BIOCHEMISTRY

THE BUILDING BLOCKS OF LIFE central carbon with an amino group (NH2), a carboxyl group Biological life survives by relying upon high-yield energy sources
(COOH), hydrogen (H), and one of 20 side groups (R) that define (such as solar radiation) to fuel life processes before releasing that
Four types of macromolecules (large, carbon-based organic
same energy as simpler, low-yield end products (such as heat).
molecules) are found in living organisms. Most are polymers— chains CAMOXYl 5IM G«OUP
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of molecules that form through dehydration synthesis (the loss of a 3HOUP J
FREE ENERGY CHANGE
water molecule). 0e0
All chemical reactions involve a change in free energy, AG. Exergonic
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A. Carbohydrates ： Energy-storing (MYCEROl FATTY ACO5
reactions release free energy (AG is negative) and are spontaneous.
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molecules containing carbon, Endergonic reactions absorb free energy (AG is positive) and are
hydrogen, and oxygen in a 1:2:1 A POVTPtPTlOE CHAIN non-spontaneous. The activation energy of a reaction refers to the
ratio. Monosaccharides, such as energy required to initiate the reaction.
the attributes of the amino
glucose (C6H12O6), are acid. ENZYMES

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single-sugar subunits often
D. Nucleic acids ： Polymers of Enzymes are biological catalysts, proteins capable of speeding
found as rings. Disaccharides
have two monosaccharide
nucleotides that encode chemical reactions without being consumed. Enzymes lower the
subunits. Polysaccharides, such genetic information. There are activation energy of a reaction (but do not affect AG, the free energy
as starch, glycogen, and two forms: deoxyribonucleic change). The substrate binds to the enzyme's active site in an induced

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acid (DNA) and ribonucleic fit, in which the enzyme changes its shape to wrap itself around the
cellulose, are long chains of
sugars.
acid (RNA). Individual substrate. Enzymatic activity can be activated or inhibited by other
nucleotides are linked by molecules.
B. Lipids ： Hydrocarbon-based molecules that are phosphodiester bonds and A. Cofactors： Some enzymes require inorganic cofactors or organic
hydrophobicinsoluble in water. There are three primary families of contain three basic parts:
lipids:

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1. Fats ： Large, energy-storing molecules, each built from two

a. One molecule of glycerol, a three-carbon alcohol.

1. Phosphate group
2. Five-carbon
deoxyribose in DNA,
ribose in RNA.
sugar:
coenzymes to react.
B. Competitive inhibitors ： Non-substrate molecules that block the
enzyme's active site.
C. Noncompetitive inhibitors: Bind to an allosteric site (receptor site

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b. Three fatty acids, long hydrocarbon chains that attach to the 3. One of four nitrogenous bases： away from the active site) and change the enzyme's
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glycerol backbone. (Hence, fats are also called a. Adenine and guanine, double-ringed purines. conformational shape so that it no longer accepts the substrate.
triglycerides.) b. Thymine and cytosine single-ringed pyrimidines.
c. RNA contains the pyrimidine uracil instead of thymine. D. Activators： Fit into an allosteric site and open the enzyme's active
2. Steroids： Four fused-hydrocarbon rings, such as cholesterol. site.
3. Phospholipids ： Glycerol with two fatty acids and a phosphate THERMODYNAMICS

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E. Feedback inhibition ： Halts enzymatic activity by an end product
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group attached (found in membranes). The first law of thermodynamics states that energy is never created or
that allosterically inhibits formation of an intermediate product.
destroyed, only transformed. The second law of thermodynamics
C. Proteins：Long polymer chains called polypeptides built from amino
states that entropy, or randomness, is always increasing. Every F. Cooperativity ： Occurs when a substrate binds to an active site,
acid subunits linked by peptide bonds. Every amino acid contains a opening additional active sites.
transformation of energy creates greater disorder.

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Every living organism is made up of cells, which are the independently, assist in biologically important reactions, and green pigment) and have a double membrane.
lowest level of structure capable of performing all the interact with membranes of neighboring cells. 2. Vacuole： Vesicle used to store water, proteins, and wastes.
activities of life. All cells arise from preexisting cells. C. Cytoplasm ： Semifluid medium called cytosol and all the 3. Cell wall： Rigid cellulose layer around the cell membrane.
CELLULAR PRECURSORS
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organelles inside the plasma membrane but outside the nucleus.

