Use the Gibbs free energy equation
Explain how enzymes affect a chemical reaction; interpret
and analyze a free energy graph
Calculate rate of enzyme activity from given data
Explain how an enzyme’s effectiveness varies with certain
environmental conditions
Explain ways in which enzyme activity is regulated by
inhibitors and activators
Explain how photosynthesis and cellular respiration are
interdependent
Explain ways in which photosynthesis and cellular
respiration are similar/different

Predict how various environmental factors affect rate of
photosynthesis or respiration (ex: oxygen concentration,
CO2 concentration, light intensity, etc)
Unit 4- Cell Division and Communication (Ch. 9-10)
What To Know...
















Chromosomes: packages of DNA; Eukaryotes have linear
chromosomes; prokaryotes have circular chromosomes;
form of DNA when cell IS dividing
Chromatin: DNA and protein complex, organized into a
long thin fiber (“ball of yarn”); form of DNA when cell is
NOT dividing
Sister Chromatids: copies of the same chromosome;
identical genetic make-up
Centromere: the mid-point on the condensed form of
chromosomes “narrow waist”
Somatic Cells: All body cells except for reproductive cells;
human somatic cells contain 46 chromosomes (diploid
cells)
Gametes: Reproductive- sperm and egg cells, human
gametes contain 23 chromosomes (haploid cells)
Centrosome: Part of the cell that aids in division,
organizes the cells microtubules
Nucleoli: Dissappear during prophase, part of nucleus
organelles inside nucleus make ribosomes
Kinetochore: Specialized structures located in the
centromere region of the chromosome; where spindle
fibers attach
Spindle: The apparatus of microtubules that helps
chromosomes to move and separate during cell division
The Cell Cycle: the life cycle of the cell; consists of G1, S,
G2, and sometimes cytokinesis; review each of these
phases
Mitosis- produces two identical daughter cells; consists of
4 stages: Prophase, Metaphase, Anaphase, Telophase
Metaphase Plate: An imaginary plane equidistant between
the spindle’s two poles
Cytokinesis: Division of the cytoplasm following mitosis
Cleavage: Cytokinesis occurs by cleavage in animal cells
Cleavage Furrow: The beginning of cell division, shallow
groove in cell, first sign of cleavage











Cell Plate: Appears in telophase in plant cells, formation
of a new cell wall between the two new cells
Haploid Cell: A cell with a single chromosome set (n)
Diploid Cell: Zygotes and all other cells with two sets of
chromosomes (2n)
Homologous Chromosomes (aka. homologues):
Chromosomes with the same length, centromere position,
and staining pattern; carrying the same “types” of genes
but perhaps different versions
Sex Chromosomes: The X and Y chromosomes that
determine gender, female= XX; male=XY
Autosomes: All other chromosomes besides X and Y
Meiosis- type of cell division that produces 4, haploid,
non-identical daughter cells; consists of two divisions of
P,M,A and T.
Synapsis: Homologues come together in prophase I
Tetrad: Four closely associated chromatids of homologous
pair
Chiasmata: X-shaped regions formed between
homologous chromosomes during crossing over
Crossing-over: The reciprocal exchange of genetic
material between non-sister chromatids during prophase
I
Cell Cycle Regulation:
 Cell Cycle Control System: A cyclically operating set of
molecules in the cell that both triggers and coordinates
key events in the cell cycle (chemicals)
 Protein kinases: Enzymes that activate or inactivate other
proteins by phosphorylating them (adding a phosphate
group)
 Cyclin: A protein two which kinase attaches. It’s named
for its cyclically fluctuating concentration in the cell. It
reacts and binds with CDKs
 Cyclin-dependent kinases (CDKs): Kinases that must
attach to cyclin to be active
 MPF: The first cyclin-CDK discovered. It helps
phosphorylate proteins. Its concentration increases as the
cell cycle progresses from G1 to M. helps the cells
complete mitosis.
 Cell Cycle Checkpoints: Send critical signals through
signal transduction pathways to regulate the cell. They
tell whether processes have been completed correctly and
if the cell should continue (G1, G2, M)







Density-dependent Inhibition: When a cell population
reaches a certain density the amount of nutrients and
growth factors available become insufficient to all
continued cell growth; cell slow or stop their growth and
division
Anchorage Dependence: Cell must be attached to a
substratum (surface, ex: other cells, bone, protein fibers)
in order to divide. Signaled to cell cycle control system via
pathways involving plasma membrane proteins and
elements of the cytoskeleton linked to them
Tumor: A mass of abnormal cells within otherwise normal
tissue
Benign Tumor: When normal cells remain at the original
site (can become malignant)
Malignant Tumor (cancer): Becomes invasive enough to
impair the function of one or more organs
Metastasis: The spread of cancer cells to sites other than
the original
Karyotype: A method of organizing the chromosomes of a
cell in relation to number, size, and type; used to detect
and diagnose chromosomal abnormalities in cells
Asexual Reproduction



