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BCHM 218 > Module 4: Mechanisms of Transcription and Translation > Flashcards

Module 4: Mechanisms of Transcription and Translation Flashcards

1
Q

What are snoRNAs?

A

Part of the sliceosome, small nuclear RNAs that play a role in gene regulattion

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2
Q

Describe 3 similarities between transcription and DNA replication

A

1) Both use a template strand as the blueprint for forming a new polypeptide
2) Both have initiation, elongation, and termination steps
3) Both replication and transcription proceed in the 5’-3’ direction

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3
Q

Describe 4 differences between transcription and DNA replication

A

1) Transcription uses rNTPs not dNTPs as “building blocks”
2) No primers are required for transcriptional initiation
3) Transcription is selective; not all the DNA is transcribed
4) Only one of the strands is used as a template in transcription for a particular RNA, which both strands of DNA are replicated simultaneously

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4
Q

T/F
RNA transcribed will be complementary to the template DNA strand and will match the sequence of the coding strand

A

True
But with U instead of T of course

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5
Q

Where is the transcriptional start site located?

A

upstream of the initiation codon (AUG)

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6
Q

What is the region between the TSS and the start codon called?

A

The 5’ untranslated region (5’UTR)

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7
Q

Transcription is catalyzed by what enzyme? In what direction?

A

By RNA polymerase in the 5’-3’ direction

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8
Q

T/F
prokaryotes have multiple RNA polymerases

A

False
They just have one: RNA Pol

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9
Q

How many subunits does RNA Pol have? List them

A

5 subunits
B, B’, w, and 2 a subunits

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10
Q

What are bacterial transcription factors called?

A

sigma factors

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11
Q

What is the RNA Pol I holoenzyme

A

The RNA polymerase core plus the sigma factor attached

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12
Q

The DNA strands are opened and separated around what structure in RNA Pol

A

The “pin” structure

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13
Q

What is the purpose of the “pin” structure

A

To open up the DNA strands, creating a DNA “bubble” that allows space for the rNTPs to pair

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14
Q

T/F
RNA Pol has a built-in proofreading mechanism

A

False

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15
Q

What is the RNA Pol error rate?

A

1 in every 100 000 bases

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16
Q

Describe kinetic proofreading

A

If an incorrect nucleotide is added, the proper H-bonding isn’t formed, causing a fray at the DNA-RNA duplex
If recognized by the RNA Pol, it can stall until phosphorolysis reverses the reaction at this base pair, allowing the correct rNTP to be paired

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17
Q

Describe nucleolytic proofreading

A

In this mechanism, RNA polymerase transcribed past the mismatched base and must “backtrack” to fix the error
The polymerase has to reverse its direction a bit, and use its endonuclease activity to hydrolyze phosphodiester backbone of the transcript upstream of the error, removing the incorrect base

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18
Q

In bacteria, what offers context specific transcription

A

Sigma factors

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19
Q

T/F
Bacteria have multiple sigma factors

A

True

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20
Q

How are sigma factors named?

A

According to their molecular weight

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21
Q

Comparisons of bacterial promoters recognized by an sigma-70 containing RNA polyermase holoenzyme have revealed similarities in short sequences located where?

A

Around -10 and -35

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22
Q

Where in the gene does the upstream promoter reside?

A

Between -40 and -60

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23
Q

T/F
Any change to the spacer region between -10 and -35 will increase trenascription

A

False
It will reduce transcription because the consensus sites won’t be on the same side of the helix

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24
Q

Give an overview of bacterial transcription

A

1) The sigma factor binds to the promoter region - and the enzyme is in the closed conformation
2) The enzyme is converted to open conformation
3) Abortive initiation occurs
4) The polymerase holds onto the transcript for more than 10 nucleotides, and creastes a stable RNA
5) The elongation phase begins
6) The promoter sequence is cleared and sigma factor falls off the polymerase
7) The polymerase is released when it encounters a termination sequence

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25
Q

How many RNA polymerases do eukaryotes have?