D. Cytoskeleton ： A system of protein filaments in the cytoplasm,
CELLS OF PROKARYOTES
Conditions on the early Earth allowed for the spontaneous abiotic
Prokaryotes include the simplest unicellular organisms and earliest
synthesis of organic compounds. This synthesis would have required including microtubules and microfilaments, that gives the cell
cells to evolve (bacteria). Major differences from eukaryotes:
an absence of atmospheric oxygen, because oxygen naturally breaks shape and helps direct movement.
A. Genetic material floats in
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down compounds and because the ozone (O3) layer today blocks the E. Ribosomes ： Proteins that work with RNA to synthesize
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the cytoplasm in a concentrated but unbounded region called the

intense UV radiation that fueled such synthesis. polypeptides. nucleoid.
A. Protobionts (collections of abiotically synthesized organic F. Cholesterol： Type of steroid (lipid with a carbon skeleton of four B. There are no
compounds) formed spontaneously as the precursors to cells. fused rings) that acts as precursor to many animal hormones. It membranebound organelles.
Protobionts such as coacervates (collections of macromolecules stabilizes the lipid bilayer of animal cells, preventing solidification
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that assemble spontaneously when shaken in water),

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microspheres (collections of protenoids), and liposomes

at low temperatures and fluidity at high temperatures.
CELL
(molecules within a lipid bilayer) can combine into larger cells or
bud into smaller ones, and can use enzymes to catalyze reactions.
TYPES OF CELLS TRANSPORT
CELLS OF EUKARYOTES PASSIVE MECHANISMS【REQUIRE NO ENERGY)

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B. The genesis of RNA, with its capacity to act as both a catalyst and
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a heredity blueprint, would have paved the way for Vie first real Eukaryotes include multicellular plants and animals and some A. Diffusion： Molecules move freely across a membrane to balance
cells. unicellular protists. Their cells contain membrane-bound organelles, a concentration gradient, from regions of high to low concentration.
CELL STRUCTURE each of which performs specific functions and increases efficiency: Diffusion of water is called osmosis.
A. Nucleus ： Membrane-bound storage site of genetic information B. Facilitated diffusion ： Molecules cross an impermeable or
A. Cell membrane ： Serves as an external barrier and encloses

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that determines heredity and directs the activities of a cell. semipermeable membrane down their concentration gradient but
organelles.
B. Mitochondria：Double-membraned power plant of the cell and the must do so via special channels.
1. The basic unit is a phospholipid molecule, with a polar
location of aerobic respiration.
phosphate group as its hydrophilic head and two nonpolar fatty
C. Smooth/rough endoplasmic reticulum (SER/RER) ： Network of
ACTIVE MECHANISMS〔REQUIRE ENERGY)
acid chains as hydrophobic tails.
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2. Individual phospholipids form a fluid phospholipid bilayer, with membranes where lipids and proteins are synthesized. Rough ER A. Active transport ： Transport of molecules from low to high
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hydrophilic heads facing out and hydrophobic tails facing in to is covered with ribosomes. concentrations across a membrane using an energy-dependent
form a nonpolar zone that separates the watery cell interior transport protein.
D. Golgi apparatus ： Organelle that packages and exports proteins
from the extracellular environment. B. Endocytosis ： Enveloping of an exterior substance within a
and lipids produced in the ER.
3. Cell membranes are semipermeable, allowing passage of membranous vesicle for admission to the cell interior.
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E. Vesicles： Sacs in which substances are transported or stored.

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gases, lipids, and small polar molecules but not charged 1. Pinocytosis： Endocytosis of dissolved liquid molecules.
F. Lysosomes ： Vesicles of digestive enzymes that degrade old
molecules (ions and proteins) or large polar molecules. 2. Phagocytosis： Endocytosis of undissolved solid matter.
cellular components.
B. Membrane proteins ： Protein molecules embedded in the bilayer
G. Plant cells contain several additional components: C. Exocytosis ： Extrusion of material from a cell by discharge from
that transport molecules unable to cross the membrane
1. Chloroplasts ： Sites of photosynthesis. Contain chlorophyll (a vesicles at the cell surface.
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Carbohydrote
Extracellular fluid choin

VocvoU Nuclear Nucleus

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Cytoplosmic NUClMlUS
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Mitochondnon
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Smooth •ndo
Chloroplash
Mudeus 也 smk
Hydrophibc reticulum Mitochondrion
Wmory pit Nudooius
region
Cytoplosm Rough
•ndopiasmk
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Mydrophobk Plosmo reticulum

mombrone Rough Ribosomes
region
•ndoplosmk
Cell wol lysosom
rotkulum
Cytoplasm Cell wall of Microvilli
odjo<n<ng Smooth membrane
Ch
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reticulum
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CELL MEMBRANE PLANT CELL ANIMAL CELL

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 CELLS (continued)
CELLULAR RESPIRATION AN OVtRVKW Of OXDATIVC RCSMUnON
1. Prophase ： Replicated chromosomes condense. Spindle forms
along cell equator. Nuclear envelope breaks down; spindle
Cellular respiration is the cellular process of oxidizing
glucose to obtain energy in the form of adenosine , 、 Cytoplasm
v.y IUUIUM :i
microtubules enter nuclear region, eventually attaching to
centromeres of chromosomes.
triphosphate (ATP). ACETYL COA | 2. Metaphase ： Chromosomes align along cell equator called the
4 Mitochond^ n

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metaphase plate but do not yet segregate to opposite poles.
GLYCOLYSIS CITRIC
Centromeres divide, freeing sister chromatids.
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Glycolysis is the oldest metabolic pathway, used by all cells, and a 3. Anaphase： Sister chromatids separate to opposite poles.
CYCLE
precursor to both the aerobic and anaerobic respiratory pathways. g<*(NADH] <*Q3 4. Telophase： Chromosomes uncoil at opposite ends and become
Glycolysis occurs in the cytoplasm. The six-carbon sugar glucose is enclosed by a reformed nuclear envelope.

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degraded to form two molecules of three-carbon pyruvate, resulting in C. Cytokinesis ： Physical division of the cytoplasm into two daughter
two NADH and two net ATP. GLUCOSE cells.
CO 』‘Cell membrane
FERMENTATION MEIOSIS
In the absence of oxygen, respiration relies on gfyeolysis to produce Meiosis produces four haploid nuclei called gametes from a single

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ATP in an anerobic process called fermentation. This process uses an diploid cell. Haploid (N) is half of the diploid number, in interphase,
organic molecule to accept the electron from NADH and reform NAD* CELL REPRODUCTION chromosomes are replicated and align in homologous pairs. Each pair
for glycolysis to run again. Much energy remains in bonds of DNA is the cell's genetic material, chromosomes are the contains a maternal and paternal homologue inherited from the
end-products, such as ethanol or lactic acid. There are three types of carriers of this genetic information. In prokaryotes, the previous generation. An important consequence of meiosis is that the
fermentation: chromosome is a single circle of DNA. In eukaryotes, each genomes are mixed and recombined

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A. Homolactic： Bacteria converts pyruvate into lactic acid.

B. Alcoholic ： Yeast and bacteria convert pyruvate into ethanol and

CO2.
chromosome is a complex of DNA and histone proteins
found in the nucleus.
BINARY FISSION
A. Meiosis I：
1. Prophase I ： Crossing-over occurs, an overlap between
homologous chromosomes at x-shaped junctures called
chiasmata and a resultant exchange of material.

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C. Heterolactic： Organisms produce lactic acid as well as other acids Prokaryotic cells reproduce via binary fission. In this process, DNA is
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replicated, and the cell splits in two roughly equal parts, each with a 2. Metaphase I： Spindle forms; joined homologous pairs line up at
and alcohols.
the center of the cell.
OXIDATIVE RESPIRATION copy of the cell's DNA.
3. Anaphase I ： Spindle shortens; chiasmata break apart, mater-
If oxygen is present, glycolysis leads to aerobic respiration, which EUKARYOTIC CELL CYCLE nal/paternal chromosomes dragged to opposite poles.

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produces a net total of 36 ATP per molecule of glucose. Eukaryotic cells reproduce via the creation of two identical diploid cells
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4. Telophase I：Chromosomes are set up at each pole; new haploid

A. Oxidation of pyruvate： Carbon dioxide splits off from pyruvate to from one diploid cell. Diploid (2N) refers to the total number of X StAGtSOMHOVSI
produce acetyl-CoA and NADH. chromosomes in autosomal (nonsexual) cells.
A. Interphase： The period between mitotic divisions during which
B. Citric acid cycle (Krebs cycle): Begins with acetyl-CoA joining

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chromosomes are not visible; comprised of three phases:
oxaloacetic acid to form citric acid, which is oxidized to CO2,
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yielding ATP, NADH, and FADH2. Oxaloacetic acid is regenerated MITOSIS Crossing R«c<xntNn«d
Ovef
for another cycle. Occurs in the mitochondria of eukaryotes and the 1 PROPHASC
2 MfTAFMASC
cytoplasm of aerobic prokaryotes. 1. ANAFHASC METAPHASf I
4 TllO*HAS€
TMf Rf ACTIONS Of TMf

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〈 )GLUCOSE cmK AOD KJttt Gi gap

phase
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|NAOH-T*CO'-
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&叫 COA 却
Synthesis pho$«
(chrotno&omM duplicated)
Oxaloocetate Citvole
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B. Meiosts II： Proceeds as a mitotic division, with each daughter cell

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from meiosis I splitting into two haploid gametes.
T»4 KMJt PHAMS Of A tUKATrOtK dUCVOl

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CELL CYCLE REGULATION
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1. Gi phase： Major period of cell growth.

