BIO 325 - EXAM 2 | FALL 2026 BOULETTE

What are the steps of replication for RNA? Include proteins used in each step.

1. Initiation

   • RNA pol binds to promoters on DNA

2. Elongation -

3. Termination

What are the steps of recombination? Include proteins used in each step.

1. Double Strand Break

   • Meiotic Prophase: Spo11 protein makes double strand break on one of chromatids

2. Resection

   • Exonuclease degrades 5’ ends on each side of break to make two 3’ single strand tales

3. First Strand Invasion

   • Dmc1 helps one of the tails invade + open other chromatid’s double helix

   • Invading strand scans for complementary sequence of sufficient length → two strands form heteroduplex(nonidentical sequences)

CROSSOVER PATHWAY

1. Form Double Holliday Junction

   • Make D loop big enough until can form complementary base pairs

   • DNA ligase forms bonds btwn adjacent ends to rejoin DNA strands w/o losing/gaining nucleotides

   • Junction = X shaped structure

2. Branch migration

   • Zip up by base pairing w/ complementary strands of parental double helix

3. Resolution of double Holliday junction

   • Resolvase breaks DNA strands at each junction, cut at each X intersection/junction

OR NONCROSSOVER PATHWAY

What is the noncrossover pathway? Include proteins used in each step.

1. Strand Displacement/Annealing

   • invading strand extends via DNA synthesis; anticrossover helicase disentangles invading/nonsister chromatid

2. DNA synthesis/ligation

   • gap is filled by DNA synthesis and sealed via DNA ligase

   • no crossing over, heteroduplex region remains in one chromatid

How does where Holliday junctions are cut contribute to crossing over?

What is a Holliday junction?

interlocked regions of two nonsister chromatids in recombination intermediates — similar base pair sequences but not the same → look like X

What is gene conversion?

The physical change of one allele in a heterozygote into the other

When can gene conversion occur?

• mismatched bases in heteroduplexes → mismatch repair

  • basically fix the mismatched base to a matching base for one of the bases

• END RESULT: see both chromatids will have the same allele

What would you see if gene conversion happened?

What are the ratios of gene conversion?

What is a forward mutation?

change wild type allele to a different allele

What is a reverse mutation?

mutant allele reverts back to wild type

What is more likely to happen: a forward or a reverse?

Forward. There are very few ways to restore function in a gene once it has been disrupted

What is a substitution?

a base at a certain position in one strand is replaced by a different base

What is a transition?

Purine replaces another purine (AG) OR pyrimidine replaces pyrimidine (CT)

What is a transversion?

purine becomes pyrimidine or vice versa

What is a deletion?

when a block of one or more nucleotide pairs is lost from a DNA molec

What is an insertion?

the addition of one or more nucleotide pairs

How do you find the mutation rate of a gene?

What did the fluctuation experiment do? What did it find?

Salvador Luria and Max Delbruck

What is the origin of bacterial resistance? Is it in response to the environment or is it mostly due to spontaneous mutations?

• if mutation occurs early, cell will produce many mutant progeny prior to plating. if mutation occurs late, we’ll see less mutant progeny on another plate → fluctuation in numbers of resistant colonies

  • diff liquid cultures spread on separate petri plates

• if resistance is a response to infection by bacteriophage, exposure should result in equal number of resistant colonies when spread on separate plates

RESULT

• bacterial resistance comes from mutations that exist before exposure to bacteriophage

What did the replica plating experiment do? What did it find?

1. invert master plates (no penicillin in medium) and imprint the colonies onto a velvet surface

2. invert a second plate (replica plate with penicillin) onto the velvet to pick up the colony imprint

3. incubate

4. only penicillin resistant colonies will grow → compare with position of colonies on the original plate

   • if mutations occur prior to exposure, all penicillin resistant colonies should grow in the same position on all replica plates

What is a genetic screen? What is an example?

What is genetic selection? What is an example?

What are the 5 natural processes that produced mutations?