one parent involved
offspring are identical to
their parent
most often used when
organism is in favorable
conditions
Sexual Reproduction



two parents involved
offspring are not identical to
each other or their parents
most often used when organism
is in unfavorable or changing
conditions
3 Stages of Cell Signaling
1. Reception: the binding of a ligand (signal molecule) to a
receptor; this binding usually changes the shape of the
receptor thereby activating it
2. Transduction: usually involves multiple steps; its a series of
chemical reactions that each stimulate a subsequent reaction;
remember “dominoes”
3. Response: “output”; final reaction in the series; the “end
goal” of the pathway; often manifested as the turning on or off
of a gene.
Termination of signal: signal molecule detaches from receptor;
shuts down reaction
Be Able To...






Identify the phases of mitosis and/or meiosis from given
diagrams
Model the phases of mitosis and/or meiosis
Explain how genetic variation is generated in meiosis
How cell signaling affects the progression of a cell
through the cell cycle
Explain how cell-cycle regulation is related to the
development of cancer cells
Identify the three parts of a signal-transduction pathway
Unit 5- Genetics (Ch. 11-12)
What To Know...







Gene: A unit of hereditary information consisting of a
specific nucleotide sequence in a DNA molecule.
Genotype: The genetic makeup of an organism. (Ex: Bb)
Phenotype: the physical traits of an organism. (Ex: Brown
fur)
Alleles: Alternate versions of a gene. (B=allele, b=
another allele)
Homozygous: having two identical alleles for a given trait
(ex:BB or bb)
Heterozygous: having two different alleles for a given
trait. (ex:Bb)
If two alleles (versions of a gene) at a particular locus
differ, the dominant allele determines the phenotype
while the recessive allele has little if any affect on the
phenotype.

Genetic experiments identify parental (P), filial 1 (F1),
filial 2 (F2)...etc. generations

Law of Segregation- Mendel’s first law, stating that allele
pairs separate during gamete formation/ meiosis, and
they randomly reform as pairs during the fusion of
gametes at fertilization (Ex: B and b)

Law of independent assortment- Mendel’s second law,
two or more genes assort independently--each pair of
alleles segregates independently of each other pair during
gamete formation. (Ex: Bb and Nn)

Monohybrid aka hybrid: an organism that is heterozygous
with respect to a single gene of interest.

Test-Cross: used to determine if an individual with a
dominant phenotype is homozygous or heterozygous

Dihybrid: an organism that is heterozygous with respect
to two genes.

Dihybrid Cross: Phenotypic Ratio= 9:3:3:1

Incomplete dominance: a type of inheritance in which F1
hybrids have an appearance that is intermediate between
the phenotypes of the parental varieties (ex: Red petals x
White petals =all Pink petaled offspring).

Codominance: A phenotypic situation in which the two
alleles affect the phenotype in separate distinguishable
ways (ex: roan horse).

Pleiotropy: the ability of one gene to have multiple
effects/ phenotypes. (ex: sickle cell gene causes many
symptoms)

Epistasis: multiple genes interact to control one trait (B=
pigment, b=no pigment, R= Red fur, r=gray fur)

Linked Genes: genes located on the same chromosome

Sex-Linked Genes: genes located on a sex chromosome (X
or Y)

Chromosome Theory of Inheritance: states that genes are
located on chromosomes and that the behavior of
chromosomes during meiosis accounts for inheritance
patterns.

Parental Types: Offspring with phenotypes that match one
of the parental phenotypes.

Recombinants: Offspring whose combination of
phenotypes are different than their parents.

Genetic Map: An ordered list of the position of genes on a
chromosome.

Map units: A measurement of the distance between
genes; one map unit is equivalent to a 1% recombination
frequency.

X-Inactivation: the silencing/shutting off of one of two X
sex chromosomes in females (Ex: calico cats)

Barr Bodies: A dense object lying along the inside of the
nuclear envelope in female mammalian cells, representing
an inactivated X chromosome.

Aneuploidy: A chromosomal mutation in which certain
chromosomes are present in extra copies or are deficient
in number.

Trisomy: When a cell has an extra copy of one
chromosome, instead of two. Ex: Trisomy 21= Down’s
Syndrome

Monosomy: When a cell has only one copy of a
chromosome, instead of two. Ex: XO= Turner’s Syndrome

Deletion: A deficiency in a chromosome resulting from
the loss of a fragment though breakage.

Duplication: Duplication of a portion of a chromosome
resulting from fusion with a fragment from a homologous
chromosome.

Inversion: Reattachment of a chromosomal fragment to
the chromosome from which the fragment originated but
in reverse orientation.

Translocation: An attachment of a chromosomal fragment
to a nonhomologous chromosome.

Klinefelter syndrome- XXY in males

Duchenne Muscular Dystrophy: A genetic disease caused
by an x-linked recessive allele.

Hemophilia: A genetic disease caused by an x-linked
recessive allele.

Sickle Cell Anemia: An autosomal recessive disease
caused by a substitution of a single amino acid in the
hemoglobin protein in red blood cells. This disease
provides an advantage in that sickle cell patients are more
resistant to getting malaria. The sickle cell trait is more
common in African populations.

Cystic Fibrosis: An autosomal recessive disease that
affects the secretory glands of the body

Huntington’s disease: an autosomal dominant disease;
neurodegenerative effects, particularly affecting muscle
coordination

Mitochondrial inheritance: Since mitochondria are
inherited solely from the mother, genes contained in
mitochondrial DNA are only passed down from the
mother.

Chi-Squared Test: a statistical test used to determine if a
null hypothesis is supported by experimental data. The
null hypothesis states that there is NO relationship
between two given variables.
Be Able To...






Predict expected phenotypic/genotypic
ratios/percentages/fractions from a given genetic cross
using punnet squares and/or addition/multiplication rules
Identify an inheritance pattern from given data or
pedigree chart; provide reasoning
Explain the different kinds of inheritance patterns
(Complete dominance, codominance, incomplete
dominance, sex-linkage, mitochondrial
Calculate recombination frequencies from given data
Develop a chromosomal map from recombination
frequency data
Calculate Chi-Square values for given data using the
equation for Chi-square; identify whether null-hypothesis
is supported or not supported and explain why/why not.
Unit 6- DNA, Protein Synthesis and Biotechnology
(Ch. 13-16)
What to Know...



Frederick Griffith experiment- first transformation
experiment using Streptococcus pneumoniae bacteria. He
transformed a harmless strain of these bacteria into a
harmful strain by making exchange between the two
strains possible.
Hershey and Chase experiment- used radioactive sulfur
and phosphorus to trace the fates of protein and DNA of
viruses (phages) that infected bacteria. They were trying
to determine which of these molecules enters a host cell
during infection.
Erwin Chargaff- his experiment uncovered the base-pair
rule; there are equal amounts of adenine and thymine in
DNA, and equal amounts of cytosine and guanine.















Meselsohn- Stahl experiment- determine that DNA
replication is semi-conservative by having bacteria
replicate in the presence of heavy nitrogen (N-15) and
then again in the presence of light nitrogen (N-14).
Watson and Crick: the scientists who built models of a
double helix to conform to the X-rays and chemistry of
DNA
The code in DNA is based on a sequence of nucleotide
bases located along the length of the DNA
molecule. There are four possible nucleotide bases:
adenine (abbreviated “A”), cytosine (“C”), guanine (“G”),
and thymine (“T”).
DNA is a double-helix, with complementary bases located
on opposing backbones bound to each other by hydrogen
bonds. A and T are complementary, and C and G are
complementary.
C and T are known as pyrimidines, which must bond with
either G or A, their complementary purine.
Genes are a specific sequences of these bases that code
for a specific product, which is often a protein.
Chromosomes consist of hundreds/thousands of genes
DNA replication is semi-conservative (composed of half of
the original and half of the new DNA); it is the process
where a template is copied in order to make a second,
identical DNA molecule for the cell (in preparation for cell
division)
Anti parallel Elongation: two strands oriented in opposite
directions elongate in opposite directions (5’ → 3’)
Leading strand: the strand where DNA polymerase can
synthesize a complementary strand continuously, moving
toward the replication fork
Lagging strand: the strand where DNA polymerase must
work in the direction away from the replication fork;
copies in short segments called Okazaki fragments
Okazaki fragments: series of fragments that are
synthesized on the lagging strand and then joined by
ligase
Helicase: enzyme that “unzips” the DNA by breaking the
weak hydrogen bonds down the middle of the molecule
DNA polymerase: enzyme that adds complementary
nucleotides during replication, proofreads newly made
DNA, and replaces any incorrect nucleotides
DNA ligase: enzyme that “glues” the Okazaki fragments
together to create one smooth strand




Telomeres: nucleotide sequence that postpones the
erosion of genes near the ends of DNA molecules
Telomerase: enzyme that lengthens telomeres in gamete
cells
A DNA sequence is converted to mRNA by a process called
transcription.
The molecule RNA polymerase binds to DNA. The region
of DNA where RNA polymerase binds is called the
promoter. Several molecules known as transcription
factors assist RNA polymerase in the process of
transcription. Together, RNA polymerase, transcription
factors, and the promoter are known as the transcription
initiation complex. The promoter called a TATA box is
crucial in forming the initiation complex in eukaryotes.












