• Shuffle
    Toggle On
    Toggle Off
  • Alphabetize
    Toggle On
    Toggle Off
  • Front First
    Toggle On
    Toggle Off
  • Both Sides
    Toggle On
    Toggle Off
  • Read
    Toggle On
    Toggle Off
Reading...
Front

Card Range To Study

through

image

Play button

image

Play button

image

Progress

1/93

Click to flip

Use LEFT and RIGHT arrow keys to navigate between flashcards;

Use UP and DOWN arrow keys to flip the card;

H to show hint;

A reads text to speech;

93 Cards in this Set

  • Front
  • Back
Name three different activities of DNA polymerases (such as pol I) in E. coli.
1. Gap filling; polymerase
2. Proofreading; 3'-5' exonuclease
3. RNA primer removal/RNase H activity; 5'-3' exonuclease
What is an Okazaki fragment and what process does it play a role in?
Short DNA fragment on lagging strand during replication or hybrid DNA-RNA fragment. Occurs in discontinuous synthesis in DNA replication.
What are topoisomerases? Name a process they are involved in.
Enzymes able to untwist DNA strands (or change helical state) by single strand transient breaks (topoisomerase I) or by double strand transient breaks (topoisomerase II).
What can you say about the processivity of bypass polymerases? How are they and other DNA repair enzymes regulated?
They are distributive enzymes (readily dissociate from DNA). They are regulated at transcriptional level (induced by DNA damage).
How can you recognize a simple transposon (insertion sequence)?
Insertion sequence possesses inverted repeats on both ends. Flanked by direct repeats (same orientation) in the target sequence.
How many DNA strands form a holiday junction?
Four
In which direction does DNA synthesis occur and in which direction does RNA synthesis occur?
DNA: 5'-3'
RNA: 5'-3'
When is the DNA replication most likely to leave a gap? If the polymerase encounters....
a. a lesion in the DNA leading strand
b. a lesion in the DNA lagging strand
b. a lesion in the DNA lagging strand
Which of the following statements about DNA replication is true?
a. Unidirectional
b. Bidirectional
c. Semiconservative
d. Continuous
e. Occurs from 3'-5'
f. Occurs from 5'-3'
g. Requires processive and distributive polymerases
h. Is highly dependent on Watson-Crick base pairing
b. Bidirectional
c. Semiconservative
f. Occurs from 5'-3'
g. Requires processive and distributive polymerases
h. Is highly dependent on Watson-Crick base pairing
Name three enzymes other than polymerases that are involved in DNA replication.
(Any three of these)
Primase, RNase, Topoisomerase, Helicase, FEN-1, Replication Protein A (RPA), SSB (Single strand binding protein)
Describe how DNA replication occurs at the lagging strand.
RNA primer hybridizes to ssDNA (synthesized by primase or RNA polymerase)
Elongation by DNA polymerase, generating Okazaki fragments
Removal of RNA primer by Pol I
Gap filling (by distributive ligase)
Nick sealing (by DNA ligase)
What is a processive polymerase?
A polymerase that carries out many additions of nucleotides before dissociating from DNA
Describe the differences between base excision repair and nucleotide excision repair.
Base excision repair:
1. Glycosidases remove the damaged base
2. AP site is repaired by excising the abasic sugar (AP endonuclease/AP lyase)
3. Gap filling (DNA polymerase)
4. Ligation (DNA ligase)

Nucleotide excision repair:
1. Endonuclease removes stretch of nucleotides
2. Gap filling (DNA polymerase)
3. Ligation (DNA ligase)
Which repair mechanism would come into play when a wrong (but undamaged) base is incorporated into newly synthesized DNA?
Mismatch repair
What is the function of bypass polymerases and how are they induced?
They ensure continued replication if a lesion is encountered by the replications machinery. Induced upon extensive DNA damage (SOS response).
The secondary structure of DNA is known as:
a. The nucleotide sequence
b. The double helix
c. The triplet codon
d. All of the above
e. None of the above
b. The double helix
The smallest structure unit of the chromosome is:
a. nanosome
b. microsome
c. nucleosome
d. all of the above
e. none of the above
c. nucleosome
In DNA replication in E. coli, which enzyme(s) exhibit(s) 3' exonuclease activity:
a. DNA ligase
b. DNA helicase
c. DNA polymerase I
d. All of the above
e. None of the above
c. DNA polymerase I
Type I DNA topoisomerase cleaves the following DNA molecule:
a. One strand of a single stranded DNA molecule
b. One strand of a double stranded DNA molecule
c. Both strands of a double stranded DNA molecule
d. All of the above
e. None of the above
b. One strand of a double stranded DNA molecule
Match the following enzymes to its function
Responsible to synthesize a short piece of RNA during DNA replication
a. DNA helicase
b. DNA ligase
c. Single strand DNA binding protein
d. Nick translation
e. Primase
e. Primase
Match the following enzymes to its function
Responsible to form a covalent bond between Okazaki fragments
a. DNA helicase
b. DNA ligase
c. Single strand DNA binding protein
d. Nick translation
e. Primase
b. DNA ligase
Match the following enzymes to its function
Orients single strand DNA toward incoming nucleotides
a. DNA helicase
b. DNA ligase
c. Single strand DNA binding protein
d. Nick translation
e. Primase
c. Single strand DNA binding protein
Match the following enzymes to its function
Responsible to unwind DNA strands ahead of DNA polymerase
a. DNA helicase
b. DNA ligase
c. Single strand DNA binding protein
d. Nick translation
e. Primase
a. DNA helicase
In prokaryotic DNA replication, which of the following is responsible for the removal of RNA primers:
a. DNA polymerase I
b. DNA polymerase II
c. DNA polymerase III
d. All of the above
e. None of the above
a. DNA polymerase I
In the active site of DNA topoisomerase I, which of the following is involved in the formation of a phosphodiester bond with DNA:
a. Threonine
b. Tryptophan
c. Tyrosine
d. All of the above
e. None of the above
c. Tyrosine
In prokaryotic DNA replication, which of the following is responsible for the formation of RNA primers:
a. RNaseA
b. RNaseB
c. RNaseC
d. All of the above
e. None of the above
e. None of the above
(Primase)
DNA transcription
a. Is an ordered and conservative mechanism
b. Proceeds in 5'-3' in the leading strand and 3'-5' in the lagging strand
c. Consists of three processes-initiation, elongation, and termination
d. All of the above
e. None of the above
c. Consists of three processes-initiation, elongation, and termination
Telomerase is involved in replication of:
a. Circular bacterial chromosome
b. Circular bacterial episomal DNA (plasmids)
c. Linear human chromosomes
d. All of the above
e. None of the above
c. Linear human chromosomes
In prokaryotic DNA replication, which of the following activity is responsible for the so called proofreading function:
a. 5' exo-nuclease
b. 3' exo-nuclease
c. First A, then B
d. First B, then A
e. None of the above
b. 3' exo-nuclease
Match the following enzymes to its function
Responsible for DNA synthesis on the leading strand
a. DNA polymerase alpha
b. DNA ligase
c. DNA polymerase III
d. DNA helicase
e. DNA topoisomerase
c. DNA polymerase III
Match the following enzymes to its function
Responsible for DNA synthesis on the leading and lagging strands
a. DNA polymerase alpha
b. DNA ligase
c. DNA polymerase III
d. DNA helicase
e. DNA topoisomerase
c. DNA polymerase III
Match the following enzymes to its function
Responsible to relieve torsional stress ahead of the replication fork
a. DNA polymerase alpha
b. DNA ligase
c. DNA polymerase III
d. DNA helicase
e. DNA topoisomerase
e. DNA topoisomerase
During replication, DNA polymerase initially incorporates 1 wrong nucleotide every ~10^6 bp. However, the overall accuracy is much higher (1 error per 10^9 bp). Why?
DNA polymerase has a proofreading ability
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?
Strand separation requires high energy and thus enzymes (such as Helicase - unwinds double-stranded DNA and Single Strand Binding Proteins (SSB) - prevents reannealing of double-stranded DNA) to occur under physiological conditions
What is the difference between processive and distributive enzymes and name an example for each.
Processive - Carries out many additions of nucleotides before dissociating from DNA (DNA Pol III).
Distributive - Readily dissociates from DNA (DNA Pol I)
Drugs that inhibit DNA synthesis usually cause cell cycle arrest at which phase?
G1 Phase
What are telomeres?
Adds TTAGG repeats (thousands) to prevent chromosomal shortening
What is a Holliday junction and in which process is it thought to be an intermediate?
Junction between four DNA strands. Intermediate in Holliday model.
What is a heteroduplex in homologous recombination?
Regions where one strand was from one duplex, and the other from the homologous duplex.
What is the importance of DNA methylation in DNA repair?
The parental strand has a higher degree of methylation that is recognized in order to repair the newly synthesized strand (and not "repair" the parental strand).
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?
Translesion synthesis
What are structural features/common characteristics of transcription factors?
DNA recognition helix and protein interaction domain
Why would the mutation risk increase if U instead of T were present in DNA?
C (which pairs with G) can get oxidized to U (which pairs with A). Since U is not part of DNA, the DNA repair system recognizes U as a damaged base and excises (repairs) it. If U were part of DNA and C got oxidized to U, the repair system would not know to excise U.
Name three features of eukaryotic mRNA.
5' terminal cap (7-methylguanine cap)
3' terminal polyA tail
methylated internal variants
splice variants
Hypothetically, why could DNA not carry out spliceosomal splicing like RNA by the mechanism discussed in class?
Requires 2'-OH which is not present in DNA
or
OH-donor site required but DNA has no T instead of U
Which statement about the Pribnow box is NOT correct?
a. It is AT rich
b. It is also called the -10 region
c. It is closely related to the TATA box
d. It is the only region in the promoter that is important for RNA transcription
e. It is highly conserved in prokaryotes
d. It is the only region in the promoter that is important for RNA transcription
Which process is mediated by small interfering RNAs?
a. Posttranslational gene silencing
b. Postranscriptional gene silencing
c. RNA splicing
b. Postranscriptional gene silencing
Match the following factors to the process it is involved in:
Sigma factor
a. RNA polymerase II-mediated transcription
b. Termination of transcription in prokaryotes
c. RNA polymerase-mediated transcription in prokaryotes
c. RNA polymerase-mediated transcription in prokaryotes
Match the following factors to the process it is involved in:
Rho factor
a. RNA polymerase II-mediated transcription
b. Termination of transcription in prokaryotes
c. RNA polymerase-mediated transcription in prokaryotes
b. Termination of transcription in prokaryotes
Match the following factors to the process it is involved in:
Transcription factors
a. RNA polymerase II-mediated transcription
b. Termination of transcription in prokaryotes
c. RNA polymerase-mediated transcription in prokaryotes
a. RNA polymerase II-mediated transcription
Name 3 unique structural features of tRNA.
Nucleosides are highly modified
Anticodon
3'-CCA acceptor arm for aminoacylation
Many non-Watson Crick base pairs
On which of the two DNA strands is daughter strand gap repair likely to occur?
Lagging strand
Which of the following statements are true? (Can be more than one)
a. The Pribnow box is AT rich
b. The Pribnow box is GC rich
c. The conserved -35 region is asymmetrical
d. The conserved -35 region is symmetrical
e. Transcription and translation are coupled in eukaryotes and prokaryotes.
f. Many RNA polymerase molecules can transcribe a gene simultaneously.
g. RNA synthesis in eukaryotes requires sigma factors.
h. RNA interferes is a mechanism of postranslational gene silencing.
a. The Pribnow box is AT rich
c. The conserved -35 region is asymmetrical
f. Many RNA polymerase molecules can transcribe a gene simultaneously.
Give two reasons why the higher error rate of RNA polymerases compared with DNA polymerases is acceptable.
(Two of the following)
Genetic code degenerate (wrong base/nucleotide may not affect protein sequence)
One amino acid substitution in protein synthesis often times without consequence
Quick degeneration and re-synthesis (high turnover rate)
Name two characteristics of rho independent termination.
GC rich palindrome upstream of 6-7 U (A on template DNA strand)
During which process occurs the formation of a 2'-5' phosphodiester bond?
Splicing
What are is the length and function of small interfering RNAs (siRNAs)?
Length: 21-23 nucleotides (or 21-30)
Function: (Postranscriptional) gene silencing (degradation of homologous mRNA sequences)
For transcription in prokaryotes versus eukaryotes, which molecule binds first to the promoter region?
Prokaryotes: RNA polymerase
Eukaryotes: Transcription factors (or TATA box protein, TBP)
Which promoter sequences are being recognized by bacterial RNA polymerase?
Assymetrical -35 region and a Pribnow Box (-10 region), which is AT rich.
How can promoter sequences be identified?
Footprinting
1. DNA protected from alkylation (dimethyl sulfate) where enzyme is bound (Pribnow and -35 region)
2. Certain nitrogens usually involved in H-bonding only gets alkylated if ssDNA
Name a characteristic of high promoter efficiency.
Increase in A:T pairs (Pribnow box) increases promoter efficiency due to weaker hydrogen bonds compared to G:C pairs.
How is it ensured that transcription occurs in one direction?
5’-terminal PPP groups of RNA chain retained (shown by radioactive labeling)
What is a difference between DNA and RNA polymerase with respect to the necessity for primers?
RNA polymerase does not require a primer, while DNA polymerase does
Which nucleoside analog do you expect would inhibit elongation: 3'-deoxyadenosine or 5'-deoxyadenoside and why?
3'-deoxyadenosine because it is missing the 3'-OH group and the 5'-phosphate. The nucleoside cannot attach as a result because RNA synthesis is 5’→3’.
Which process do intercalating chemotherapeutics inferfere with?
Replication and transcription by inhibiting RNA and DNA polymerase
Would the use of ITP instead of GTP during in vitro transcription increase, decrease or not affect termination efficiency?
Decrease termination efficiency because amino group missing compared with G, and I:C pairs are weaker than G:C pairs (2 vs. 3 H-bonds).
What is the TATA box?
Promoter sequence at region -27. Similar to Pribnow box (-10 region) in prokaryotes.
Does coupled transcription-translation occur in prokaryotes, eukaryotes or both?
Prokaryotes due to lack of compartmentalization (nucleus)
What statement can you make regarding the degree of RNA modification in prokaryotes versus eukaryotes?
In prokaryotes, protein translation often occurs without RNA modification. In eukaryotes, extensive RNA modifications are possible.
What is splicing?
Excision of intron (noncoding) sequences
What is a putative advantage of splicing?
Increases protein diversity relative to prediction from genome
What sequence is required for the attachment of amino acids onto tRNAs?
CCA sequence
Why is rRNA originally transcribed as one unit?
Because the components are present in a 1:1:1 ratio and must by regulated in same way, so it makes the process simpler and less energy is wasted.
How can you distinguish prokaryotic from eukaryotic rRNA?
Prokaryotic rRNA: 23S, 5S, 16S
Eukaryotic rRNA: 28S, 5.8S, 18S
The bacterial RNA polymerase usually binds which of the following promoters:
a. The -10 region and -25 region
b. The -10 region and -35 region
c. The -10 region and -45 region
d. The -10 region and -55 region
e. The -10 region and -65 region
b. The -10 region and -35 region
In prokaryotic tRNA processing, which of the following is responsible for the formation of the 5'-terminus of all tRNA:
a. RNase D
b. RNase P
c. RNase III
d. All of the above
e. None of the above
b. RNase P
______________ is a GC rich stem loop followed by an A rich segment
Rho independent terminator
Bacterial transcription almost always initiates with the following:
a. A or C
b. A or T
c. C or G
d. All of the above
e. None of the above
e. None of the above
Match the following to the process it is involved in:
Responsible for cleavage of one strand of a double stranded DNA molecule
a. The beta subunit of the bacterial RNA polymerase
b. The beta prime subunit of the bacterial RNA polymerase
c. Type I DNA topoisomerase
d. Type II DNA topoisomerase
e. DNA polymerase III
c. Type I DNA topoisomerase
Match the following to the process it is involved in:
Responsible for cleavage of both strands of a double stranded DNA molecule
a. The beta subunit of the bacterial RNA polymerase
b. The beta prime subunit of the bacterial RNA polymerase
c. Type I DNA topoisomerase
d. Type II DNA topoisomerase
e. DNA polymerase III
d. Type II DNA topoisomerase
Match the following to the process it is involved in:
Responsible for biosynthesis of bacterial genome
a. The beta subunit of the bacterial RNA polymerase
b. The beta prime subunit of the bacterial RNA polymerase
c. Type I DNA topoisomerase
d. Type II DNA topoisomerase
e. DNA polymerase III
e. DNA polymerase III
Is responsible for the formation of the 5' end of mature bacterial tRNA
a. RNase D
b. RNase P
c. RNase III
d. All of the above
e. None of the above
b. RNase P
The origin of replication in E. coli chromosome contains three direct repeats of a 13 base-pair sequence rich in:
a. A and C
b. A and G
c. G and C
d. All of the above
e. None of the above
e. None of the above
Transcription almost always initiates with the following:
a. Purines
b. Pyrimidines
c. Purines and pyrimidines
d. All of the above
e. None of the above
a. Purines
Responsible for DNA synthesis on the leading strand
a. DNA polymerase alpha
b. DNA polymerase delta
c. All of the above
d. None of the above
b. DNA polymerase delta
Responsible for DNA synthesis on the lagging strand
a. DNA polymerase alpha
b. DNA polymerase delta
c. All of the above
d. None of the above
a. DNA polymerase alpha
The beginning of a transcription process:
a. Operator
b. Promoter
c. Repressor
d. Rho protein factor
b. Promoter
In the secondary DNA structure, the complimentary chains of the double helix are:
a. Parallel to each other
b. Anti-parallel to each other
c. Perpendicular to each other
d. All of the above
e. None of the above
b. Anti-parallel to each other
A typical prokaryotic promoter is made of a -35 consensus sequence of TTGACA and a -10 consensus sequence rich in:
a. A and T
b. A and G
c. G and C
d. G and T
e. C and T
a. A and T
The origin of replication in E. coli contains three direct repeats of a 13 base-pair sequence rich in:
a. A and T
b. A and G
c. G and C
d. G and T
e. C and T
a. A and T
In prokaryotic DNA replication, which of the following activity is responsible for the so called proofreading function:
a. 5' exo-nuclease
b. 3' exo-nuclease
c. First A, then B
d. First B, then A
e. None of the above
b. 3' exo-nuclease
In prokaryotic tRNA processing, which of the following is responsible for the formation of the 5' end:
a. RNase D
b. RNase P
c. RNase III
d. All of above
e. None of the above
b. RNase P
Transcription almost always initiates with the following:
a. A or T
b. A or G
c. G or C
d. All of the above
e. None of the above
b. A or G