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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
How many RNA polymerases do eukaryotes have?
3
26
What is the product of RNA Pol I
Ribosomal RNA (rRNA) precursors. Is responsible for transcribing rRNAs
27
What is the product of RNA Pol II
Messenger RNA (mRNA) are protein coding genes
28
What is the product of RNA Pol III
Smaller functional RNAs (tRNA, snRNA)
29
What regions in eukaryotic genes have or attract transcription factors
There is one in the general eukaryotic core promotor and there are regulatory sequences both upstream and downstream that bind gene-specific transcription factors
30
T/F Only RNA Pol II uses a TATA binding protein
False All three kinds of RNA polymerase use TATA binding proteins
31
Describe the TATA binding protein
The TBP binds to a 5' TATAAA sequence (AKA the TATA box) near position -30 of the promoter region
32
T/F All genes are under TBP transcription initiation, even if they don't have a TATA box
True
33
Describe how genes with no TATA box are under TBP transcription
TBP-associated factors (TAFs) recognize the promoter region of the gene and recruit TBP there
34
Describe the structure of the TATA binding protein
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
35
TFII indicates a transcription factor for which RNA polymerase?
RNA Pol II
36
Briefly describe Electrophoretic Mobility Shift Assays (EMSA)
Fragments of DNA of a known sequence are incubated with the protein of interest and then analyzed on a non-denaturing polyacrylamide
37
Explain the differences in pre-mRNA processing in prokaryotes and eukaryotes
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
38
List the features of a mature mRNA
5' cap 3' Poly A tail A coding region
39
What is the first modification made to pre-mRNA
The addition of a 5' cap
40
What is the 5' cap made of. What is its purpose
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
41
List the order of pre-mRNA modifications
1) Addition of 5' Cap 2) Addition of Poly A tail 3) Splicing
42
What is the start codon
AUG
43
What are the stop codons?
UAA UAG UGA
44
What are the 3 important characteristics of the genetic code?
It is degenerate It is robust It is universal
45
Describe the meaning of a degenerate code
Is one in which several codons have the same meaning - Ex., multiple codons code for the same amino acid
46
How does having a degenerate code allow it to be robust?
Because it allows the DNA to absorb single-base mutations with minimal consequences to the protein it encodes
47
How is the genetic code universal?
All organisms use the same genetic code with only a few minor modifications
48
What are the 5 rules of the genetic code?
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
49
A long sequence of triplet nucleotides with no stop codons is known as what?
An open reading frame (ORF)
50
What is a transition mutation?
Where a purine is replaced by another purine, or a pyrimidine is replaced by another pyrimidine
51
If there is a transition mutation in the third position of a codon, what is likely to occur?
Nothing. This rarely causes a change
52
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
Not really anything, both G and A are polar, and therefore the polarity of the protein is reserved
53
If there is a transition mutation in the first position of a codon, what is likely to occur?
An amino acid change may occur, but one that is chemically similar to the original
54
What are the 4 point mutations?
1) Silent 2) Missense 3) Nonsense 4) Non-stop
55
Describe a silent mutation
A point mutation where the amino acid has no change due to it
56
Describe a missense mutation
A single-base substitution that leads to the replacement of one amino acid to another
57
Describe a nonsense mutation
Results in a premature stop due to the creation of a stop codon
58
Describe a nonstop mutation
Mutation causes a loss of a stop codon
59
What are the three stages of translation?
Initiation Elongation Termination
60
Describe the structure of tRNA
Relatively small Single stranded RNA tRNA folds back on itself to produce a secondary structure, similar to a clover, with 4 arms
61
What are the four arms of a tRNA molecule
Amino acid arm D arm T arm Anticodon arm
62
Describe the amino acid arm of tRNA
contains a CCA sequence at the 3' terminus The amino acids attach to the 3' terminal A residue
63
Describe the anticodon arm of tRNA
On the 5' end of the moleucle Contains a 3' nucleotide sequence that base pairs with the complementary mRNA
64
What is the anticodon for Met?
5' CAU 3' UAC
65
what is an aminoacyl-tRNA?
When a tRNA is "charged" because it has its amino acid bound to it
66
T/F tRNAs carry specific amino acids
True
67
T/F there is one aminoacyl-tRNA syntheses for each type of codon
False There is one aminoacyl-tRNA synthetases for each one of the amino acids, so some need to recognize multiple codons
68
What is Wobble Base pairing?
The noncannonical base pairing that can only happen in the 3rd position of the mRNA codon
69
What is the "wobble position"
The nucleotide in the third position of the codon, which can vary without affecting the encoded amino acid
70
When the first base of the anticodon (5' --> 3') is _______, base pairing is specific and tRNA only recognizes one codon
C or A
71
When the first base is ________, base pairing is less specific and tRNA can recognize two different codons
U or G
72
When the first base of an anticodon is ______, tRNA can recognize three different codons
I
73
Where does the interaction between tRNA and mRNA take place?