RNA polymerase then “reads” along one strand of DNA
(known as the “template”), matching the complementary
nucleotide bases (uracil “U” replaces T in RNA) to those of
the template. These complementary bases are made by
RNA polymerase into a strand of mRNA.
Introns: DNA of eukaryotic genes contains sequences of
nucleotides that are not involved in coding proteins; will
be “cut” out
Exons: “Important” DNA sequences that code for proteins
that are spliced together
Splicesomes:
Made of a variety of proteins and several
small nuclear ribonucleoproteins (snRNPs) that recognize
the splice sites
snRNPs: helps recognize the splice sites
Alternative RNA splicing: Proteins of different sizes and
different amino acid sequences can be made from a single
mRNA strand due to different ways of grouping the bases
as introns or exons.
Transfer RNA is a folded piece of RNA containing, in part,
three nucleotide bases on one side (anticodon) and a site
where amino acids bond on the opposite end.
tRNA is specific to both the amino acid it binds to and also
to its anticodon. The anticodon is complementary for a
specific codon in mRNA.
Every three consecutive nucleotides on an mRNA molecule
make up a codon. Each codon in mRNA codes for 1 of 20
specific amino acids (protein monomers) in a protein
chain.
In ribosomes, mRNA is decoded and used to create an
amino acid chain in a process called translation.
When an mRNA molecule is read by a ribosome, it passes
through until it reaches the codon “AUG”, which can codes
for the amino acid methionine.
The ribosome, one codon at a time, attaches the specific
tRNA molecule to its complementary
codon. Simultaneously, the amino acid on this tRNA
molecule forms a peptide bond with the previously







attached amino acid. This process repeats as a long
protein chain is formed until the ribosome encounters a
“stop” codon in the mRNA, which stops the process of
translation.
Mutations: mistakes in the sequence of DNA, or
chromosome as a whole
Base pair substitutions: replaces one nucleotide and its
partner with another pair of nucleotides and can cause
missense or nonsense mutations
Base pair insertions or deletions: additions or losses of
nucleotide pairs in a gene and may produce a frameshift
mutation
Frameshift mutation: when a nucleotide is deleted or
inserted causing the reading frame of codons to shift
Missense mutation: codes for an amino acid but not
necessarily the right amino acid
Nonsense mutation: changes an amino acid codon into a
stop codon nearly always leading to nonfunctional
proteins
Mutagens: physical or chemical agents that can cause
mutations
Gene Regulation- ch. 15
 Operon- the entire stretch of DNA required for production
of a protein(s); include the promotor region, operator,
and the genes they control
 Promotor- a region on the DNA that marks the start of a
gene(s)
 Operator- region on the DNA to which a repressor binds
 Repressor- a protein (coded for by a regulator gene) that
binds to an operator and blocks transcription of another
gene(s)
 Corepressor- a small molecule that cooperates with a
repressor protein to switch an operon off
 Repressible operon- usually on but can be turned off by
attachment of a repressor (ex: trp operon)
 Inducible operon- usually off but can be turned on by
removing the repressor (ex: lac operon)
 Inducer: a molecule that inactivates the repressor and
turns on transcription
 Epigenetic inheritance- inheritance of traits transmitted
by mechanisms not directly involving a nucleotide
sequence.






Non-coding mRNAs (ncRNA)- mRNA that is transcribed
but not translated; instead it is used to regulate other
mRNA transcripts and/or genes
microRNA (miRNA)- a type of ncRNA that can bind to
complementary mRNAs and either degrade it or block its
transcription until a later time
small interfering RNA (siRNA)- a type of ncRNA that can
block the transcription of genes → this is called RNA
interference, or RNAi.
Oncogenes:
cancer causing genes
Proto-oncogenes:
normal cellular genes that code for
proteins that stimulate normal cell growth and division;
mutations may occur in these genes which can lead to
cancer
P53 gene: encodes a tumor-suppressor protein; mutations
in this gene can lead to cancer
Biotechnology
 Gel Electrophoresis: the process of separating DNA
fragments that have been cut by restriction enzymes. This
is due to the DNA being negatively charged and when a
current is run through the gel the fragments will go
towards the positive end. The bigger fragments will stay
closer to the wells they are placed in while the smaller
fragments will move further away. It helps identify the
differences in people because everyone has their own
unique restriction sites.
 Polymerase Chain Reaction (PCR): Multiple copies of a
small DNA sample can be made for further study.
 Transformation- a change in genotype and phenotype due
to the assimilation of external DNA by a cell; often
accomplished using vectors (for example, a DNA plasmid)
Be Able To…






Understand and explain results and conclusions from the
major historical experiments involving DNA.
Use base-pair rule to create a complementary DNA,
mRNA, tRNA and/or amino acid sequence.
Predict and explain the effects of a mutation
Explain the different ways in which genes are regulated
Predict/identify organisms that have been transformed in
a transformation experiment
Draw conclusions from a DNA fingerprinting experiment