AP Biology Review Sheet

Gene Expression and Regulation

1. Structure of DNA – (deoxyribonucleic acid) double helix twisted shape of genetic
material discovered by Watson, Crick, and Franklin.
a. Subunits of Nucleotides.
i. a phosphate.
ii. a nitrogenous base – linked with phosphodiester bonds between the
sugars and phosphates.
1. Adenine – purine; (double-ring shape).
2. Guanine – purine; (double-ring shape).
3. Cytosine – pyrimidine; (single-ring).
4. Thymine – pyrimidine; (single-ring).
iii. 5 carbon sugar (deoxyribose).
b. Antiparallel Strands – one runs 3’ to 5’ the other runs 5’ to 3’ sides of phosphates
and sugars (backbone), rungs of paired bases with hydrogen bonds in between.
c. Base Pairing Strands – Complementary.
i. A – T (2 hydrogen bonds).
ii. G – C (3 hydrogen bonds).
d. Location of DNA
i. In eukaryotes DNA is found in nucleus on multiple linear chromosomes (a
chromosome IS a strand of DNA with proteins and others).
ii. In prokaryotes DNA is not in a nucleus and is usually a single circular
chromosome.
iii. Prokaryotes, viruses, and eukaryotes can contain plasmids (small
extrachromosomal DNA that is double stranded DNA).
2. DNA Replication – process of making exact copies of DNA for mitosis or meiosis (semi-
conservative process).
a. Enzyme (DNA helicase) unzip strands by breaking hydrogen bonds.
b. “Spare” nucleotides are added bidirectionally to bond complementarily with use
of DNA polymerases.
c. DNA polymerase can only add to the 3’ to 5’ side and new DNA is made in the 5’
to 3’ direction.
d. Replication bubbles open up and a replication fork is created because bubble is
in one half and it has one side 3/5 and one 5/3.
e. RNA primers must be laid down to start process.
i. RNA primase makes primers.
f. Leading strand makes DNA continuously (3/5).
g. Lagging strand makes DNA discontinuously (5/3).
i. Okazaki Fragments – lagging strands made in pieces of nucleotides.
h. Lagging strand requires enzyme (DNA ligase) to fuse fragments.
3. Flow of Genetic Information – Central Dogma of Biology.
a. DNA – transcription (in nucleus) – RNA – translation (in cytoplasm) – Proteins.
4. RNA – (ribonucleic acid) single stranded genetic material made of nucleotides.
a. Ribose Sugar.
 b. Nucleotides – Uracil instead of Thymine.
i. A – U.
ii. C – G.
c. mRNA – carries genetic information from DNA to the ribosome.
d. rRNA – part of ribosomes with catalytic functions.
e. tRNA – binds and transports amino acids to the ribosomes and are used in
translation.
f. RNAi – molecules used for gene expression regulation (turning genes on and off).
5. DNA Transcription
a. mRNA is made in the nucleus; RNA polymerase enzyme reads DNA (3’ to 5’) and
creates complementary mRNA.
i. TATA Box where RNA polymerase binds and begins.
ii. Transcription Factors – proteins that enhance transcription and help RNA
polymerase into correct shape.
iii. Elongation – adding of RNA nucleotides; does not stay attached to DNA.
iv. Termination – ends when RNA pol reaches a termination sequence.
6. mRNA Editing
a. Introns cut out; exons are left and spliced together using spliceosomes (snRNP’s).
b. Add poly-A tail to 3’ and GTP cap to 5’.
c. Each 3 nucleotide sequences are called a codon.
d. Go to ribosome (free or in rough ER).
7. Translation
a. mRNA code is read and matched with tRNA (brings amino acids) to construct a
polypeptide using the ribosome.
i. Have a corresponding amino acid for that codon of mRNA.
b. Initiation – mRNA 5’ end attaches to small ribosome.
i. tRNA with anticodon UAC attaches to start codon AUG.
ii. Large ribosomal subunit binds and tRNA is in P site.
c. Elongation – new tRNA enters A site.
i. Peptide bond forms when amino acid is transferred from tRNA in P site to
A site.
ii. Translocation occurs and tRNA in A site moves to P.
d. Termination – ribosome encounters stop codon (UAA, UAG, UGA).
i. If in ER – polypeptide is released into ER, then to Golgi complex, vesicle to
cell membrane, then exocytosis (may be given signals for exit).
e. Free ribosomes typically make products for the cell and are not exported.
8. Genetic Mutations – error in genetic code; change of DNA sequence (may be inheritable
if in egg or sperm).
a. Point Mutations – one nucleotide error (substitutions).
i. Nonsense Mutations – original codon becomes a stop codon (stops
protein synthesis).
ii. Missense Mutations – original codon becomes altered and produces a
different amino acid.
 iii. Silent Mutation – codon code changes but codes for the same amino acid
(no change in protein sequence).
9. Gene Rearrangements – DNA sequences that have been altered.
a. Insertion or Deletion – gain or loss of DNA or a gene.
i. Frame Shift Mutations – one or more bases deleted or inserted.
b. Duplications - extra copy of genes is caused by unequal crossing over during
meiosis or chromosome rearrangements.
c. Inversions - changes occur in the orientation of chromosomal regions.
d. Translocations - 2 different chromosomes (or 1 chromosome in two different
places) break and rejoin so that DNA sequence or gene is lost, repeated, or
interrupted.
e. Transposons - gene segments that can cut/paste themselves throughout the
genome.
10. Gene Regulation – Prokaryotes and Eukaryotes
a. Prokaryotes
i. Inducers (turn genes on) and repressors (turn genes off) – small
molecules that interact with regulatory proteins or regulatory sequences.
1. Regulatory proteins inhibit gene expression by binding to DNA
and blocking transcription (negative control).
2. Regulatory proteins stimulate gene expression by binding to DNA
and stimulating transcription (positive control) or binding to
repressors to inactivate repressor function.
b. Eukaryotes
i. Transcription factors bind to DNA sequences and regulatory proteins.
1. Some of these transcription factors are activators (increase
expression), while others are repressors (decrease expression).
2. The combination of transcription factors binding to the regulatory
regions at any one time determines how much, if any, of the gene
product will be produced.
11. Immunity – plants, invertebrates, and vertebrates have multiple, nonspecific immune
responses.
a. Mammals – specific immune responses triggered by natural or artificial agents
that disrupt dynamic homeostasis.
i. Mammalian Immune System – cell mediated and humoral responses.
1. Cell-Mediated Response – target intracellular pathogens when
antigens are displayed on the outside of the cells.
2. Humoral Response – produce antibodies against specific antigens.
b. Antigens – recognized by antibodies to the antigen; proteins produced by B cells,
and each antibody is specific to a particular antigen.
i. Second Exposure to Antigen – fast and enhanced immune response.
12. Viruses – nonliving agents capable of infecting cells in a host cell.
a. Bacteriophage – virus that infects bacteria.
b. Replication – Lytic and Lysogenic Cycle; Viruses inject DNA or RNA into host cell.
 i. Viruses have highly efficient replicative capabilities that allow for rapid
evolution.
ii. Viruses replicate via the lytic cycle, allowing one virus to produce many
progenies simultaneously.
1. Virus replication allows mutations to occur through usual host
pathways.
iii. RNA viruses lack replication error-checking mechanisms; has higher rates
of mutation.
iv. Related viruses can combine/recombine information if they infect the
same host cell.
v. Some viruses are able to integrate into the host DNA and establish a
latent (lysogenic) infection.
vi. Genetic information in retroviruses is a special case and has an alternate
flow of information: from RNA to DNA.
1. Made possible by reverse transcriptase, an enzyme that copies
the viral RNA genome into DNA.
2. DNA integrates into the host genome and becomes transcribed
and translated for the assembly of new viral progeny.