Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

M.Phil. Preparatory Flashcards > Mol biology2 > Flashcards

Mol biology2 Flashcards

1
Q

What happens in conservative, semi-conservative and dispersive DNA replications?

A

Conservative (From heavy and light), semi-conservative (hybrid and light), dispersive (hybrid only)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Who verified the semi-conservative model of DNA replication?

A

Matthew Meselson and Franklin Stahl in 1957

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What type of centrifuge was used in the Meselson and Stahl DNA replication experiment?

A

Cesium chloride based equilibrium density gradient

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What happens to an overwound DNA?

A

It becomes positively super-coiled

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What happens to an underwound DNA?

A

It becomes negatively super-coiled

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Name the four substrates of DNA polymerase enzymes?

A

dTTP, dATP, dCTP, and dGTP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the two important requirements of DNA polymerase enzyme

A

A template strand and primer with 3’-OH end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How does the DNA polymerase enzyme achieves polymerization?

A

Mg2+ ion draws electrons from the 3’-OH allowing nucleophilic attack by the OH group onto the pyrophosphate. The other Mg ion stabilizes the pyrophosphate for release.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the nature of DNA replication?

A

Semidiscontinous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

If the polymerases cannot initiate DNA replication on their own then how does the process begins?

A

Primase synthesizes the primer strand which is used by the polymerases to construct the DNA strand.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Explain the role of each of these two enzymes during DNA replication in bacteria. 1. DNA poly 3 and 1

A

DNA poly 3 (Polymerization)
DNA pol 1 (Gap filling and fragment removal)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the major unwinding helicase of bacteria?

A

dnab product or DNAb helicase (forms a ring around the single strand of DNA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How many subunits does a dnab helicase ring contains?

A

6

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What happens during the initiation of DNA replication in E.coli?

A

DnaA binds to the oriC site and melts the DNA, after this the DnaB is loaded into the lagging strand and unwinding begins.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What synthesizes both new strands at the replication fork of bacteria?

A

DNA poly 3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Is primer used by both leading and lagging strands?

A

Yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the primer requirements of the leading and lagging strand?

A

The continuous strand needs a primer one time only but the lagging strand multiple primers.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Where is the primer attached?

A

5’ end of the DNA strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is a primosome?

A

Complex of helicase with primase. One opens the double helix and the other subsequently synthesizes RNA primer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is the nature of the primer in bacterial DNA replication?

A

RNA in nature added to the 5’ end of the terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How does the DNA polymerases synthesize DNA without violating the 5’ to 3’ rule in bacteria?

A

They loop the lagging DNA strand onto itself in such a way that the orientation is the same as the leading strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the trombone model of DNA replication?

A

In this model the DNA is synthesized and periodically collapsed and vice versa during replication (okazaki fragments)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What does recent studies on the trombone model tells us?

A

2 enzymes work on the lagging strands and 1 on the leading strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the large replication machinery of bacteria?

A

DNA polymerase 3 holoenzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What helps the DNA poly 3 to remain attached to the strands and move over the molecule?

A

Beta clamp in bacteria and PCNA in eukaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is a non-catalytic part of DNA poly 3 in bacteria?

A

Beta clamp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What happens to the beta clamp at the okazaki strand?

A

It is periodically renewed after each cycle of fragment development

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

How does a circular beta clamp gets loaded into the DNA strand?

A

It is ATP bound and the loop is open through which DNA strand can pass and once it’s inside the wall of the beta clamp loop wall, the ATP is hydrolyzed and the loop closes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What do you know about the DNA poly 1 in bacterial DNA replication?

A

It’s single unit and performs repair, fragment and primer removal, etc. functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are the components of DNA poly 3 holoenzyme?

A
  1. Clamp loader
  2. Two beta clamps
  3. Helicase
  4. Two core polymerase
  5. Two/three subunits holding the beta loader
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is the direction of DNA poly 1 exonuclease activity?

A

3 to 5 and vice versa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What contributes to the high fidelity of DNA replication in bacteria?

A
  1. Nucleotide selection
  2. Exonuclease activity
  3. Mismatch repair
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is the direction of primer removal?

