Quiz #9

Question 1

What are five general requirements for DNA replication?

Answer 1

1. Enzyme that can catalyze DNA synthesis from deoxyribose, called DNA polymerase, all organisms contain many DNA pols
2. Mg+ ions (required for enzyme function)
3. dNTPs (deoxyribose triphosphates)
4. a free 3’-OH end in the correct position to act as a primer for DNA synthesis
5. a template for base pairing

Question 2

Who found the first DNA polymerase?

Answer 2

Arthur Kornberg

Question 3

What kind of reaction powers polymerization?

Answer 3

loss of phosphates is an exergonic reaction that powers polymerization

coupling of this exergonic reaction to synthesis is necessary, order is being created

Question 4

What is the mechanism of DNA replication?

Answer 4

in dsDNA, the two strands are antiparallel and complementary

enzyme that replicates DNA, DNA polymerase will only add nucleotides to an existing nucleotides free 3’-OH (DNA polymerase cannot initiate synthesis of a polynucleotide)

replication proceeds in both directions from each origin, until the entire molecule is copied

Question 5

What is the initiation step of DNA replication?

Answer 5

the DNA helix is unwound by a helicase that acts at origins of replication

topoisomerase: moves in front of fork, to help relieve strain due to twisting caused by helicase

single-stranded binding proteins prevent single strands from reannealing, and are easily displaced by DNA pol

Question 6

How does topoisomerase work?

Answer 6

it cuts one strand, lets the DNA unwind by one turn, and then it “mends” the cut

Question 7

What is the elongation step of DNA replication?

Answer 7

primase synthesizes a 5-10 nt RNA primer, complementary to DNA template, it doesn’t need a 3’-OH

sliding clamp: keeps DNA pol on the template

DNA polymerase III synthesizes the new DNA in 5’ –> 3’; direction

the new DNA strand starts from the 3’ OH of the RNA

Question 8

What are Okazaki fragments?

Answer 8

the lagging strand contains many short segments of the newly synthesized DNA, called Okazaki fragments

the enzymes skip to the next available template, making an ordered array of Okazaki fragments (the latest one synthesized, is closest to the fork)

Question 9

How can Okazaki fragments be converted into a single continuous strand?

Answer 9

DNA pol I removes the RNA, one nucleotides at a time, from the 5’ end, and it replaces it with DNA (adding to the 3’ end of the adjacent DNA)

DNA ligase seals the gap between the sugar-phosphates of the adjoining pieces of DNA

Question 10

What are three methods of proofreading and repairing DNA?

Answer 10

Proofreading corrects errors during DNA replication

Mismatch repair fixes mispaired bases, and small insertions or deletions that happen during DNA synthesis

Nucleotide Excision Repair is used to remove pyrimidine dimers formed by UV radiation and some other defects involving modified nucleotides that cause a significant distortion in the DNA helix

Question 11

What is the process of proofreading?

Answer 11

when incorrect pairing occurs during DNA synthesis, DNA pol III can detect and remove mismatched bases

occasionally, incorrect base inserts and polymerase forms phosphodiester bond

polymerase detects a mis-pairing of bases, and removes the nucleotide using 3’–>5’ exonuclease activity

Question 12

What is exonuclease?

Answer 12

an enzyme that removes nucleotides from the end of the polymer

Question 13

What is the process of mismatch repair?

Answer 13

is active shortly after the synthesis of DNA strand, and the mismatch is deleted in the newly synthesized DNA

new DNA is cut on both sides of mismatch by an endonuclease, the mispaired nucleotide and a few neighbors are excised

DNA pol III fills the gap, DNA ligase seals the “nick” in the backbone

Question 14

What is the process of nucleotide exclusion repair?

Answer 14

an endonuclease enzyme cuts the DNA (on each side of the modified nucleotides) and removes all bases between cuts

DNA pol I replaces missing nucleotides

DNA ligase seals the free end

pyrimidine dimer: covalent bond forms between adjacent pyrimidine bases

Question 15

What are the two accepted definitions of a gene?

Answer 15

a functional unit of heredity that determines an observable trait or characteristic (= phenotype) of an organism

the DNA sequence that determines the chemical structure of a specific polypeptide or RNA molecule

Question 16

Who was Gregor Mendel?

Answer 16

was the first to propose a “particulate” mechanism of inheritance

found that crossing two distinct varieties of pea plants resulted in offspring that resembled one of the two parents, the dominant parent

Question 17

Who was Sir Archibald Garrod?

Answer 17

the idea that genes are (somehow) responsible for the manufacture of proteins was first proposed in 1902 by Garrod

alkaptonuria causes a build up of the amino acids phenylalanine and tyrosine, as well as a by-product that turns urine dark blue/black

he hypothesized that the phenotype was due to the absence of an enzyme required for a specific metabolic pathway

Question 18

What were the steps in Beadle and Tatum’s experiment isolating mutants of a fungus?

Answer 18

1. Minimal medium: media has glucose, salts, vitamins, but cells must synthesize all amino acids by themselves
2. Complete medium: this media has all amino acids supplied, each culture is started with one cell that survived the X-rays, each contains one potential mutant strain
3. Minimal medium: Strain C cannot grow when all amino acids are removed, next they tested to see which amino acid it cannot make
4. This particular mutation, Strain C, affects the cells’ ability to synthesize arginine (Arg)

Question 19

What was the conclusion that Beadle and Tatum came to?

Answer 19

showed that each mutant was deficient in a single enzyme that catalyzed a specific step in the biosynthesis of the required amino acid, thus supporting their hypothesis

Question 20

What are some differences between transcription and translation in prokaryotes vs. eukaryotes?

Answer 20

in prokaryotes, transcription and translation occur in the same space, translation of mRNA can even start before transcription has finished

in eukaryotic cells, the nuclear envelope separates transcription and translation, eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA