Nucleotides Test 1

Front 1

During replication, DNA polymerase initially incorporates 1 wrong nucleotide every ~106bp. However, the overall accuracy is much higher (1 error per 109bp). Why?

Back 1

Repair mechanisms are present to decrease the incidence of an error during replication

Front 2

In which direction is DNA being synthesized biosynthetically?

Back 2

5’ – 3’ direction. If replication occurred 3’ – 5’, could not proofread because no PPP.

Front 3

Double-stranded DNA is fairly stable and strand separation usually requires high energy. Instead of high temperature, how do organisms cope with this “problem” during replication?

Back 3

Through the use of enzymes

Front 4

What is an Okazaki fragment and in which process does it play a role?

Back 4

An Okazaki fragment is a short fragment of DNA created on the 3’ – 5’ lagging strand during DNA replication. It’s role is to allow the lagging strand to be replicated in the 5’ – 3’ direction.

Front 5

Name three activities of DNA polymerases.

Back 5

Polymerase (gap filling)
5’ – 3’ exonuclease activity (proofreading)
3’ – 5’ exonuclease activity ( primer removal, RNAse H)

Front 6

Name a process in which DNA ligase plays a role.

Back 6

Ligation of Okazaki fragments

Front 7

Name a process in which DNA topoisomerase is important.

Back 7

Untwisting of parental strands in DNA replication

Front 8

Which functional group of DNA ligases and topoisomerases is thought to play a catalytic role?

Back 8

Phenolic hydroxyl group on the Tyr residue.

Front 9

What is the importance of the 5’ → 3’ exonuclease activity of DNA polymerase I in E. coli?

Back 9

Primer removal, RNAse H activity

Front 10

What is the difference between processive and distributive enzymes and name an example for each.

Back 10

Processive- carries out multiple nucleotide additions before disassociating Ex. Pol III
Distributive- readily dissociates from DNA Ex. Pol I

Front 11

Does DNA synthesis occur in one or two directions from the ori?

Back 11

In both directions from the ori.

Front 12

Drugs that inhibit DNA synthesis usually cause cell cycle arrest at which phase?

Back 12

G1

Front 13

What are telomeres?

Back 13

TTAGGG repeats added to the ends of linear chromosomes to protect the ends from shortening and losing genetic information.

Front 14

Why is it advantageous that thymine rather than uracil is a DNA base?

Back 14

If U was used instead of T in DNA, it would increase the risk of mutation. C can easily be oxidized to form U. If this occured, then U would base pair with A instead of C with G which would result in unrecognized errors in transcription.

Front 15

Which promoter sequences are being recognized by bacterial RNA polymerase?

Back 15

-35 region and the Pribnow Box

Front 16

How can promoter sequences be identified?

Back 16

The -35 region and Pribnow box are both highly conserved regions that the promoters can recognize.

Front 17

Where does the σ factor play a role?

Back 17

Specific σ factors recognize classes of genes in Prokaryotes. Along with a Polymerase they bind to the promoter to initiate transcription.

Front 18

Name a characteristic of high promoter efficiency.

Back 18

Several RNS polymerases can initiate transcription simultaneously.

Front 19

How is it ensured that transcription occurs in one direction?

Back 19

The -35 region is asymmetrical and the enzyme can recognize the direction of transcription.

Front 20

What is a difference between DNA and RNA polymerase with respect to the necessity for primers?

Back 20

DNA requires a primer, RNA does not require a primer.

Front 21

Which nucleoside analog do you expect would inhibit elongation: 3’-deoxyadenosine or 5’-deoxyadenosine and why?

Back 21

3’- deoxyadenosine because it is missing the PPP (triphosphate)

Front 22

Which process do intercalating chemotherapeutics interfere with?

Back 22

They interfere with replication and transcription.

Front 23

What is the basis for ρ-independent termination of transcription in prokaryotes?

Back 23

GC rich palindrome upstream of 6-7 U (A on template DNA). RNA forms a stem-loop secondary structure which results in termination.

Front 24

Would the use of ITP instead of GTP during in vitro transcription increase, decrease or not affect termination efficiency?

Back 24

ITP would diminish termination efficiency because I:C pairs are weaker than G:C pairs (2 vs. 3 H bonds)

Front 25

What is the TATA box?

Back 25

Promoter sequence for transcription in Eukaryotes.

Front 26

What are common characteristics of transcription factors?