A

5’ to 3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is the direction of bacterial DNA proofreading?

A

3’ to 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is an important difference between bacterial DNA replication initiation and eukaryotic initiation?

A

Bacterial DNA replication takes place at one site only whereas in case of eukaryotes, it takes place at multiple sites called replicons.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the importance of acetylated histones in case of eukaryotic DNA replication?

A

Least acetylated DNA are in heterochromatin form and are usually transcribed late

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What is ARS?

A

Autonomous replicating sequences are specific sequences of DNA that can initiate DNA replication.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Do vertebrates contain the ARS?

A

No, the site of DNA replication in vertebrates is associated with epigenetic factors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are the steps of DNA replication in yeast?

A
  1. ORC protein complex binds the origin
  2. Pre-RC complex binding (MCM protein complex)
  3. Activation of the replication complex by CDK or protein kinases
  4. Activation of helicase, which are two in number and move oppositely as the DNA is replicated
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

How many polymerases have been isolated from the eukaryotic cells?

A

5 (alpha, beta, gamma, delta, and epsilon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What eukaryotic polymerase replicates the mitochondrial DNA?

A

Poly gamma

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What eukaryotic polymerase is involved in DNA repair?

A

Poly beta

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

What subunits of the eukaryotic polymerases are associated with DNA polymerization/replication?

A

Alpha, delta, and epsilon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Are okazaki fragments present in eukaryotic DNA replications?

A

Yes, but they’re much smaller than those found in prokaryotic DNA replication.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What polymerase is linked with the leading strand?

A

Epsilon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What polymerase is linked with the lagging strand?

A

Delta

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What’s the role of poly alpha

A

Forms complex with primase and helps in DNA replication initiation. Binds to the unwound DNA strands containing the SSB alternate RPA. Primase forms the primer and poly a extends it.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What is PCNA?

A

The sliding clamp of eukaryotic cells aka alternate of prokaryotic beta clamp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is the clamp loader in case of eukaryotes?

A

RFC

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What happens when the poly a has extended the lagging strand primer?

A

It detaches from it and is replaced by the PCNA-delta complex, which will complete the remaining part of the okazaki fragment.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What is the ultimate fate of the primer in eukaryotic okazaki fragment?

A

It is displaced by the delta polymerase and cut by FEN-1 and after this the nick left is filled by the DNA ligase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What is the molecular belt of eukaryotic cells?

A

PCNA due to it’s ability to orchestrate multiple complexes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What eukaryotic polymerases have 3’ to 5’ exonuclease activity?

A

Epsilon, delta, and gamma

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is replication foci?

A

Localized regions of replication forks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is the composition of the nucleosome core?

A

Octameric in nature comprised of H3H4 tetramers and H2A/H2B dimers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What is CAF-1?

A

Histone chaperone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What are the two repair pathways in nucleotide excision?

A

Transcription coupled pathway and global genomic pathway

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What could be the cause of nucleotide base excision?

A

Dimer formation with the strands and chemical group attachment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What transcription factor is involved and how does it work in nucleotide base excision?

A

TF2H has helicase activity which opens the affected strand after this endonucleases nick the strand , the strand is detached and polymerases rebuild the excised area with new strand, ligase binds the nick left by polymerase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

What mediates the transcription pathway of NER?

A

Stalled RNA polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

What mediates the global genomic pathway in NER?

A

XBC subunit of TF2H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

What happens in Base excision repair?

A

A faulty base is removed and replaced with the correct one

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What is the important enzyme of the base excision mechanism?

A

DNA glycosylase (cleaves off the glyosidic bond holding the base to the deoxyribose sugar)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

Why nature favored thymine over uracil in RNA?

A

One reason is the difficulty faced by the repair machinery of the DNA which gets a hard time when confronted by uracil formed by cytosine conversion.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

How is mismatch repair done when the enzymatic machinery fails to recognize it?

A

It causes distortion in the double helix structure of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What enzyme binds to the two double strands that have a break (non-homologous)?

A

Ku enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

What is the 2nd step in DNA double strand repair (non-homologous)?

A

Recruitment of DNA-PKcs (catalytic unit with kinase activity) on the breaks which then brings the breaks closer and hence the DNA ligase IV can finally work to repair the break

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

What is the predominant form of repair in DNA double strand break?