In the ribosome
74
Where is the peptidyl transferase center located in the ribosome; what is its function?
Found in the 60s subunit; functions as a catalyst for peptide bond formation between adjacent amino acids in the growing polypeptide chain
75
Where is the decoding center located within the ribosome; what is its function?
Located in the 40s subunit; is where the aminoacylated tRNAs read the genetic code by base pairing with each codon
76
What occurs at the A site of a ribosome?
Where the aminoacyl-tRNA binding occurs
77
What occurs at the P site of a ribosome?
Where the peptidyl-tRNA binding occurs
78
What occurs at the E site of a ribosome?
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
What is the Shine-Delgano Sequence?
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
T/F There are two tRNAs for methionine in all organisms
True There is one initiation one and one coding for the Met residue in an internal position in a peptide
81
What is the tRNA for an initiation Met called?
tRNA ^fMet
82
Why can't the tRNA ^fMEt add a Met residue into the polypeptide?
Because the addition of the formyl group means that the N group is blocked and cannot be added to the chain
83
What is a polycistonic mRNA?
A single transcript that codes for more than one protein
84
What is monocistonic mRNA?
a transcript that cones for only one protein
85
What does it mean to say that bacterial genes can be non-overlapping or overlapping?
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
Provide an example of an overlapping start and stop codon, depending on the reading frame
5' AUGA
87
What is a Kozak sequence?
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
T/F In both eukaryotes and prokaryotes, a single mRNA can be translated by multiple ribosomes silultaneously
True Allows for each transcript to be used to produce multiple copies of that protein
89
A single mRNA transcript bound by multiple ribosomes is called what?
A polysome
90
What kind of energy is used in elongation?
GTP
91
How does an aminoglycoside function?
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
How doe aminonucleosides function?
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
What are release factors required for?
For a transcript to be released from a ribosome
94
What are the primary release factors in prokaryotes? In eukaryotes?
RF-1 and RF-2 in pro. eRF1 in eu
95
RF-1 recognizes what stop codons?
UAG and UAA
96
RF-2 recognizes what stop codons?
UGA and UAA
97
What is a bacterial operon?
A unit of genetic expression consisting of one or more constrained genes and the operator and promoter sequences that regulate their transcription
98
What is the lac operon?
Is a polycistronic mRNA, containing two regulatory regions and three genes that are the lac genes
99
What are the two regulatory regions in the lac operon?
lac l and lac O
100
What are the three lac genes?
Lac Z, Lac Y, and Lac A
101
Describe lac l
Encodes for the lac repressor protein, which interacts with lac O to regulate transcription
102
Describe lac O
Is the lac operator, which doesn't code for a gene product but interacts with lac l to regulate transcription
103
Describe lac Z
Codes for protein B-galactosidase, which catalyzes cleavage of lactose into its components
104
Describe lac Y
Codes for the galactoside permease protein, which insterts into the bacterial plasma membrane and imports lactose into the cell
105
Describe lac A
Codes for the protein thiogalactose transacetylase, which modifies toxic galactosides that are imported along with lactose, removing them from the cell
106
T/F The lac operon acts in cis and the lac repressor acts in trans
True
107
The binding of the lac repressor to the lac operator is an example of what?
Negative regulation
108
Where are the three operator regions in the lac operon?
O1 - just 3' of the promoter region O2 - in the lac Z gene O3 - 5' of the promoter
109
T/F Th lac repressor always binds to O1 and O2 or O2 and O3
False It always binds with O1 and then either O2 or O3 as its second
110
How is the lac operon activated?
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
What is the function of allolactose?
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
What is the role of effectors in Negative Regulation?
Causes a conformational change that results in an increase or decrease in transcription
113
How does an effector activate a molecule in negative regulation?
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
What is positive regulation?
Regulation that activates the operon
115
The positive regulation of the lac operon is modulated by what protein?
cAMP receptor protein (CRP)
116
Describe the role of the effector in positive regulation
Effectors bind an activator (rather than a repressor) to cause a conformational change that results in an increase or decrease in transcription
117
How does an effector cause inactivation of an activator in positive regulation?
Binding of the effector reduces the affinity of the activator for DNA, therefore inhibiting expression
118
How does an effector cause activation of an activator in positive regulation?
cAMP binds to the activator CRP, which increases expression
119
What is the activator of the lac operon?
CRP
120
Global regulation can occur through what?
The binding of a common transcriptional activator The removal of a common repressor bound to DNA
121
Describe how distant regulation occurs
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
Proteins that make protein-protein interactions to influence transcription are called?
Coactivators and corepressors
123
How do coactivators work?
Act as a bridge between the activator and the RNA polymerase to activate transcription

BCHM 218 (2 decks)

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