Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

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.

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

mRNA’s discovery

A

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

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

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

rRNA

A

Ribosomal RNA; facilitates the interaction between tRNA and mRNA

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

tRNA

A

Transfer RNA; carries amino acids to create proteins

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

mRNA

A

RNA that ‘codes’ for a series of amino acids

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

Transcription

A

DNA is turned into mRNA

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

Translation

A

mRNA is turned into a protein

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

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

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

Template strand vs. coding strand

A

The strand that serves as the template for RNA synthesis

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

Coding strand

A

The strand not involved in transcription

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

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

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

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

What monomers does RNAP use?

A

rNTP, versus DNA which uses dNTP

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

Bacterial RNAP components

A

holoenzyme

Core enzyme, sigma factor

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

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

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

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

Transcription unit

A

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

promoter
RNA-coding region
terminator

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

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

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

RNA transcript

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Upstream
The side of the start site towards the promoter towards the 5' end.
26
Downstream
The side of the start site towards the coding region towards the 3' end.
27
Bacterial promoter structure
contain consensus sequences, recognizable sequences at different upstream regions of their promoters
28
Specific Consensus sequences in bacteria
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.
29
Promoter strength
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.
30
Effect of promoter strength
RNAP can still bind at weak promoters, but its gene will be transcribed much less
31
Initiation of bacterial transcription
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
32
Significance of consensus sequences to initiation
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
33
RNAP Explore
RNAP loosely attaches to DNA so it can locate a consensus sequence
34
Closed-promoter complex
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.
35
Open-promoter complex
RNAP opens a transcription bubble at the promoter
36
Elongation in bacterial transcription
sigma factor dissociates from the core enzyme The growing transcript is made 5' to 3'. T to A and A to U
37
Transcription bubble
Opened by RNAP at promoter during initiation very small, and rewinds behind the RNAP This peels the RNA transcript off
38
Termination in bacteria
Transcription ends when the terminator sequence has been transcribed There are two forms of termination in bacteria: Rho-dependent and intrinsic
39
Intrinsic termination
The formation of a hairpin structure stalls the RNAP and causes it to dissociate, ending termination
40
Terminator sequence composition in bacterial mRNA
Terminators are GC rich, and are followed by a string of uracil (UUUUUUU in the mRNA)
41
Hairpin / stem-loop structure
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
Rho-dependent termination
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
Rho factor
an enzyme that breaks down H-bonds and acts as a helicase
44
Polycistronic
Bacterial RNA can be polycistronic. Polycistronic RNA contains multiple genes. During translation, this RNA creates several proteins at once.
45
RNAP II
The main RNAP in eukaryotes. produces gene product transcripts / mRNA
46
RNAP in eukaryotes
Eukaryotes has 3 types of RNA polymerase. Each type is used to produce different types of RNA. RNAPII is the main one
47
Initiation in eukaryotes
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
TATA box initiation
a GTF called TFIID binds the TATA box. TFIID recruits other GTFs
49
Core Promoter
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
TATA box
The most common type of Eukaryotic consensus sequence During initiation, a GTF called TFIID binds the TATA box. TFIID recruits other GTFs
51
RNAII and initiation
RNAII doesn't recognize the promoter. It requires proteins called transcription factors to initiate transcription.
52
Transcription factors
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
GTFs
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
Regulatory transcription factors
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
Enhancers and silencers
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
Enhancer
A cis-acting DNA element. When bound by an activator, it increases transcription of its nearby gene.
57
Silencer
A cis-acting DNA element. When bound by a repressor, it decreases transcription of its nearby gene.
58
Activator
A trans-acting element; regulatory transcription factor Binds an enhancer DNA element to increase transcription
59
Repressor
A trans-acting element; regulatory transcription factor Binds a silencer DNA element to decrease transcription
60
Pribnow Box
The -10 TATAAT sequence in prokaryotes, a promoter consensus sequence
61
Goldberg Hogness Box
The "TATAA" box in eukaryotes, a promoter consensus sequence
62
RNAPI
The Eukaryotic RNAP that makes rRNA.
63
Polyadenylation signal
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
How does the polyadenylation signal end transcription?
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
Use of RNA end modifications
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
3' end modification
A string of AAAAAA on the 3' end of an mRNA, terminated by a hydroxyl group (Poly-A tail)
67
Poly-A polymerase
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
5' end modification
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
Exons
coding regions of mRNA
70
Introns
non-coding regions of mRNA
71
RNA splicing
Removal of introns from mRNA to create a continuous coding sequence
72
Intron structure
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
Intron 5' splice site
GU
74
Intron 3' splice site
AG
75
Self-splicing introns
The intron RNA itself can catalyze its own excision, without the need for additional proteins or other RNA molecules.
76
Ribozyme
RNA capable of enzymatic activity
77
Group I intron removal process
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
Group II intron removal process
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
General removal steps of self-splicing introns
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
Spliceosomal intron
These can't catalyze their own excision; they require another structure, the spliceosome.
81
Spliceosome formation
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
snRNA
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
Spliceosomal intron removal
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
Insertion editing
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
Substitution editing
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
Crick & Brenner experiment
Chemically induced mutations that resulted in frameshift mutations in bacteriophages Growth/no growth results showed that codons were 3 nucleotides and commaless
87
In-vitro protein synthesis
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
polynucleotide phosphorylase
catalyzes the cell-free synthesis of RNA No DNA needed Links available RNA nucleotides together in random order
89
PolyU experiment
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
RNA homopolymer
a long string of the same base
91
RNA heteropolymer codon experiments
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
Triplet binding assay
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
Degeneracy
the same amino acid is coded for by more than one codon

Biol251 (8 decks)

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