A

NHEJ aka Non-homologous end joining

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What is a promoter?

A

It’s the site on DNA where RNA polymerase binds to initiate transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

What is the direction of the movement of RNA poly on the DNA template strand?

A

From 3’ to 5’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

What’s the polymerization direction of RNA synthesized from the template DNA strand?

A

From 5’ to 3’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

Why helps in ensuring the irreversible reaction needed for protein or nucleic acid polymerization?

A

The pyrophosphate released by the nucleotide triphosphates decomposition is broken by hydrolysis and tremendous free energy is released which ensures the irreversibility of the reactions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

Why are RNA polymerases said to be processive?

A

They are required to stay attached to the template DNA strand over a long stretch of the strand.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

Is the RNA poly movement along the template strand continuous?

A

No, it’s discontinuous!

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

What is meant by upstream and downstream in template strand context?

A

Upstream DNA is that portion which lies towards the 3’ end and downstream towards the 5’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

What does negative and positive values indicate in the DNA sequence codes?

A

Positive means downstream and negative represents upstream

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

Where are the genes for initiation located wrt to upstream and downstream?

A

Upstream or towards the 3’ end of the template strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

Where are the genes for termination and transcription located?

A

Downstream or towards the 5’ end of the template strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

What are upstream and downstream in context of RNA synthesis

A

Vice-versa of template strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

What’s the most common type of conserved sequence in bacterial genome?

A

-35 consensus sequence (TTGACA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

Where is the second most conserved sequence located in bacterial genome?

A

-10 bases from the initiation point

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

Why is the second most conserved sequence important?

A

It’s within the promoter region at -10 bases from the initiation site (+1) and helps in melting the DNA during RNA synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

What is another name for the second most conserved sequence and what’s it’s sequence?

A

Pribnow box and it is comprised of the TATAAT sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

Where are both -35 and -10 elements located?

A

Upstream and in the promoter region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

What sigma factor is known as the “housekeeping sigma factor”?

A

Sigma 70

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

What is the role of sigma 70 factor?

A

Initiates most of the gene transcription in bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

What’s the role of ring shaped Rho factor in bacterial transcription?

A

Terminates the transcription process (also takes place via termination sequences) by detaching the RNA from the polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

Where does distinction between eukaryotic and prokaryotic transcription arises?

A

Transcription factor requirements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

What is the portion of DNA called which transcribes into mRNA?

A

Transcription unit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

What do you know about rDNA?

A

rRNA forming DNA portion also forms nucleoli in nucleolus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

How many rRNA are there in the eukaryotic ribosome?

A

4 (three in the large subunit and one in the small subunit)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

What are the three subunits of the large eukaryotic ribosome?

A

28S, 5.8S, and 5S RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

What is the subunit of the large eukaryotic ribosomal subunit?

A

18S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

What is formed by the three subunits of the eukaryotic ribosome?

A

60S large subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

What is formed by the single subunit of the ribosome?

A

40S small subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

What enzyme synthesizes the ribosome subunits?

A

RNA poly 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

Which of the three large ribosomal subunit is synthesized outside the nucleus?

A

RNA poly 3 synthesizes the 5S subunit from a different RNA precursor

98
Q

What proteins associate with pre-rRNA during transcription?

A

snoRNP

99
Q

What is the protein-snoRNA complex called?

A

snoRNPs or small nucleolar ribonucleoproteins

100
Q

What is an important function of snoRNPs and other like proteins

A

To cleave the 5’ end of the pre-rRNA

101
Q

What is the primary transcript for the pre-rRNA?

A

45S molecule

102
Q

What is the cleavage pattern of the 45S molecule?

A

45 > 41 > 32 > 28S and 5.8S

103
Q

What is the most frequent form of modification done to the pre-rRNA molecule

A

Conversion of uridine to psuedouridine and methylation of the ribose at the 2’ site of the sugar.

104
Q

What snoRNAs decide the uridine isomerization and methylations?

A

Box C/D (methylation) and Box H/ACA (isomerization)

105
Q

In what form are the tRNA genes found throughout the genome?