Back 26

Contain both DNA recognition helix and protein interaction domains

Front 27

 What is a Holliday junction and in which process is it thought to be an intermediate?

Back 27

o Homologous recombination
o Holliday junction formed from 4 DNA strands
o Forms Holliday intermediate

Front 28

 What is a heteroduplex in homologous recombination?

Back 28

o Regions where one strand was from one duplex, the other from the homologous duplex; caused by reciprocal inversion

Front 29

 How can you recognize a transposon in the genome?

Back 29

o Insertion sequence has inverted repeats at both ends
o Insertion sequences are flanked by direct repeats in the same orientation in target sequence

Front 30

 Name different types of DNA repair processes.

Back 30

o Direct repair
 Cyclobutane thymine dimmer photoreactivation
• Formed by [2+2] cycloaddition
• Photolyase binds
• Light absorption (300-500nm)  cleavage
• Photolyase dissociates
• Demethylation
 Demethylation- alkyltransferases (methyl guanine methyl transferase) reverse this process
o Excision Repair
 Base Excision Repair
• Part of DNA excised by DNA glycosylase
• Removal of damaged base by specific glycosidases
• Repair of AP sites left after removal of damaged base (or by spontaneous hydrolysis);
o AP endonucleases & lyases excise abasic sugar
o Gap filling (DNA polymerase, pol 
o Ligation (DNA ligase)
 Nucleotide excision repair
• Excises several nucleotides
• Excision repair of photodimers
• Endonucleases excise
• Gap filling by DNA polymerase
• Ligation

Front 31

o Special Cases of Nucleotide Excision Repair

Back 31

 Transcription coupled repair- only occurs if you need proteins around
• Lesions also block transcription
• Transcribed regions are repaired faster
 Mismatch repair
• If wrong base is incorporated (undamaged)

Front 32

 What is the importance of DNA methylation in DNA repair?

Back 32

o How to recognize newly synthesized strand (and not “repair” parental strand)?
 A: Look at methylation pattern! Higher degree of methylation in parental strand.

Front 33

 Sometimes damaged DNA is not repaired yet by direct or excision repair when the replication complex approaches a lesion. Which repair mechanism(s) can come into play?

Back 33

o Translesion synthesis, recombination repair by daughter strand gap repair, double-strand break reapir, or repair of replication forks

Front 34

 What are bypass polymerases, what statement can you make about their processivity?

Back 34

o Bypass polymerases are only induced upon extensive DNA damage (SOS response) and readily dissociates from DNA (distributive)

Front 35

 Does coupled transcription-translation occur in prokaryotes eukaryotes, or both?

Back 35

o prokaryotes

Front 36

 What statement can you make regarding the degree of RNA modification in prokaryotes versus eukaryotes?

Back 36

o More dramatic

Front 37

 Name features of eukaryotic mRNA.

Back 37

o 5’-terminal cap
o 3’-terminal poly(A) tail
o Methylated internal variants
o Splice variants

Front 38

 Name 3 unique structural features of tRNA.

Back 38

o Nucleosides are highly modified
o Anticodon
o 3’-CCA acceptor arm for aminoacylation
o many non-Watson-Crick base pairs

Front 39

 What is splicing?

Back 39

o excision of intron sequences
o Creation of several splice variants possible ie. Exon between two introns-> modified functionality ie. Depending on cell type
o Increased protein diversity relative to prediction from genome, more variability for organism
o Other ways to generate protein diversity: posttranslational modifications

Front 40

 Why could not DNA be spliced by the mechanism discussed in class?

Back 40

o No 2’-OH

Front 41

 What is a putative advantage of splicing?

Back 41

o Creation of several splice variants possible- modified functionality depending on cell
o Increased protein diversity relative to prediction from genome

Front 42

 Which sequence is for the attachment of amino acids onto tRNAs?

Back 42

o CCA required for attachment of amino acids

Front 43

 Why is rRNA originally transcribed as one unit?

Back 43

o want unit 1:1:1 ratio (of the S segments)

Front 44

 How can you distinguish prokaryotic from eukaryotic rRNA?

Back 44

o Prokaryotes
 28S rRNA 5.8S rRNA 18S rRNA
o Eukaryotes
 23S rRNA 16S rRNA 5S rRNA

Front 45

 What are small interfering RNAs?

Back 45

o 21-23 ribonucleotides long
o Facilitate sequence specific gene suppression via RNA interference (of homologous genes)