A

3

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26
Q

What is the product of RNA Pol I

A

Ribosomal RNA (rRNA) precursors. Is responsible for transcribing rRNAs

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27
Q

What is the product of RNA Pol II

A

Messenger RNA (mRNA) are protein coding genes

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28
Q

What is the product of RNA Pol III

A

Smaller functional RNAs (tRNA, snRNA)

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29
Q

What regions in eukaryotic genes have or attract transcription factors

A

There is one in the general eukaryotic core promotor and there are regulatory sequences both upstream and downstream that bind gene-specific transcription factors

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30
Q

T/F
Only RNA Pol II uses a TATA binding protein

A

False
All three kinds of RNA polymerase use TATA binding proteins

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31
Q

Describe the TATA binding protein

A

The TBP binds to a 5’ TATAAA sequence (AKA the TATA box) near position -30 of the promoter region

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32
Q

T/F
All genes are under TBP transcription initiation, even if they don’t have a TATA box

A

True

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33
Q

Describe how genes with no TATA box are under TBP transcription

A

TBP-associated factors (TAFs) recognize the promoter region of the gene and recruit TBP there

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34
Q

Describe the structure of the TATA binding protein

A

TBP is saddle-shaped, and sits on the DNA double helix upon binding. The “stirrups” of the saddle are in contact with the minor groove on the TATA box sequence

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35
Q

TFII indicates a transcription factor for which RNA polymerase?

A

RNA Pol II

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36
Q

Briefly describe Electrophoretic Mobility Shift Assays (EMSA)

A

Fragments of DNA of a known sequence are incubated with the protein of interest and then analyzed on a non-denaturing polyacrylamide

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37
Q

Explain the differences in pre-mRNA processing in prokaryotes and eukaryotes

A

In prokaryotes, mRNA can be directly transcribed and directly translated by ribosomes
In Eukaryotes, transcription and pre-mRNA processing takes place in the nucleus, and the mature mRNA has to exit the nucleus to the cytoplasm to be translated

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38
Q

List the features of a mature mRNA

A

5’ cap
3’ Poly A tail
A coding region

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39
Q

What is the first modification made to pre-mRNA

A

The addition of a 5’ cap

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40
Q

What is the 5’ cap made of. What is its purpose

A

Is a residue of 7-methylguanosine and keeps mRNA protected by preventing recognition of the 5’ end by exonucleases, as well as mediates the binding of the mRNA to the ribosome

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41
Q

List the order of pre-mRNA modifications

A

1) Addition of 5’ Cap
2) Addition of Poly A tail
3) Splicing

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42
Q

What is the start codon

A

AUG

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43
Q

What are the stop codons?

A

UAA
UAG
UGA

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44
Q

What are the 3 important characteristics of the genetic code?

A

It is degenerate
It is robust
It is universal

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45
Q

Describe the meaning of a degenerate code

A

Is one in which several codons have the same meaning
- Ex., multiple codons code for the same amino acid

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46
Q

How does having a degenerate code allow it to be robust?

A

Because it allows the DNA to absorb single-base mutations with minimal consequences to the protein it encodes

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47
Q

How is the genetic code universal?

A

All organisms use the same genetic code with only a few minor modifications

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48
Q

What are the 5 rules of the genetic code?

A
  1. It is non-overlapping
  2. It does not contain pauses
  3. The genetic code is read in triplets
  4. It is read in a linear fashion
  5. The code is resistant to mutations
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49
Q

A long sequence of triplet nucleotides with no stop codons is known as what?

A

An open reading frame (ORF)

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50
Q

What is a transition mutation?

A

Where a purine is replaced by another purine, or a pyrimidine is replaced by another pyrimidine

51
Q

If there is a transition mutation in the third position of a codon, what is likely to occur?

A

Nothing. This rarely causes a change

52
Q

If there is a transition mutation in the second position of a codon, from an A to a G, what would occur to the polarity of the amino acid

A

Not really anything, both G and A are polar, and therefore the polarity of the protein is reserved

53
Q

If there is a transition mutation in the first position of a codon, what is likely to occur?

A

An amino acid change may occur, but one that is chemically similar to the original

54
Q

What are the 4 point mutations?

A

1) Silent
2) Missense
3) Nonsense
4) Non-stop

55
Q

Describe a silent mutation

A

A point mutation where the amino acid has no change due to it

56
Q

Describe a missense mutation

A

A single-base substitution that leads to the replacement of one amino acid to another

57
Q

Describe a nonsense mutation

A

Results in a premature stop due to the creation of a stop codon

58
Q

Describe a nonstop mutation

A

Mutation causes a loss of a stop codon

59
Q

What are the three stages of translation?

