Lecture 7: Replication

Question 1

deoxyribonucleotide triphosphate (dNTP)

Answer 1

• nucleotide

Question 2

How do prokaryotes replicate their DNA?

Answer 2

• DNA polymerase unzips helix
• 5’–>3’ in both directions
• replication forks and bubbles (see notes)

Question 3

synthesis of leading strand (2 steps) (4 key enzymes/proteins involved in first step, SHPT; 1 involved in second)

Answer 3

1. DNA is opened and primed:
   - primase makes RNA primer (~10 nucleotides long)
   - topoisomerase removes twists
   - helicase opens double helix
   - single strand DNA binding proteins keeps strands separated
2. DNA polymerase III makes leading strand 5’–>3’

Question 4

synthesis of lagging strand (5 steps)

Answer 4

1. RNA primer is added
2. first fragment synthesized
3. next fragment is synthesized (okazaki fragments)
4. replace primer (DNA primer I replaces RNA with DNA and goes 5’–>3’)
5. gap is closed by DNA ligase

Question 5

How does DNA replication occur in Eukaryotes? What is the problem that eukaryote cells run into at the end of replication?

Answer 5

• similar to prokaryotes except larger and more linear chromosomes with multiple replication forks
• at the end of replication a problem occurs where there are missing nucleotides at the 5’ end because chromosomes shorten during replication

Question 6

telomer and telomerase

Answer 6

• telomer: portion of strand (end piece) missing DNA (the unreplicated 5’ end)
• telomerase binds to a 3’ end and adds nucleotides to lengthen telomer several times; has its own RNA template
• extended DNA acts as a template for DNA polymerase III

Question 7

DNA repair:

• during replication
• immediately after replication
• anytime

Answer 7

• during: DNA polymerase proofreads DNA; wrong nucleotides are excised and replaced
• immediately after replication: mismatched repair occurs on new strand
• anytime: repair of damaged DNA

Question 8

enzymes involved in DNA repair (3): state role

Answer 8

• nucleases: excision
• DNA polymerase: replacement
• ligase: linkage

Question 9

genotype vs phenotype

Answer 9

genotype: sequence code for protein
phenotype: physical trait produced by protein

Question 10

List the types of mutations (4)

Answer 10

• silent
• missense
• nonsense
• frameshift

Question 11

explain the following mutation type and the result of it: silent

Answer 11

• change in nucleotide sequence that does not impact the amino acid specified by codon
• result: no change in phenotype

Question 12

explain the following mutation type and the result of it: missense

Answer 12

• change in nucleotide sequence that changes amino acid specified by codon
• result: change in primary structure of protein (could be beneficial, neutral, or deleterious)

Question 13

explain the following mutation type and the result of it: nonsense

Answer 13

• change in nucleotide sequence that results in an early stop codon
• result: breakdown of mRNA or a shortened polypeptide; usually deleterious

Question 14

explain the following mutation type and the result of it: frameshift

Answer 14

• addition/ deletion of a nucleotide

- result: reading frame is shifted altering meaning of all subsequent codons; almost always deleterious

Question 15

differentiate between DNA I and DNA III

Answer 15

• dna polymerase I: removes RNA primer with DNA

- dna polymerase iii: adds nucleotides to make new strand