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Biol251 > Transcription > Flashcards

Transcription Flashcards

1
Q

Why must DNA use an intermediate molecule?

A

DNA is in the nucleus; this is so that the DNA is shielded from the cell environment, and from enzymes in the cytoplasm.

Protein creation takes place in the cytoplasm, however. So DNA must not directly create proteins.

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2
Q

mRNA’s discovery

A

RNA synthesis preceded phage protein synthesis, and that RNA is complementary to phage DNA

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3
Q

Gene expression

A

the creation of proteins from DNA

DNA gets transcribed into mRNA
mRNA gets translated into a protein

Non-coding RNA is also involved in gene expression

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4
Q

rRNA

A

Ribosomal RNA; facilitates the interaction between tRNA and mRNA

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5
Q

tRNA

A

Transfer RNA; carries amino acids to create proteins

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6
Q

mRNA

A

RNA that ‘codes’ for a series of amino acids

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7
Q

Transcription

A

DNA is turned into mRNA

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8
Q

Translation

A

mRNA is turned into a protein

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9
Q

Similarity between transcription and DNA replication

A

Uses DNA as a template for base-pairing
Phosphodiester bonds connect the RNA nucleotides
There is a 5’ to 3’ direction of synthesis

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10
Q

Differences between DNA replication and transcription

A

Product (dsDNA vs RNA)
Scale (whole genome vs single genes)
Monomer (deoxyribonucleic acids vs ribonucleic acids)
Base pair (A-T vs A-U, T-A)
Key enzyme (DNA polymerase vs RNA polymerase)
Primer (needs primer vs doesn’t need primer)
Template (both strands vs one strand)

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11
Q

Template strand vs. coding strand

A

The strand that serves as the template for RNA synthesis

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12
Q

Coding strand

A

The strand not involved in transcription

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13
Q

Why is the coding strand called that?

A

the RNA will be the same as the coding strand, save for uracil in place of thymine

they will also have the same parallelism.

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14
Q

Typical representation of DNA sequences in the context of transcription

A

DNA sequences are typically represented as coding strands.

If you don’t see the prime labels, it is assumed to be 5’ to 3’ left to right.

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15
Q

RNAP

A

RNA polymerase
works similarly to the DNA polymerases.

Goes 5’ to 3’
catalyze the addition of nucleotide triphosphates into growing nucleotide chains

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16
Q

What monomers does RNAP use?

A

rNTP, versus DNA which uses dNTP

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17
Q

Bacterial RNAP components

A

holoenzyme

Core enzyme, sigma factor

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18
Q

Bacterial RNAP core enzyme

A

2a, 1b, 1b’, and 1w
Contains the active site
Has an inactive form; must be paired with a coenzyme, the sigma factor

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19
Q

Bacterial RNAP sigma factor

A

Coenzyme to core enzyme

Only when the sigma factor combines with the core enzyme is the enzyme active.

Recognizes and binds to the promoter sequence

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20
Q

Bacterial RNAP sigma factor use

A

there are several different types of sigma factors.

These different sigma factors recognize different types of promoter sequences.

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21
Q

Transcription unit

A

Contains the start and end of a gene, plus the gene itself

promoter
RNA-coding region
terminator

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22
Q

Significance of transcription units

A

RNAPs only transcribe the sequence containing the desired genetic information.

So, all genes must have “starts” and “ends”

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23
Q

+1 site

A

The site where transcription begins

The RNAP binds to the DNA template at the promoter.
This defines where they lay down the first nucleotide.
This site is the +1 site.

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24
Q

RNA transcript

A

The transcribed mRNA
Contains the RNA-coding region and the terminator

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25
Q

Upstream

A

The side of the start site towards the promoter
towards the 5’ end.

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26
Q

Downstream

A

The side of the start site towards the coding region
towards the 3’ end.

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27
Q

Bacterial promoter structure

A

contain consensus sequences, recognizable sequences at different upstream regions of their promoters

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28
Q

Specific Consensus sequences in bacteria

A

One is -35 from the +1 site. TTGACA

Another is -10 from the +1 site. TATAAT (Pribnow box)

Consensus sequences may not be those exactly.