A

Irregularly scattered in clusters and in tandem sequences

106
Q

What is unusual about the RNA poly 3 enzyme?

A

It can recognize promoter region within the transcribed portion of the genes

107
Q

What enzyme catalyzes the formation of the tRNA transcript?

A

RNA poly 3**

108
Q

What endonuclease enzyme is required for processing the tRNA transcript and what’s unique about it?

A

It’s called the ribonuclease P and is present in both pros and eukars and is composed of both RNA (cleaves off the pre-tRNA) and protein subunits

109
Q

What enzyme synthesizes the mRNA transcript?

A

RNA poly 2

110
Q

Why are the proteins in transcription initiation termed “general transcription factors”?

A

Same array of proteins are associated with other organisms too.

111
Q

Where does the TATA binding protein binds in the DNA?

A

To the TATA sequence (minor groove)

112
Q

TBF is basically a subunit of?

A

TF2D protein

113
Q

The enzyme TF2H phosphorylation facilitates?

A

Uncoupling of the RNAP2 from the promoter area and move downstream

114
Q

What CTD is phosphorylated by TF2H?

A

Serine at position 5

115
Q

What CTD is phosphorylated by P-TEFb?

A

Serine at position 2

116
Q

What is the importance of serine 2 and 5 phosphorylation?

A

2 recruits mRNA slicing and polyadenylation proteins and 5 5’capping formation

117
Q

How does the mRNA synthesis terminates?

A

Unclear

118
Q

What are some elongation factors that bind with the RNAP2 complex after initiation?

A

TF2S, P-TEFb, and ELL

119
Q

What experiment suggests the nature of mRNA slicing during post-transcription?

A

DNA-RNA hybridization (non complementary DNA sequence causes bulging of the complex)

120
Q

What is the precursor of GMP in the methyl-guanosine capping?

A

GMP

121
Q

Where are the methyl groups transferred by the capping enzymes?

A

On the 7th position of the guanosine and on the 2nd carbon of the RNA ribose

122
Q

What happens in the polyadenylation?

A

It’s a mRNA processing step which takes place at the 3’ end of the mRNA molecule. First the nascent mRNA is cleaved by an endonuclease and after that a enzyme adds the adenine nucleotides from the ATP molecule.

123
Q

What is the nature of splice sites in mRNA?

A

Ancient evolutionary consensus sequences

124
Q

What are the consensus sequences at the 5’ and 3’ ends?

A

G/GU at the 5’ and AG/A at the 3’ end

125
Q

What are the polypyrimidine tract?

A

Consensus sequence of poly TTTTT near the 3’ end of mRNA

126
Q

What is an important thing to remember regarding the upstream and downstream concepts?

A

They are with respect to the promoter or consensus sequence under consideration not the terminals necessarily

127
Q

Although splice sites contain data that helps in splicing, then why is it still not sufficient in various situations?

A

Exonic splicing enhancers are special sequences within the exons which help in their recognition from the introns in case the normal machinery ignores them.

128
Q

True or False? Introns are self splicing in many cases?

A

True

129
Q

What is an example of self splicing introns?

A

Tetrahymena (group 1 introns) and group 2 introns

130
Q

What happens in mRNA self splicing?

A

Intronic adenosine attacks the 5’ spice site, intron gets detached, the free 3’ OH from the free exon attacks the 3’ end of the 3’ splice site, intron completely detached in lariat form, the two exons ligate with each other.

131
Q

What is the relationship between SnRNP and spliceosomes?

A

They’re associated and do the splicing process in eukaryotes.

132
Q

What group of introns form lariat during exon splicing?

A

Group 2 introns

133
Q

What are the snRNPs of the eukaryotic splicing of mRNA that leave the complex at the end?

A

U4 and U1

134
Q

What snRNPs remain at the splicing of mRNA till the end?

A

U2, U5, U6

135
Q

What is the function of the U2 snRNP?

A

Binds the branching point where the lariat forming adenosine is located

136
Q

What is the function of the U5 snRNP?

A

It holds the 5’ Exonic end in place and also the 3’ terminal of the other exon at the end of splicing.

137
Q

What is the function of U6?

A

Hypothesized to be a ribozyme inhibited by U4, once it leaves the snRNP binds the U2 and helps in the lariat formation

138
Q

What is sm protein?

A

A 7 ringed protein inside the snRNP

139
Q

What binds the ESE portion during the eukaryotic splicing of mRNA?

A

SR protein

140
Q

What binds the polypyrimidine sequence near the 3’ splice end of the intron in eukaryotic mRNA splicing?

A

U2AF

141
Q

What is the importance of introns?

A

They act as spacer element within genes and provide safe site for splicing. They also shuffle between genes bringing evolutionary changes in gene expression and diversity or new gene formation.

142
Q

What do you understand by gene shuffling?

A

When unrelated genetic sequences combine or shuffle between each other

143
Q

What is the number of combination possibility for the codons?

A

4^3 (64) possibilities

144
Q

How do we know the codons are non-overlapping in nature?

A

Take the example of sickle cell anemia, which occurs due to one amino acid mutation. So if the code is overlapping then one mutation should affect three consecutive codons but in practice this is not the case.

145
Q

How do we know that amino acid can be served by more than one codon?

A

44 triplet combinations of the codon are extra and the number of amino acids synthesized is 20

146
Q

What are synonymous and non-synonymous mutations?

A

The former is a mutation type which doesn’t affect the phenotype and the other does

147
Q

What’s a degenerate codon?

A

Codons which can code for more than one type of amino acids

148
Q

What’s non-sense mutation?

A

Premature termination

149
Q

What happens in frameshift mutation?

A

Insertion or deletion type of mutation can put the polymerase enzyme into incorrect reading frame

150
Q

Which of the three codons are same between similar amino acids?

A

The first two are very similar and the last or third codon has the highest variability

151
Q

Why does the tRNA folds into clover-leaf like shape?

A

Because of complementary sequences

152
Q

What part of the tRNA accepts amino acids?

A

3’ end OH

153
Q

What part of the tRNA has the greatest variability?

A

Variable arm

154
Q

Why doesn’t the loops form hydrogen bonds with each other?

A

Nucleotides are concentrated in this region and hence they disrupt the hydrogen bond formation

155
Q

What part of tRNA are a subject of recognition?

A

The loops

156
Q

Where is the CCA sequence located in tRNA?

A

3’ end of the molecule

157
Q

What arms form continuous double helix structure in tRNA?

A

The amino acid and T’C arms

158
Q

What arms form partially continuous arms?

A

The anti-codon and D arm

159
Q

Name the different arms of tRNA?

A

Variable arm, T and D arms, anticodon arm

160
Q

In total how many codons code for amino acids?

A

61 codons

161
Q

What is the basic principle of wobble hypothesis?

A

One tRNA can serve multiple amino acid due to the flexibility of the third nucleotide on the codon of mRNA. For the first two nucleotides the steric requirement is very strict

162
Q

Inosine I of the anti-codon can pair with?

A

A, U, and C

163
Q

What is the name of the enzyme catalyzing the attachment of amino acid at the 3’ end of the tRNA?

A

Aminoacyl-tRNA synthetase or aaRS

164
Q

Explain the steps of tRNA charging?

A

1st step = amino acid + AMP
2nd step = amino acyl AMP + tRNA

165
Q

What makes the tRNA charging thermodynamically favorable?

A

Release of PPi in the first step is used in hydrolysis and hence provides the necessary energy required to derive the reaction to product formation.

166
Q

How does a ribosome places itself in the right reading frame?

A

With the help of AUG or start codon

167
Q

All aa-tRNAs enter the A site except?

A

Methionine based tRNA

168
Q

What is the large subunit of the bacterial ribosome?

A

50s

169
Q

What is the small subunit of the bacterial ribosome?

A

30s

170
Q

What sequence is used by the bacterial ribosome to align properly on the mRNA?

A

Shine-Dalgarno sequence

171
Q

To what sequence is the Shine-Dalgarno complementary?

A

The 3’ end of the 16s ribosomal subunit

172
Q

What is the function of IF3

A

Prevents premature joining of the 50s subunit and also irrelevant aa-tRNA

173
Q

What is the function of IF2?