A

Initiation
Elongation
Termination

60
Q

Describe the structure of tRNA

A

Relatively small
Single stranded RNA
tRNA folds back on itself to produce a secondary structure, similar to a clover, with 4 arms

61
Q

What are the four arms of a tRNA molecule

A

Amino acid arm
D arm
T arm
Anticodon arm

62
Q

Describe the amino acid arm of tRNA

A

contains a CCA sequence at the 3’ terminus
The amino acids attach to the 3’ terminal A residue

63
Q

Describe the anticodon arm of tRNA

A

On the 5’ end of the moleucle
Contains a 3’ nucleotide sequence that base pairs with the complementary mRNA

64
Q

What is the anticodon for Met?

A

5’ CAU
3’ UAC

65
Q

what is an aminoacyl-tRNA?

A

When a tRNA is “charged” because it has its amino acid bound to it

66
Q

T/F
tRNAs carry specific amino acids

A

True

67
Q

T/F
there is one aminoacyl-tRNA syntheses for each type of codon

A

False
There is one aminoacyl-tRNA synthetases for each one of the amino acids, so some need to recognize multiple codons

68
Q

What is Wobble Base pairing?

A

The noncannonical base pairing that can only happen in the 3rd position of the mRNA codon

69
Q

What is the “wobble position”

A

The nucleotide in the third position of the codon, which can vary without affecting the encoded amino acid

70
Q

When the first base of the anticodon (5’ –> 3’) is _______, base pairing is specific and tRNA only recognizes one codon

A

C or A

71
Q

When the first base is ________, base pairing is less specific and tRNA can recognize two different codons

A

U or G

72
Q

When the first base of an anticodon is ______, tRNA can recognize three different codons

A

I

73
Q

Where does the interaction between tRNA and mRNA take place?

A

In the ribosome

74
Q

Where is the peptidyl transferase center located in the ribosome; what is its function?

A

Found in the 60s subunit; functions as a catalyst for peptide bond formation between adjacent amino acids in the growing polypeptide chain

75
Q

Where is the decoding center located within the ribosome; what is its function?

A

Located in the 40s subunit; is where the aminoacylated tRNAs read the genetic code by base pairing with each codon

76
Q

What occurs at the A site of a ribosome?

A

Where the aminoacyl-tRNA binding occurs

77
Q

What occurs at the P site of a ribosome?

A

Where the peptidyl-tRNA binding occurs

78
Q

What occurs at the E site of a ribosome?

A

The exit site, where the tRNA molecule is released after the growing peptide chain is transferred to the next aminoacyl-tRNA in the P site

79
Q

What is the Shine-Delgano Sequence?

A

An initiation signal of 4-9 purine residues situated 8-13 nucleotides from the 5’ side of the start codon that guides the 5’ AUG to its correct position on the ribosome

80
Q

T/F
There are two tRNAs for methionine in all organisms

A

True
There is one initiation one and one coding for the Met residue in an internal position in a peptide

81
Q

What is the tRNA for an initiation Met called?

A

tRNA ^fMet

82
Q

Why can’t the tRNA ^fMEt add a Met residue into the polypeptide?

A

Because the addition of the formyl group means that the N group is blocked and cannot be added to the chain

83
Q

What is a polycistonic mRNA?

A

A single transcript that codes for more than one protein

84
Q

What is monocistonic mRNA?

A

a transcript that cones for only one protein

85
Q

What does it mean to say that bacterial genes can be non-overlapping or overlapping?

A

Means that in some genes there will be an open reading frame that is distinct from another and will have a separate Shine-Delgarno sequence, and that others will have open reading frames for the genes that overlap with one another. They will likely have overlapping start and stop codons

86
Q

Provide an example of an overlapping start and stop codon, depending on the reading frame

A

5’ AUGA

87
Q

What is a Kozak sequence?

A

The presence of a purine nucleotide 3 residues before the start codon and a G residue following the start codon

Is thought to enhance translation

88
Q

T/F
In both eukaryotes and prokaryotes, a single mRNA can be translated by multiple ribosomes silultaneously

A

True
Allows for each transcript to be used to produce multiple copies of that protein

89
Q

A single mRNA transcript bound by multiple ribosomes is called what?

A

A polysome

90
Q

What kind of energy is used in elongation?

A

GTP

91
Q

How does an aminoglycoside function?