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29
Q

Promoter strength

A

The better a match promoter sequence is to TTGACA or TATAAT, the stronger a promoter it is.

This means the RNAP binds better to begin transcription.

Less match means being a weak promoter, and binding weakly.

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30
Q

Effect of promoter strength

A

RNAP can still bind at weak promoters, but its gene will be transcribed much less

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31
Q

Initiation of bacterial transcription

A

RNAP explores
RNAP recognizes & binds to promoter using sigma factor
RNAP positioned at +1 site
RNAP opens transcription bubble
open-promoter complex is created
first nucleotide laid at +1 site

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32
Q

Significance of consensus sequences to initiation

A

allow the bacterial RNAP to tightly bind to the template at that region

The distance between them places the enzyme’s active site at the +1 site

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33
Q

RNAP Explore

A

RNAP loosely attaches to DNA so it can locate a consensus sequence

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34
Q

Closed-promoter complex

A

The sigma factor has bound the consensus sequence.
The RNAP’s active site is aligned with the +1 site.
The DNA is ds, and RNAP is over the promoter.

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35
Q

Open-promoter complex

A

RNAP opens a transcription bubble at the promoter

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36
Q

Elongation in bacterial transcription

A

sigma factor dissociates from the core enzyme
The growing transcript is made 5’ to 3’.
T to A and A to U

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37
Q

Transcription bubble

A

Opened by RNAP at promoter during initiation
very small, and rewinds behind the RNAP
This peels the RNA transcript off

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38
Q

Termination in bacteria

A

Transcription ends when the terminator sequence has been transcribed

There are two forms of termination in bacteria: Rho-dependent and intrinsic

39
Q

Intrinsic termination

A

The formation of a hairpin structure stalls the RNAP and causes it to dissociate, ending termination

40
Q

Terminator sequence composition in bacterial mRNA

A

Terminators are GC rich, and are followed by a string of uracil (UUUUUUU in the mRNA)

41
Q

Hairpin / stem-loop structure

A

many RNA regions are complementary to each other. they fold to create a hairpin structure

The terminator sequence in bacteria is designed to produce this structure.

The structure stalls RNAP, terminating transcription

42
Q

Rho-dependent termination

A

Rho factor binds somewhere upstream of the terminator sequence

RNAP forms the hairpin structure, and is stalled
Rho factor catches up with the RNAP
It destroys the H-bonds between the RNA-DNA hybrid

very rare

43
Q

Rho factor

A

an enzyme that breaks down H-bonds and acts as a helicase

44
Q

Polycistronic

A

Bacterial RNA can be polycistronic.
Polycistronic RNA contains multiple genes.
During translation, this RNA creates several proteins at once.

45
Q

RNAP II

A

The main RNAP in eukaryotes. produces gene product transcripts / mRNA

46
Q

RNAP in eukaryotes

A

Eukaryotes has 3 types of RNA polymerase.
Each type is used to produce different types of RNA.
RNAPII is the main one

47
Q

Initiation in eukaryotes

A

GTFs recognize the promoter. They bind to the promoter.

RNAPII recognizes the GTFs and is recruited to the core promoter.

The GTFs align the RNAPII active site to the start site, forming the pre-initiation complex.

48
Q

TATA box initiation

A

a GTF called TFIID binds the TATA box. TFIID recruits other GTFs

49
Q

Core Promoter

A

located about 30 bp upstream of the start site.

contains one or more consensus sequences

location determines where RNAPII binds to the DNA, and where the start site is

most common consensus sequence is a TATA box, aka a Goldberg-Hogness box

50
Q

TATA box

A

The most common type of Eukaryotic consensus sequence

During initiation, a GTF called TFIID binds the TATA box. TFIID recruits other GTFs

51
Q

RNAII and initiation

A

RNAII doesn’t recognize the promoter.

It requires proteins called transcription factors to initiate transcription.