A

GTP bound and needed for attachment of the first methionine based tRNA

174
Q

What is the function of IF1?

A

Prevents the initiator tRNA from entering the wrong site and stabilizes the 30s subunit on the mRNA

175
Q

What is the form of methionine found in bacteria?

A

N- Formylmethionine

176
Q

In what step is the IF1 and IF3 released in bacterial initiation?

A

2nd step

177
Q

What are the subunits of ribosome in eukaryotes?

A

60s and 43s

178
Q

What is different about prokaryotic and eukaryotic initiation of translation?

A

In eukaryotes the eIFs and aa-tRNA bind in advance to the 43s subunit of the ribosome

179
Q

What’s the function of eIF4E

A

Binds the 5’ methyl-guanosine cap of mRNA

180
Q

What initiation factor removes double strands from the mRNA?

A

eIF4A

181
Q

What makes the mRNA strand circular during initiation?

A

eIF4G

182
Q

What is the final subunit after the large 60s has joined the 43s complex on mRNA?

A

80s

183
Q

What is another GTP bound initiation factor which releases bound GTP?

A

eIF5B

184
Q

When does the large 60s subunit joins the 43s complex in eukaryotic initiation?

A

When the AUG is detected by the complex and eIF2s GTP is hydrolyzed along with eIF5B GTP with release of all other eIFs

185
Q

What is the energy behind the ribosome function?

A

GTP hydrolysis

186
Q

Where is the 16s ribosomal subunit located?

A

Inside the small subunit side

187
Q

Explain these two important features of ribosomes; helicase activity and tunnel

A

Helicase makes sure the mRNA is in linear and not in secondary form whereas the tunnel helps the polymerized peptide to translocate within the ribosome.

188
Q

What are important first step factors of elongation initiation (bringing tRNA to the A site)?

A

GTP bound EF-Tu in bacteria and eIF1A in eukaryotes

189
Q

What ribosome active site holds the growing peptide chain?

A

P-site

190
Q

What carries a nucleophilic attack in the formation of peptide bond in elongation?

A

The aa-tRNA N group

191
Q

Does the peptide bond formation within the ribosome requires energy input?

A

No it doesn’t require energy from outside but is catalyzed by peptidyl transferase

192
Q

What is peptidyl transferase?

A

Enzymatic domain of the large subunit (60s), ribozyme in nature due to association with tRNA in P site

193
Q

Where is the peptide bond formed in three of the ribosome active sites?

A

A site

194
Q

What happens in step 2 of elongation?

A

Transfer of the nascent polypeptide chain from the tRNA in the P site to the aminoacyl‐tRNA of
the A site, forming a dipeptidyl‐tRNA in the A site and a deacylated tRNA in the P site

195
Q

What happens during ribosome translocation?

A

It moves with respect to the mRNA codons and the EF-G bound GTP is hydrolyzed

196
Q

What is the feature of translocation during elongation in translation?

A

6 degree ratchet like movement

197
Q

Is it true that tRNAs can remain in hybrid forms during translocation in protein translation?

A

Yes, it’s true!

198
Q

At what steps are GTP utilized during protein translation?

A

During aa-tRNA assembly in A site and during translocation

199
Q

What is one of the most destructive types of mutation?

A

Frameshift mutation (one base pair deleted or inserted)

200
Q

How many codons act as stop codons?

A

Three

201
Q

What are the stop codons?

A

UAA, UAG, UGA

202
Q

How does termination takes place when tRNA doesn’t recognize any of the stop codons?

A

Through termination factors such as class 1 and 2 RFs

203
Q

What class RF binds with the A site of the ribosome?

A

Class 1

204
Q

What is the termination sensing mechanism in eukaryotic

A

They’ve a special class 1 termination factor which recognizes all three stop codons e.g. eRF1

205
Q

What are the key steps of class 1 RF in termination?

A
  1. The RF binds the mRNA codon and induces conformational changes
  2. The link between the nascent polypeptide change and tRNA is affected resulting in the release of the polypeptide chain.
  3. Hydrolysis of RF3 or eRF3 GTP results in the release of the RF
  4. Final step includes, release of deacylated tRNA, mRNA, and ribosome subunit disassembly.
206
Q

True or false? Transcription and translation takes place simultaneously in bacteria?