1. depurination

2. deamination

3. x-rays

4. UV light

5. oxidation

What is depurination?

a purine base is hydrolyzed (taken out) of the deoxyribose-phosphate backbone → apurinic site can’t specify a complementary base → get random base

What is deamination?

the removal of an amino (—NH₂)

• change C to U

• if replicated, may alter C:G → T:A (transition mutation)

How do X-rays/cosmic rays lead to natural mutations in DNA?

breaks sugar phosphate backbone → leads to deletion or improper religation

How can UV light exposure lead to natural mutations in DNA?

causes adjacent thymine residues to become chemically linked and form thymine dimers → substitutions

How can irradiation lead to natural mutations in DNA?

create free radicals/oxidation → alter bases → substitution

What is the difference between mutations that arise spontaneously vs because of a mutagen?

What is a mutagen?

a physical or chemical agent that raises the frequency of mutations above the spontaneous rate

What is homology dependent repair?

What is base excision repair? How does it work?

What is nonhomologous end joining? How does it work?

What is mismatch repiar?

How do trinucleotide repeats get inherited?

Why do unstable repeats happen?

How does the Ames test work?

Can a chemical induce His+ revertants of special His- mutant strains of Salmonella?

• His- can only grow if histidine is supplied SO only revertants can grow on plates w/o histidine

Why does the Ames test use rat liver enzymes?

to simulate the mammalian metabolism that bacteria lack — this metabolism can turn nonhazardous chemicals into mutagenic substances

• allows us to better assess the scope of harm to humans

What types of mutants does the Ames test look for?

Revertants

What does it mean when complementation occurs?

What phenotype would you see when complementation occurs?

What does it mean when complementation does not occur? What phenotype would you see?

What is a complementation group? Are they in the same or different genes?

How do you use a complementation table to find the number of genes and complementation groups?

What did Benzer’s experiment with T4 phage show about complementation?

What did Benzer’s experiment with T4 phage show about recombination?

What did Benzer’s experiment with T4 phage show about mutations?

How do all of the results from Benzer’s experiment relate to each other?

Why did Benzer have a control group? What was it?

How can deletion mapping show where mutations are? How would you solve this kind of problem?

What are hotspots?

What did Garrod find? Using what experiment/technique?

What did Beadle and Tatum find? Using what experiment/technique?

How do you use a supplementation table to find the biochemical pathway?

What does it mean if a mutant cannot grow on something in a supplementation table?

What does it mean if a mutant can grow on something in a supplementation table?

If there is a block at any step of the pathway, how does that affect the concentration of intermediates in the pathway?

What did Yanofsky find? Using what technique/experiment?

What did Crick and Brenner find in 1955? Using what experiment/technique

What is the term for the process of using DNA to make RNA?

Where are promoters in relation to genes? What do they do when activated?

Where are enhancers in relation to genes? What do they do when activated?

What is the coding strand? How can you determine which one it is?

What is the template strand? How can you determine which one it is?

When/in what cells will you find exons and introns?

When will you only find exons?

What is the difference between primary transcript and mature mRNA

What is the term for the process of using mRNA to create proteins?

What makes up mRNA?

What is the importance of mRNA modifications?

What kinds of modifications are added to mRNA?

Is mRNA single stranded or double stranded?

What are the 5’ and 3’ UTRs? How do they relate to exons?

What do spliceosomes do?

Where is transcription happening?

Where is RNA processing happening?

Where is translation happening?

What does a tRNA do?

Where does the amino acid attach to a tRNA? What is it called?

Where is the anticodon position?

Structure of tRNA

What is wobble? Why is it important?

How do you find the codon sequence that will pair with the anticodon sequence

What do the stop codons look like in DNA vs RNA?

What is the importance of post-translational modifications?

How are they modified?

What is a silent mutation?

What is a missense mutation?

What is a conservative missense mutation?

What is a nonconservative missense mutation?

What is a nonsense mutation?

What is a frameshift mutation?

What is an extensive missense mutation?

What is an immediate nonsense mutation?

What is an amorphic (null) mutation?

What is a hypomorphic mutation?

What is a neomorphic mutation?

What is ectopic expression?

What is haploinsufficiency?

What is an antimorphic (dominant-negative) mutation?