2. S phase：Chromosome replication takes place, producing pairs of Cells divide in order to maintain a surface-to-volume ratio so that the
Fumorote sister chromatids (identical chromosomes) that are each cell has enough surface area to absorb nutrients and expel wastes
u-Keloglataraie connected by a centromere. relative to its volume.
A. The cell cycle is regulated internally by checkpoints at the Gi, G2,
3. G2 phase： Synthesis of cell machinery in preparation for cell

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[FAD Succincie _.
division.
and M phases. The checkpoints halt cell division until overridden
**»*.^-wSvcc inyl-CoA NADR B. Mitosis (M) phase： The division of genetic material and cellular (e.g., when the M checkpoint halts anaphase until the sister
chromatids are properly aligned).
U-P {3OP contents.
1. Cyclin-dependent kinases (enzymatic complexes that activate
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enzymes responsible for cell division) regulate the checkpoints,
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activating enzymes by phosphorylating them (changing their

shape and opening their active sites).

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INTERPHAStX^X
2. The kinases are in turn regulated by cydin, a protein present in
the celts at variable (cycling) concentrations.
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B. External signals can also regulate cell division.

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C. Chemiosmotic (oxidative) phosphorylation ： In mitochondria,

1. Growth factors are proteins that originate in one cell type and
electrons from NADH and FADFhflow through an electron transport
promote division in another cell type.
chain from high to low energy states through energy-releasing
2. Density-dependent inhibition stops cells from dividing once they
steps, establishing an electrochemical proton gradient across the
reach a certain density over a given surface area.
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inner membrane of mitochondria. O2 accepts the electrons to form

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3. Anchorage dependence prevents cells from dividing unless they

water. ATP is synthesized when H+ ions diffuse back across the
MHAPHASC attach to specific surfaces.
membrane through embedded proteins.
C. Cancer cells are cells that ignore cell cycle regulations and divide
TK STAGfS OF MITOSIS unchecked.
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 MOLECULAR GENETICS
NUCLEIC ACIDS THE CENTRAL DOGMA

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A. DNA occurs most often as a double helix, a spiral staircase-shaped molecule composed of two The process of gene ex pression/protein synthesis follows a specific order
nucleotide chains hydrogen・bonded to each other. A. DNA is transcribed into mRNA.
B. mRNA is then translated into protein.
1. One of these chains always ends with a free 3'・OH group, while the other always ends with a free

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5*-phosphate group.
2・The chains bind in opposing directions: the 5* end of one chain is hydrogen-bonded to the 3' end of its
partner.

DNA >mRNA $ PROTEIN

B. in double-stranded DNA, adenine hydrogen-bonds to thymine, and guanine hydroge bonds to cytosine.

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TtANSCmPTlON TKANUAT10N
1. Therefore, the proportion in DNA of adenine is always equal to that of thymine, and the proportion of
guanine is always equal to that of cytosine: A = T, G = C.
2. There is always an equal proportion of purines (A, G) and pyrimidines (C, T).
GENE REGULATION
DNA REPLICATION
Gene regulation in prokaryotes： Prokaryotes have genes organized in an operon contain- ing all the genes

AGCCTAT must pair with the chain TCGGATA). 北

A. Complementarity： The base sequence of one chain of DNA completely determines the sequence of its
partner in the double helix. Each chain is a complementary mirror image of the other (e.g., the chain

B. Semiconservative replication： After one onApoiynwov*

in a metabolic pathway, a promoter, and an operator (on-off switch). The operator controls whether RNA
polymerase will bind to the promoter and transcribe RNA. The operator can be controlled by both negative
and positive gene regulation.
A. Negative gene regulation：

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round of replication, the original pair is
1. Repressible operons are regulated by repressor proteins (encoded elsewhere than the operon).
not conserved. Each strand becomes
These proteins bind to the operator and prevent genetic transcription. Corepressors regulate the
part of a new duplex.
repressor proteins by binding onto an allosteric site.
1. when a DNA molecule rep cates, it separates at one end to form a replication fork. Each strand
a. Repressible operons function in anabolic pathways that synthesize end products from starter

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serves as a template for synthesis of a new strand・
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reactants.
2. DNA polymerase is
b. The end product itself can act as the corepresson so that once enough products are synthesized
enzyme that catalyzes the replication process, it moves along each DNA strand from the 5* to 3*
the machinery shuts off.
direction, so new strands are synthesized 5' end first, 3’ end last.
2. Inducible operons are also controlled by repressor proteins, but an inducer binds to an allosteric site
3. The leading DNA strand is synthesized continuously.