A

It binds to the decoding center of the small ribosomal subunit and causes inappropriate flipping of either A1492 or A1493, which kills bacteria though errors in translational fidelity by causing misfolded proteins

92
Q

How doe aminonucleosides function?

A

They bind to the ribosomal A site and participate in peptide bond formation, but then the growing peptide chain is transferred to the antibiotic, and does not engage in translocation. The antibiotic dissociates from the ribosome and therefore prematurely stops protein synthesis

93
Q

What are release factors required for?

A

For a transcript to be released from a ribosome

94
Q

What are the primary release factors in prokaryotes? In eukaryotes?

A

RF-1 and RF-2 in pro.
eRF1 in eu

95
Q

RF-1 recognizes what stop codons?

A

UAG and UAA

96
Q

RF-2 recognizes what stop codons?

A

UGA and UAA

97
Q

What is a bacterial operon?

A

A unit of genetic expression consisting of one or more constrained genes and the operator and promoter sequences that regulate their transcription

98
Q

What is the lac operon?

A

Is a polycistronic mRNA, containing two regulatory regions and three genes that are the lac genes

99
Q

What are the two regulatory regions in the lac operon?

A

lac l and lac O

100
Q

What are the three lac genes?

A

Lac Z, Lac Y, and Lac A

101
Q

Describe lac l

A

Encodes for the lac repressor protein, which interacts with lac O to regulate transcription

102
Q

Describe lac O

A

Is the lac operator, which doesn’t code for a gene product but interacts with lac l to regulate transcription

103
Q

Describe lac Z

A

Codes for protein B-galactosidase, which catalyzes cleavage of lactose into its components

104
Q

Describe lac Y

A

Codes for the galactoside permease protein, which insterts into the bacterial plasma membrane and imports lactose into the cell

105
Q

Describe lac A

A

Codes for the protein thiogalactose transacetylase, which modifies toxic galactosides that are imported along with lactose, removing them from the cell

106
Q

T/F
The lac operon acts in cis and the lac repressor acts in trans

A

True

107
Q

The binding of the lac repressor to the lac operator is an example of what?

A

Negative regulation

108
Q

Where are the three operator regions in the lac operon?

A

O1 - just 3’ of the promoter region
O2 - in the lac Z gene
O3 - 5’ of the promoter

109
Q

T/F
Th lac repressor always binds to O1 and O2 or O2 and O3

A

False
It always binds with O1 and then either O2 or O3 as its second

110
Q

How is the lac operon activated?

A

Via leaky expression
Some B-galactosidase and galactoside permease is present even when lactose isn’t present, and when it is, these few existing molecules enable lactose from the medium to enter the cell

111
Q

What is the function of allolactose?

A

To induce the lac operon by binding t a site on the lac repressor, causing a conformational change resulting in dissociation of the repressor from the operator

112
Q

What is the role of effectors in Negative Regulation?

A

Causes a conformational change that results in an increase or decrease in transcription

113
Q

How does an effector activate a molecule in negative regulation?

A

The effector bidns to the repressor and induces a conformational change that results in the repressor’s dissociation from that molecule, allowing transcription to proceed

114
Q

What is positive regulation?

A

Regulation that activates the operon

115
Q

The positive regulation of the lac operon is modulated by what protein?

A

cAMP receptor protein (CRP)

116
Q

Describe the role of the effector in positive regulation

A

Effectors bind an activator (rather than a repressor) to cause a conformational change that results in an increase or decrease in transcription

117
Q

How does an effector cause inactivation of an activator in positive regulation?

A

Binding of the effector reduces the affinity of the activator for DNA, therefore inhibiting expression

118
Q

How does an effector cause activation of an activator in positive regulation?

A

cAMP binds to the activator CRP, which increases expression

119
Q

What is the activator of the lac operon?

A

CRP

120
Q

Global regulation can occur through what?

A

The binding of a common transcriptional activator
The removal of a common repressor bound to DNA

121
Q

Describe how distant regulation occurs

A

Through the process of ‘DNA looping’ where the activator binds to a DNA binding region distant from the promoter and the DNA folds over so it can make contact with the transcriptional machery

122
Q

Proteins that make protein-protein interactions to influence transcription are called?

A

Coactivators and corepressors

123
Q

How do coactivators work?

A

Act as a bridge between the activator and the RNA polymerase to activate transcription

BCHM 218 (2 decks)

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