52
Q

Transcription factors

A

Proteins which affect transcription. There are two types; one, GTFs, help RNAPII initiate transcription; the other, regulatory transcription factors, affect the rate of transcription

53
Q

GTFs

A

A set of interacting proteins called the TFII (transcription factors for RNAPII)

recognize and bind promoter, and are recognized by RNAPII, allowing transcription to begin

“general” because they assemble at RNAPII’s core promoters

54
Q

Regulatory transcription factors

A

aka “trans-acting elements”

Proteins bind to distal control elements to affect the rate at which transcription is initiated

ACTIVATORS: bind to enhancers to increase initiation
REPRESSORS: bind to silences to reduce initiation

55
Q

Enhancers and silencers

A

Distal DNA elements which are far away from the promoter.

They help form or prevent the pre-initiation complex.

They are exclusive to eukaryotes.

An enhancer is bound by an activator.
A silencer is bound by a repressor.

56
Q

Enhancer

A

A cis-acting DNA element.

When bound by an activator, it increases transcription of its nearby gene.

57
Q

Silencer

A

A cis-acting DNA element.

When bound by a repressor, it decreases transcription of its nearby gene.

58
Q

Activator

A

A trans-acting element; regulatory transcription factor

Binds an enhancer DNA element to increase transcription

59
Q

Repressor

A

A trans-acting element; regulatory transcription factor

Binds a silencer DNA element to decrease transcription

60
Q

Pribnow Box

A

The -10 TATAAT sequence in prokaryotes, a promoter consensus sequence

61
Q

Goldberg Hogness Box

A

The “TATAA” box in eukaryotes, a promoter consensus sequence

62
Q

RNAPI

A

The Eukaryotic RNAP that makes rRNA.

63
Q

Polyadenylation signal

A

Eukaryotic terminators have a polyadenylation signal, AAUAAA

It serves as a cleavage signal when transcribed, and also allows the poly-A tail to be attached to pre-mRNA.

64
Q

How does the polyadenylation signal end transcription?

A

When the signal is transcribed into mRNA as AAUAAA, an endonuclease is attracted.

It cuts the bond between mRNA and RNAPII.

The RNAPII continues to transcribe; the mRNA peels off.

65
Q

Use of RNA end modifications

A

protect the mRNA, allowing them to survive in the cytoplasm for longer

facilitate mRNA export, allowing them to leave the nucleus faster

play a role in translation initiation

66
Q

3’ end modification

A

A string of AAAAAA on the 3’ end of an mRNA, terminated by a hydroxyl group (Poly-A tail)

67
Q

Poly-A polymerase

A

Polyadenylation signal in pre-mRNA serves as a signal for the poly-A polymerase enzyme

PAP.E adds the poly-A tail, and poly-A binding proteins attach to the tail

68
Q

5’ end modification

A

A 5’ cap is also added to the 5’ end of the mRNA

The cap is m7G, a specialized methylated guanine

Attaches via a unique 5’ to 5’ bond

69
Q

Exons

A

coding regions of mRNA

70
Q

Introns

A

non-coding regions of mRNA

71
Q

RNA splicing

A

Removal of introns from mRNA to create a continuous coding sequence

72
Q

Intron structure

A

Introns begin with GU (donor sequence)
Introns end with AG (acceptor sequence)
These consensus sequences allow intron-exon borders to be recognized.

Within the intron is the branch point (A). It is usually an adenosine.

73
Q

Intron 5’ splice site

A

GU

74
Q

Intron 3’ splice site

A

AG

75
Q

Self-splicing introns

A

The intron RNA itself can catalyze its own excision, without the need for additional proteins or other RNA molecules.

76
Q

Ribozyme

A

RNA capable of enzymatic activity

77
Q

Group I intron removal process

A

A free guanine attaches to an active site within the intron.

The guanine carries a hydroxyl group with it.

The hydroxyl group attaches to the 5’ splice site.

The 5’ splice site is cut.

The 3’ end of the now-free exon has a free hydroxyl group.

The 3’ hydroxyl of exon 1 attaches to the 3’ splice site at the 5’ end of exon 2.

78
Q

Group II intron removal process

A

A (within the intron) is a branch point with a reactive adenine (A).