A

True!

207
Q

What’s an operon?

A

It’s a gene complex of bacterial genome with specific function

208
Q

What’s a polycistronic mRNA?

A

One which contains information for more than one peptide

209
Q

What is the type of regulation in case of operon?

A

Allosteric regulation by tryptophan or lactose

210
Q

What are the key components of operon?

A
  1. Structural genes 2. Operator 3. Regulatory gene 4. Promoter
211
Q

Which one is an inducer operon?

A

Lactose

212
Q

What happens in repressor operon?

A

Tryptophan binds with the repressor acting as a co-repressor and inhibits the genes encoding tryptophan synthesizing enzymes

213
Q

What happens in case of inducer operon?

A

Lactose binds with repressor and prevents its binding with the operator hence allowing the synthesis of enzymes degrading lactose. Here the metabolite is acting as an inducer of gene expression

214
Q

What encodes the beta galactosidase enzyme which breaks lactose?

A

Z gene

215
Q

What encodes the galactoside permease, which allows lactose influx inside bacteria?

A

Y gene

216
Q

What gene encodes the enzyme thiogalactoside transacetylase?

A

A gene

217
Q

What is a catabolic based operon gene regulation?

A

Lac operon

218
Q

What is an anabolic based gene regulation?

A

Trp operon

219
Q

The mechanism of repressor based regulation in operon is considered as?

A

Negative control

220
Q

What is the relationship between glucose and cAMP

A

Inverse

221
Q

How does cAMP overcomes the effect of glucose inhibition of lac operon?

A

It binds a CRP protein forming the complex cAMP-CRP, which binds to DNA allowing formation of the lac proteins

222
Q

What regulates the expression of lac operon?

A

Glucose concentration

223
Q

What is the principle of attenuation in operon regulation?

A

Attenuation is the process of transcription termination with formation of two different types of secondary structure. One terminates the transcription shortly after initiation.

224
Q

Where does attenuation takes place on the operon?

A

Ladder sequence

225
Q

What are riboswitches?

A

They are mRNAs which bind metabolites which might ultimately affect their termination or translation

226
Q

Where is the +1 position of lac operon located

A

Inside the operator

227
Q

Where is the cAMP-CRP binding region located on the lac operon?

A

Upstream with respect to operator

228
Q

What is the ladder sequence?

A

It’s a specific sequence within the trp operon that works via attenuation

229
Q

How does ladder sequence causes transcription termination in trp operon?

A

It forms a hairpin loop like structure which restrains the polymerase from further progression downstream on operon.

230
Q

What’s an important fact to remember regarding operon attenuation

A

The transcription actually initiates and is terminated downstream

231
Q

What is glucose effect?

A

It’s a positive effect which downregulates other sugar operons in bacteria

232
Q

How does glucose induces it’s effect?

A

It blocks the adenylate cyclase enzyme, which synthesizes the cAMP hence preventing the CRP-cAMP complex formation needed for the activation of the lac operon

233
Q

Is attenuation ladder sequence also present in Lac operon?

A

No, the primary means of regulation in lac operon is repressor and catabolite activator protein (CAP).

234
Q

What is the function of attenuator?

A

Another name for a stop signal in trp operon

235
Q

Is glucose effect present in lac trp operon case?

A

No, it relies on repressor and attenuator sequence

236
Q

What is the function of LacI?

A

Controls repressor production

237
Q

What is the form of lactose in the operon regulation?

A

Allolactose

238
Q

How is positive control regulated?

A

Presence of glucose prevents the binding of an activator (CAP) to the promoter hence transcription cease

239
Q

What’s the main difference between negative and positive regulation of operon?

A

In one a protein directly restricts the transcription whereas in case of positive an activator protein is repressed instead of the operon directly

240
Q

Why is glucose based repression positive and not negative?

A

Negative regulation of lac operon results in the catabolism of lactose whereas in positive the catabolic operon is repressed hence in this context it’s positive regulation.

M.Phil. Preparatory Flashcards (22 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions