Module 2 - DNA replication & Chromosome structure

Describe 3 enzymatic activities that DNA polymerase 1 undertakes:

1) 5'->3' (forward) DNA-dependant polymerase activity, requiring a 3' primer site and a template strand 2) 3'->5' (reverse) exonuclease activity that mediates proofreading 3) 5'->3' (forward) exonuclease activity that mediates nick translation during DNA repair 4) 5'->3' (forward) RNA-dependant DNA polymerase activity

DNA polymerases catalyse DNA synthesis, list three requirements for this enzyme to operate: (What do you need for a PCR reaction?)

1. Nucleotide base pairs (A, T, G, C) 2. Mg2+ 3. A Template DNA strand 4. A DNA strand with a free 'OH group on the end

List and describe each of the three alternate forms of duplex nucleic acid chains?

B form = most common form of DNA, right handed double helix structure A form = less common, thicker, duplex with shorter gaps between base pairs Z form = left handed helix structure, caused by long stretches of alternating purines & pyrimidines

Describe three characteristics of a telomere:

Occur at the ends of eukaryotic chromosomes. Protect from degrading effect of deoxyribonuclease. Prevent fusion of chromosomes. Facilitate complete replication at the ends of DNA molecules. Contain repetitive sequences and a distinct structure.

What enzyme is responsible for producing a new RNA strand in a transcription bubble?

RNA Polymerase

Explain briefly why the genetic code is degenerate and explain the difference between partial and complete degeneracy:

The occurrence of more than one codon per amino acid is called degeneracy. Most amino acids are specified by more than one codon - the multiple codons are usually similar in their nucleotide sequence. Two types of degeneracy: 1) Partial degeneracy = changing the 3rd base from one purine to another or one pyrimidine to another will often not alter the amino acid specified. Changing from a pyrimidine to a purine (and vice versa) is more likely to alter the amino acid. 2) Complete degeneracy = occurs when any of the four bases could be substituted as the 3rd base without altering the amino acid.

What is the purpose for the addition of the 5' 7-methyl guanosine cap on eukaryotic pre-mRNA molecules? a) It prevents the degradation of the sequence by nucleases b) It prevents the degradation of the sequence by lysosomes c) It guides the pre-mRNA sequence out of the plasma membrane d) All of these e) None of these

a) It prevents the degradation of the sequence by nucleases

Genetic material must perform which three essential functions? a) Replication, mutation, gene expression b) Replication, adaption, mutation c) Transcription, translation, storage d) Transcription, translation, replication e) None of the above

a) Replication, mutation, gene expression

Three levels of condensation are required to package metaphase chromosomes. In order of complexity, lowest to highest, they are: a) Supercoiling into 11nm nucleosomes, 30nm chromatin fibre condensation, scaffold formation b) 30nm chromatin fibre condensation, supercoiling into 11nm nucleosomes, scaffold formation c) Scaffold formation, supercoiling into 11nm nucleosomes, 30nm chromatin fibre condensation d) Supercoiling into 11nm nucleosomes, scaffold formation, 30nm chromatin fibre condensation e) Scaffold formation, 30nm chromatin fibre condensation, supercoiling into 11nm nucleosomes

a) Supercoiling into 11nm nucleosomes, 30nm chromatin fibre condensation, scaffold formation

In a nucleosome, the DNA is wrapped around a) histones b) ribosomes c) polymerase molecules d) a thymine dimer

a) histones

The spontaneous loss of of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage? a) nuclease, DNA polymerase, DNA ligase b) telomerase, primase, DNA polymerase c) telomerase, helicase, single-strand binding protein d) DNA ligase, replication fork proteins, adenylyl cyclase

a) nuclease, DNA polymerase, DNA ligase

In analysing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules? a) A = G b) A + G = C + T c) A + T = G + C d) A = C

b) A + G = C + T

Which of the following codons is most often recognized as the start codon for the translation? a) GUA b) AUG c) CUG d) UUG e) AAG

b) AUG

A biochemist isolates, purifies, and combines in a test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture? a) DNA polymerase b) DNA ligase c) Okazaki fragments d) primase

b) DNA ligase

Nitrogenous bases are held together in the centre of the DNA molecule by what type of chemical bond? a) Phosphodiester b) Hydrogen c) Peptide d) Ionic e) Covalent

b) Hydrogen

DNA replication occurs in which manner? a) Conservative b) Semi-Conservative c) Dispersive d) Conservative and Semi-Conservative e) Semi-Conservative and Dispersive

b) Semi-Conservative

DNA Ligase serves what purpose? a) To break hydrogen bonds in the DNA structure b) To seal single stranded breaks in the DNA double helices c) To seal double stranded breaks in the DNA single helices d) All of the above e) None of the above

b) To seal single stranded breaks in the DNA double helices

The template DNA strand below will produce which new strand of DNA: 3'-ATCGGGAAATTCGGA-5' a) 3'-ATCGGGAAATTCGGA-5' b) 5'-ATCGGGAAATTCGGA-3' c) 5'-TAGCCCTTTAAGCCT-3' d) 3'-TAGCCCTTTAAGCCT-5' e) 5'-UAGCCCUUUAAGCCU-3'

c) 5'-TAGCCCTTTAAGCCT-3'

Which of the following enzymes catalyses DNA synthesis? a) DNA Ligase b) DNA Helicase c) DNA Polymerase d) DNA Gyrase e) None of these

c) DNA Polymerase

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesised? a) the origins of replication occur only at the 5' end b) helices and single-strand binding proteins work at the 5' end c) DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand d) DNA ligase works only in the 3'-5' direction

c) DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand

In his work with pneumonia-causing bacteria and mice, Griffith found that: a) the protein coat from pathogenic cells was able to transform nonpathogenic cells b) heat-killed pathogenic cells caused pneumonia c) some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic d) the polysaccharide coat of bacteria caused pneumonia

c) some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic

The elongation of the leading strand during DNA synthesis: a) progresses away from the replication fork b) occurs in the 3'->5' direction c) does not require a template strand d) depends on the action of DNA polymerase

d) depends on the action of DNA polymerase

E. coli cells grown on 15N medium are transferred to 14N medium and allowed to grow for two more generations. DNA extracted from these cells is centrifuged. What density distribution of DNA would you expect in this experiment? a) one high-density and one low-density band b) one intermediate-density band c) one high-density and one intermediate-density band d) one low-density and one intermediate-density band

d) one low-density and one intermediate-density band

Which of the following must be present in order for DNA polymerase to be active? a) Mg2+ b) dNTPs c) Existing DNA template with a free 3' end d) A and C e) All of the above

e) All of the above