The A attaches to the 5’ splice site. A lariat is formed.

The 3’ hydroxyl of exon 1 attaches to the 3’ splice site at the 5’ of exon 2.

The intron is released as a lariat.

79
Q

General removal steps of self-splicing introns

A

Bond between 3’ end of exon 1 and 5’ end of intron is broken

Bond between 3’ end of exon 2 and 5’ end of intron is broken

The intron is folded into a secondary structure to facilitate these breaks.

80
Q

Spliceosomal intron

A

These can’t catalyze their own excision; they require another structure, the spliceosome.

81
Q

Spliceosome formation

A

snRNAs combine with a protein to form snRNP (small nuclear ribonucleoproteins).

snRNPs interact with other proteins to form the spliceosome.

The spliceosome is made of several snRNPs.

snRNPs recognize slicing signals on pre-mRNA.

They do this through binding the consensus RNA sequences.

82
Q

snRNA

A

Element of the spliceosome, functions as a ribozyme

The snRNA are U rich, so the varieties of snRNP are referred to as U1, U2, U4, U5, U6

83
Q

Spliceosomal intron removal

A

U1 binds to the 5’ splice site. U2 binds to the branch point.
U2 recruits more snRNPs: the U4/U6*U5 complex.
U6 displaces U1. U6 tries to interact with U2, causing U4 to get squeezed out.
U6 interacts with U2, causing the A branch site to form a lariat with 5’.
The free 3’ hydroxyl of the exon attacks the 3’ splice site.
The exons are joined together by U5.
The lariat is released and degraded.

84
Q

Insertion editing

A

The mRNA has a complementary pairing with a gRNA (guide RNA).

Loops form in gRNA where it has non-complementary regions.

Endonuclease makes cuts in the mRNA where there are loops in the gRNA.

The mRNA now has a template strand.
The “gaps” are filled in.

85
Q

Substitution editing

A

Adenosine to inosine editing occurs in pre-mRNA coding for receptors in brain tissue.
Adenosine deaminase catalyzes the AI conversion.
Inosine reads as a G. It becomes GC instead of AT.

86
Q

Crick & Brenner experiment

A

Chemically induced mutations that resulted in frameshift mutations in bacteriophages

Growth/no growth results showed that codons were 3 nucleotides and commaless

87
Q

In-vitro protein synthesis

A

A cell-free translation system
Ribosomes, amino acids, but no mRNA
When you insert mRNA, its protein is created
An enzyme, polynucleotide phosphorylase, catalyzes the cell-free synthesis of RNA

88
Q

polynucleotide phosphorylase

A

catalyzes the cell-free synthesis of RNA

No DNA needed
Links available RNA nucleotides together in random order

89
Q

PolyU experiment

A

Long UUUUUUU mRNA created using polynucleotide phosphorylase

used 20 test tubes, each filled with a different amino acid. For each individual experiment, 19 test tubes were “cold” and one was radioactively tagged.

Tubes contained bacterial extracts with all components necessary for translation

Each tube contains one labeled amino acid

A radioactive protein was only found in one of the tubes, the one UUU codes for

The amino acid in that tube is utilized by the UUU codon

This technique was used for other homopolymers

90
Q

RNA homopolymer

A

a long string of the same base

91
Q

RNA heteropolymer codon experiments

A

The A & C were polymerized in a specific ratio, experimentally
poly-AC codons can have 6 different amino acids
These amino acids were in proportions determined by the probability of multiple incorporations of each nucleotide, based on their ratio

don’t reveal the ORDER of bases in each codon.
They only reveal the composition

92
Q

Triplet binding assay

A

Synthetic RNA is produced
A mixture of ribosomes and one labeled amino acid is created
RNA is added into the mixture

This mixture is passed through a filter
The charged tRNAs bound to a ribosome get stuck on the filter
The unbound ribosomes and unbound tRNA passes through the filter

Radioactivity at filter was analyzed
If the radioactivity in the filter is high, the codon codes for the amino acid

93
Q

Degeneracy

A

the same amino acid is coded for by more than one codon

Biol251 (8 decks)

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