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on the repressor protein and inactivates it, triggering transcription.
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4. The lagging DNA strand is synthesized discontinuously in segments of nucleotides called Okazaki
fragments, which later join together with the help of DNA ligase. a. Inducible operons function in catabolic pathways that break down nutrients.
b. The nutrient itself sometimes acts as the inducer, such that enzymes are only created when they
will be used.

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B. Positive gene regulation：
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1. An activator protein binds to an operator and helps RNA polymerase attach to the promoter.
GENE EXPRESSION (PROTEIN SYNTHESIS' 2. Molecules can control the activator by bin ding to an allosteric site and ope ning its active site,
A. RNA transcription allowing the activator to bind onto the operator
1. The region of DNA
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Gene regulation in eukaryotes： Eukaryotic gene regulation occurs at several levels.
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encoding the desired gene

is unzipped, and the A. Modifications on chromatin： Chromatin is a tightly packed form of DNA. Modifications on chromatin can
enzyme RNA poly ・ merase prevent or promote tran scripti on by altowing or barring access to in dividual genes.
copies the nucleotide 1. DNA methylation (the attachment of a CH3 methyl group to DNA bases) inhibits genetic expression.
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2. Histone ocetylation (the addition of a COCH3 acetyl group to the DNA-binding histone proteins)
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sequence to make a strand

of messenger (m) RNA. loosens the grip of histones on chromatin and allows transcription.
Though the two strands of TRANSCRIPTION B. Control elements ： Distal control elements ("enhancersw) and proximal control elements are both
DNA proteins that bind to DNA at specific (non-coding) DNA binding domains. Control elements activate

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are complementary, only one strand (the template strand) is transcribed into mRNA.
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2. Non codi ng seque nces of mRNAcalled introns are removed, an dthe remaini ng sequenc ・
transcription by attaching to RNA polymerase and forming a transcription initiation complex along the
es, called exons, are spliced together. promoter.
3. The mRNA leaves the nucleus. C. Steroid hormones： Steroid horm ones coordinate express io n of multiple related genes by binding to
B. Translation specific receptors that activate transcription in those genes.

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1. A ribosome (a complex of ribosomal (r)RNA and pro ・ tein) D. Regulatory proteins ： Regulatory proteins can control the rate of degradation of mRNA and can block
binds to an mRNA transcript and reads a triplet of nucleotides, mRNA translation by preventing ribosomes from binding to mRNA. Proteastomes are protein complexes
called a codon. that can recognize and degrade proteins, thereby curtailing their activity.
2. The ribosome binds the matchi ng anticodon of a transfer
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(t)RNA molecule, which is attached to a spe・ cific amino acid,

into the ribosome's A-site.
3. Sequential mRNA codons call new tRNA-amino acids into the MUTATION
A-site, shifting previous tRNA-amino acids to the P-site # where A. Point mutations ： Mutations that affect single genes through a base-pair substitution, dele・ tion, or
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they link to form a polypeptide chain insertion.

until a "stop" codon is reached.
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STRUCTURE OF A (RNA MOtECUlE

1. Deletions or insertions that are not in a multiple of three cause a frameshift mutation, in which all
downstream codons are altered.
Nucleus Amino acids 2. Point mutations may have no effect, may improve or damage the protein, may create a novel protein,
or may create a nonfunctional one.
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Valine = Mothioninc
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B. Chromosomal mutations： Mutations that affect an entire organism.

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1. Nondisjunction： An error in chromosomal distribution during meiosis, which results in aneuploidy, or
gametes with an abnormal chromosome count
mRNA : tRNA
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2. Polyploidy： A mutation in which gametes contain more than two full sets of chromo・ somes.
Ribosome O Chain
wtthp bonds
Polyploidy is generally less fatal (or altering) than aneuploidy.
3. Mutations can also occur on individual chromosomes. These include:
a. Deletion： A chromosomal fragment gets detached during cell division;
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O Transaiption of ❷!RNA txnds to ❸ Ribosome takes tRNA 0 Proiem winds in b. Duplication： That same fragment joins its homologous chromosome;
mRNA from DNA its amino ocid for next mRNA codon 2°, 3° slruclures
c. Inversion： That fragment gets reinserted backward; or
d. Translocation： That fragment gets attached to a nonhomologous chromosome.
AN OVERVIEW OF PROTEIN SYNTHESIS 4. The effects of chromosomal mutation are often fatal or can result in genetic disease but in rare cases
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may improve an organism's fitness.

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 MEIMDELIAN GENETICS
Genetics is the study of the heredity of organisms. A gene is MENDEL'S FIRST LAW (LAW OF SEGREGATION) occurred because the dominant allele determines the phenotype
the basic unit of heredity；an allele is one of two or more alter in heterozygotes by masking the recessive allele.
A. Single-trait crosses ： Mendel took two different strains of true-
2. Then, Mendel crossed two Fi plants. 3/4 of the plants in F2, the
native forms of a specific gene. breeding pea plants, one with green peas
second generation of pea plants, showed the dominant trait; 1/4
INTRODUCTION and one with yellow peas, and crossed showed the recessive.
them. In modern terms, this monohybrid B. From these results, Mendel came up with three postulates:
A. Until the 20th century, scientists believed that traits from the parents

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cross used homozygous plants, having
would blend in the offspring (e.g., a tall father and short mother 1. Alternative forms of a trait are controlled by different alleles of the
the same allele inherited from each gene responsible for that trait.
results in a child of medium height). Eventually, all members of a
parent. 2. When gametes (haploid reproductive cells) form in diploid
species would look the same.
1. The first-generation plants, Fi, were
B. Gregor Mendel, by crossing different strains of garden peas and individuals, the two alternative alleles for a gene segregate from
heterozygous (having inherited two

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analyzing the results, created the genetic theory still used today. each other.
different alleles of a gene) but showed
3. Every gamete has an equal chance of receiving either member of
only one trait This
an allele pair.
MENDEL'S SECOND LAW (LAW OF INDEPENDENT ASSORTMENT) 1. Phenotype is intermediate between the two parental phenotypes (incomplete dominance).

A. Mendel also conducted several multi-trait (dihybrid) 2. Phenotype resembles homozygous dominant, but is still distinguishable from it (partial dominance).

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crosses, in which he crossed peas that were heterozygous 3. Both parental phenotypes can be identified in the offspring (codominance).
for two genes. C. Pleiotropy： Instance when a gene produces more than one phenotypic effect.

B. in each case, he observed a 9:3:3： 1 phenotype ratio and WW06 WWOg WwGO D. Sex chromosomes： Specific chromosomes that dictate the sex of certain organisms (the remaining
concluded that genes located on different chromosomes chromosomes are called autosomes).
assort independently of one another.
GENETICS
A. Genotype： The genes an in dividual has.
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1. in humans, there are two sex chromosomes, X and Y.
a. Males possess one each of X and Y chromosomes.
b. Females possess two X chromosomes.
2. Sex-linked inheritance：In humans, a male expresses all traits unique to the X chromosome he inherits

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B. Phenotype： The physical appearance of an individual.
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B. Incomplete dominance ： sometimes heterozygous from his mother. Males are afflicted with X-linked disorders because there is no counterpart on the Y
chromosome to express the functional allele.
genotypes result in phenotypes that do not precisely
resemble one pare nt. TRAIT CtOSS
GAf(N W>SMOOTH wVWl

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B. DNA ligase glues the cut fragments in solution with phosphodiester cloned gene is re-excised using restriction enzymes.
PLASMIDS
bonds, creating a piece of recombinant DNA containing both the
Plasmids are self-replicating rings of bacterial DNA. A plasmid can be
gene and the plasmid.
used as a cloning vector, in which a gene of interest is spliced into that
C. Transformation of the plasmid reintroduces the recombinant DNA

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plasmid and reintroduced into the bacteria for mass replication.
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into bacteria by electroporation, an electric shock that temporarily

A. Restriction enzymes (enzymes that cut DNA at specific sequences)
makes the bacteria's plasma membrane permeable.
cut open the plasmid and excise the gene of interest from its host
D. Bacterial growth in culture replicates the gene (within the plasmid).
DNA.
The recombinant plasmid DNA is isolated from the bacteria, and the

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 ments migrate at differential rates: shorter fragments travel farther analyzes whole molecules of mRNA rather than fragments of DNA cut
POLYMERASECHAINREACTION
down the gel than longer ones do. by restriction enzyme digest.
A PCR (polymerase chain reaction) can be used to clone DNA in vitro.
A. Heating the gene of interest separates it into single strands. D. A DNA ladder is run in one of the wells, containing fragments of
B. Cooling the solution allows the gene to bind with primers that are benchmark sizes used to identify the sizes of the other fragments.
complimentary to the ends of the target gene. E. The gel is dyed with a solution that binds to DNA and makes it glow
C. DNA polymerase adds new nucleotides to the primers, creating new under ultraviolet light. The DNA glows pink under the light and can
copies of the target gene. be physically cut from the gel and isolated.
D. Reheating the products continues in cycles such that new DNA is
BLOTTING

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created in mass.
Southern blotting, an extension of electrophoresis, pulls DNA
GEL ELECTROPHORESIS fragments from an electrophoresis gel onto a piece of nitrocellulose
Gel electrophoresis is used to isolate DNA fragments by size.
paper by the capillary action of an alkaline solution. The paper is
A. DNA cut with restriction enzymes is placed in wells at the end of a
removed, and a radioactive probe of single-stranded DNA binds to the

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gel, and this gel is bathed in an aqueous solution. target DNA. The radioactive DNA shows up on a piece of film placed
B. An electrical charge is passed through the gel, pulling the polar
onto the paper.
DNA molecules through the gel.
C. Variations in size among DNA fragments make the frag Northern blotting is similar to Southern blotting except for the fact that it

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Evolution is the process by which species change gradually population. B. Sexual selection ： Individuals with traits that appeal to sexual
over time. It arises from processes of selection that favor 2. Bottleneck effect ： Only a few individuals of a species survive a
partners are more likely to pass on those traits to succeeding
individuals having certain favorable traits over those lacking disaster. generations. Various traits may be preserved not because they enhance
those favorable traits. C. Gene flow ： Movement of genes from one population to another survivorship but because they increase reproductive success.

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NEO-DARWINIAN THEORY through migration of individuals between populations and/or mating C. Artificial selection： Humans intentionally breed animals to enhance
between separate populations. specific traits.
A. Principle of variation ： Variations in morphology, physiology, and
behavior occur among individuals in any given population. TYPES OF SELECTION COEVOLUTION
B. Principle of heredity ： Offspring resemble parents more than they A. Natural selection ： Individuals produce more offspring than can Coevolution is the long-term evolutionary adjustment of one group of

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resemble other members of the population. survive. Because individuals compete for limited resources, those organisms to another.
C. Principle of selection ： Individuals with certain traits more with favorable variations and traits are more successful at passing A. Predator-prey interactions：Both plants and animals develop special
successfully survive and reproduce, passing those traits to the next on those traits to succeeding generations. Over time, those traits defenses when they interact competitively with other organisms.
generation. become prevalent, while disadvantageous traits occur with
B. Symbiosis ： A relationship in which two kinds of organisms
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decreased frequency.
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EVOLUTIONARY FACTORS 1. Directional selection ： Selection favors an extreme phenotype,

consistently live together.
A. Mutation ： A permanent change in a celKs DNA, causing diversity 1. Commensalism： A relationship in which one individual is closely
the frequency of which increases over time.
among individuals. associated with another and benefits without doing harm to the
2. Stabilizing selection ： Selection acts to eliminate both extreme
B. Genetic drift ： A random change in the frequency of alleles. Two host.
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phenotypes. The frequency of the intermediate phenotype

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instances of genetic drift cause individuals' genes to be unnaturally 2. Mutualism： A relationship that benefits both organisms involved.
increases over time. 3. Parasitism： A type of predation in which one organism lives in or
overexpressed:
3. Disruptive selection：Selection acts to eliminate the intermediate on a host and benefits while harming the host
1. Founder effect： Only a few individuals of a species start a new
phenotype from a population, favoring the extremes.

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POPULATION GENETICS
Population genetics is the study of the properties of genes in when there are no limits on its rate of growth. N is the population size; represented by：
populations (as opposed to in individuals). dN/dt is the rate of change in population size over time; and r： is the

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p2(a) + 2pq(ab) + q2(b) = 1
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POPULATIONS population's capacity for growth. or

B. Carrying capacity ： dN/dt = rN[(K - N)/K]; the size at which a 1 = (p + q)2 = p2 + 2pq + q2
A. Size ： Small populations are more likely to go extinct because
population stabilizes in a particular environment, based on available
random events or disturbances may affect the population
resources, predation, competition, and niche.
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disproportionately. Also, inbreeding may eliminate the genetic
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A. Population： An interbreeding group of the same species.

diversity necessary for the population to thrive. HARDY-WEINBERG PRINCIPLE 1. Every species has a niche defined by its lifestyle factors (e.g.,
B. Dispersion ： Widely spaced populations may not thrive because In the absence of mutation, migration, genetic drift, and nonrandom behavior, habitat, predation).
individuals may not interact often enough to reproduce sufficiently. selection, allele and genotype frequencies remain constant in a 2. Overlap of niches results in competition until competitors are
random-mating population. Dominant alleles do not replace recessive
eliminated or displaced into a different niche.
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POPULATION GROWTH ones because the frequencies do not change. Mathematically:

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If the frequency of allele a is p, and the frequency of allele b is q, then B. Community： All the populations (biotic factors) in an area.
A. Biotic potential：dN/dt = nN; the rate at which a population increases
the genotype frequencies after one generation of random mating are C. Ecosystem： All the biotic and abiotic factors in an area.
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D. Biome： A large region with distinct plant and animal life. c. Oceanic/pelagic zone： Surface layers of the open ocean. into atmosphere. Plants transpire, also sending water into
1. Tropical rain forest ： Infertile soil but heavy rainfall; dense d. Aphotic/abyssal zone： Deep-water areas; no sunlight. atmosphere as vapor. Water vapor condenses into clouds and
precipitates into rain. Rain falls back to Earth, collects on land as
vegetation. Greatest biodiversity of any biome. lO.Freshwater： Ponds, lakes, rivers; tied closely to terrestrial
runoff or groundwater, and runs back into oceans.

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2. Savanna ： Open grassland with scattered trees; transitional habitats. Lakes in temperate regions see thermal stratification.
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• Carbon cycle ： Plants incorporate airborne CO2 into organic

between rain forest and desert; found primarily in Africa. <3% of the Earth's surface.
compounds. Primary consumers eat plants. When organisms die,
3. Desert： Sparse, arid; large daily fluctuation in temperature. ECOLOGICAL SUCCESSION their carbon is locked into fossil fuels or decomposed by microbes.
4. Chaparral： Coastal area with short evergreen shrubs; mild, rainy
Communities change through an orderly process of succession. Burning of fossil fuels, decomposition of organisms, and cellular
winter; hot, dry summer. A. Pioneer organisms move into an uninhabited area.

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• Nitrogen cycle: Nitrogen-fixing bacteria convert atmospheric N2 gas

5. Temperate grassland ： Rich soils, abundant precipitation, B. With succession, the community's biomass, complexity, species
diversity, and capacity to process nutrients all increase. into ammonium (NH4+). Nitrifying bacteria convert ammonium into
agriculturally productive; covers much of the Americas.
C. The result is a stable climax community.
nitrites (NO2_) and nitrates (NO3_), which are assimilated by plants,
6. Temperate deciduous forest： Deciduous trees (drop leaves every
which are then eaten by animals. After plant or animal death,
ENERGY FLOW
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winter); warm, rainy summer; cool winter. decomposers (bacteria, fungi) convert nitrogen back to ammonium
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7. Energy in an ecosystem flows among organisms of different trophic

Taiga： Northern coniferous forest with long, cold winter. (NH4+). Denitrifying bacteria process nitrogenous compounds back
levels. Primary producers (plants, chemosynthetic bacteria) have the into atmospheric N2 gas.
8. Tundra： Cold; little precipitation or vegetation; permafrost exists
most biomass, followed by primary consumers (herbivores) and • Phosphorous cycle：Phosphorous-containing rocks weather into soil;
near the surface; covers -20% of Earth's land area.
secondary and tertiary consumers (carnivores, omnivores). Finally,
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9. Marine： Salt water; covers -75% of Earth's surface;

plants take up phosphates (PO43-) from soil. Animals eat plants;
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decomposers (saprophytes) break down organic remains and excretions. decomposers break down dead plants and animals, returning
home to 10% of living species. Divided into zones: Only 10% of a trophic level's energy flows to the next; the rest is lost to phosphates to soil. Leaching removes phosphates from soil via water
a. Intertidal/littoral zone ： Shorelines and coasts; subject to respiration, heat, and so on. that runs into lakes and streams. Sedimentation forms new
periods of wet and dry. CYCLES IN THEENVIRONMENT phosphorous-containing rocks.

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b. Neritic zone： Shallow waters to the continental shelf.

• Water cycle ： Solar energy causes water to evaporate from oceans

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