Chapter 17: Transcription and Translation Flashcards
1
Q
DNA Replication occours during _______ (general, not cell cycle)
A
Cell division. DNA is copied to be transferred to daughter cells.
2
Q
Expression of information encoded in DNA (__________) is part of _________ expression
A
Genes, genome expression
3
Q
RNA is synthesized in the _______ direction
A
5’ to 3’
4
Q
This enzyme is responsible for synthesizing RNA from DNA using the template strand
A
RNA polymerase
5
Q
RNA Polymerase ________ require a primer to begin transcription, unlike DNA polymerase
A
Does not
6
Q
RNA Polymerase synthesizes RNA in the _______ direction
A
5’ to 3’
7
Q
Bacteria have ___ type(s) of RNA Polymerase, and eukaryotes have ___ type(s) of RNA Polymerase
A
1
3 (I, II, and III)
8
Q
RNA has the nucleotide base ___ instead of ____
A
Uracil (U), Thymine (T)
9
Q
____ is the first phase of transcription
A
Initiation
10
Q
In prokaryotes, a _________ must bind to the DNA promoter, and RNA Polymerase
must bind to the _____ before beginning transcription
A
Sigma protein, Sigma protein
11
Q
In prokaryotes, RNA Polymerase and Sigma protein bind to form a ________
A
Holoenzyme
12
Q
In prokaryotes, the sigma protein of the Holoenzyme binds to ______ segments on DNA that help start transcription
A
Promoter
The promoter segments are where the holoenzyme will bind before reading the DNA template and transcribing
13
Q
In Prokaryotes, __________ bind to promoters with slightly different DNA base sequences. This allows the organism to __________ in response to environmental changes.
A
different sigma proteins
activate certain genes
14
Q
Which component of a holoenzyme makes initial contact with promoter segments
A
Sigma protein
15
Q
Bacterial (prokaryote) promoter sequences are DNA sequences __________ of ___________
A
upstream, open reading frames
16
Q
Sigma proteins act as a ________ factor for _______ in prokaryotes
A
regulatory, RNA polymerase
Sigma proteins guide RNA Polymerase to specific promoter sequences.
17
Q
True or False: Most Bacteria only have 1 type of Sigma protein
A
False
18
Q
Promoter sequences are _____ base pairs long
A
40-50
19
Q
Bacterial promoters have 2 key regions: the ____ box and the ____ box
A
-10 box, -35 box
20
Q
The -10 box is found _________ and consists of the sequence _ _ _ _ _ _
A
10 bases upstream from the transcription start site (+1 site)
TATAAT
21
Q
The -35 box is found _________ and consists of the seuence _ _ _ _ _ _
A
35 bases upstream from the transcription start site (+1 site)
TTGACA
22
Q
The +1 site is where __________
A
Transcription’s start site lies
23
Q
True or False: all bacterial promoters have a -10 box and a -35 box, the rest of the promoter sequence varies
A
True
24
Q
Name the 3 Phases of Transcription in Prokaryotes:
A
Initiation, Elongation, Termination
25
During the Initiation phase in prokaryotic transcription, these two steps happen.
Sigma protein binds to DNA promoter, RNA polymerase binds to Sigma to form holoenzyme.
Sigma protein guides holoenzyme to a promoter sequence.
26
The _____ dissociates from _____ once transcription in prokaryotes is complete.
sigma protein, the core enzyme (RNA Polymerase)
27
During the Elongation phase of transcription in bacteria (prokaryotes), these steps happen:
RNA polymerase moves along the DNA template in the 3' to 5' direction and synthesizes primary transcript in the 5' to 3' direction
28
During the termination phase of transcription in bacteria (prokaryotes), these steps happen:
Holoenzyme reads a stop codon, which causes it to produce hairpins instead of a monomer of primary transcript
Holoenzyme will then detach from the DNA template
The sigma protein will dissociate from the holoenzyme
29
Key differences between transcription in prokaryotes and eukaryotes (4 bullets)
- Eukaryotes have 3 types of RNA Polymerase
- Eukaryotes have more diverse promoters, including TATA box at -30
- Eukaryotes have Basal transcription factors instead of Sigma proteins
- Occours in nucleus in eukaryotes, Cytoplasm in prokaryotes
30
Transcription occours in the _____ in eukaryotes and in the ______ in prokaryotes(bacteria)
Nucleus, cytoplasm
31
The protein-coding regions of eukaryotic genes are interrupted by non-coding regions. What are the coding regions called and what are the non-coding regions called.
Coding regions: Exons
Non-Coding regions: Introns
Exons are interrupted by introns
32
Context: Eukaryotic Genes
_____ are interrupted by ______
Exons are interrupted by introns.
33
The product of transcription in both Prokaryotes and Eukaryotes is called ________
Primary transcript
34
True or False: Exons always translate into proteins
IGNORE THIS CARD
False! Exons always express mRNAs, but not necessarily proteins.
IGNORE THIS CARD
35
This process removes introns from pre-mRNA
RNA splicing
36
This protein binds to other proteins of this same type to form a spliceosome.
snRNP (small nuclear ribonucleoproteins)
37
Spliceosomes catalyze this reaction:
Splicing reaction, which removes introns from pre-mRNA
38
A ______ functions as the catalytic unit in the spliceosome.
Ribozyme
39
Describe the 4 steps for RNA splicing
1: snRNPs bind to start and end of an intron and do branch site within the intron
2: More snRNPs join to form a spliceosome
3: The intron is cut from the exon, the intron forms lasso shape at branch point
4: The spliced out intron is released, and the remaining exons in the pre-mRNA sequence are joined together
40
The splicing process allows different _______ and therefore _____ to be produced from a single gene
mRNAs, proteins
41
pre-mRNA transcripts are also processed by:
The addition of a 5' cap and a poly(A) tail
42
The 5' cap serves as a:
Recognition signal for translation machinery
Helps extend mRNA lifespan by protecting against degredation
43
poly(A) tail function:
Extends the life of an mRNA by protecting it from degredation
Serves as termination signal for transcription
44
Components of a mature mRNA from the 5' to 3' end
5' end: [5' cap, 5' untranslated region (UTR), coding region, 3' untranslated region (UTR), poly(A) tail.] : 3' end
45
Difference of RNA Polymerase in eukaryotes vs. prokaryotes:
Eukaryotes have 3 types of RNA polymerase that produce a different class of RNA (mRNA, tRNA, rRNA)
Prokaryotes have only 1 type of RNA polymerase
46
Difference of promoter structure in eukaryotes vs. prokaryotes
Eukaryotes promoter structures are more variable and longer, and often include a TATA box about -30 from the +1 site
Prokaryotes typically contain a -35 box [TTGACA] and a -10 [TATAAT] box
47
Difference of proteins that associate with promoters in eukaryotes vs. prokaryotes
Eukaryotes have many general transcription factors
Prokaryotes have different version of Sigma proteins that bind to different promoters
48
Difference in RNA processing in eukaryotes vs. prokaryotes
Eukaryotes have extensive RNA processing. Several steps occur to mature pre-mRNA before export to cytoplasm
- 1: Enzyme catalyzed addition of 5' cap
- 2: Splicing (intron removal) by spliceosomes to produce mRNA
- 3: Enzyme catalyzed addition of poly(A) tail to 3' end on mRNA
Prokaryotes very rarely have RNA processing
49
Difference in Translation in eukaryotes vs. prokaryotes
Eukaryotes: Initiation and termination are more complex. Elongation is similar to bacteria
Prokaryotes: Initiation and termination are less complex. Elongation is similar to prokaryotes
50
In eukaryotes, transcription and translation are _____
Separated
Transcription and RNA processing occurs in the nucleus
Translation of mature mRNA occurs in the cytoplasm
51
tRNAs are the link between ______ and _______
mRNAs and Amino Acids
52
aminoacyl tRNA synthetases
This enzyme "charges" tRNA by catalyzing the addition of amino acids to tRNAs using ATP
53
tRNA is covalently linked to its _________
corresponding amino acid
54
A tRNA that is covalently linked to its corresponding amino acid is called a:
aminoacyl tRNA
55
tRNA structure
3' end binding site for amino acids
Anti-codon (base pair triplet) that pairs with codon on mRNA
56
There are ____ amino acids with ___ codons and ___ types of tRNA
20 amino acids, 61 codons, 40 tRNA
57
tRNA has a ______ shape
Cross with circles on ends
58
Ribosomes contain _____ and ______
Proteins and ribosomal RNA (rRNA)
59
Ribosomes can be separated into a _____ and a ______
Small subunit
Large subunit
60
The small subunit of a ribosome has this function:
Holds the mRNA in place during translation
61
The large subunit of a ribosome has this function:
Where peptide bonds form
62
The active site of the ribosome is made entirely of _________
ribosomal RNA (rRNA)
63
A ribozyme is:
An enzyme that catalyzes peptide bond formation
Made of rRNA
64
The three sites of a ribosome are:
A site (acceptor site)
P site (peptide site)
E site (exit site)
65
Function of the ribosome A site
Accepts aminoacyl tRNA into ribosome for elongation process
66
Function of the P site of a ribosome
Peptide bond is formed between polypeptide and the amino acid of aminoacyl tRNA
67
The initiation of translation begins with a _ _ _ codon
AUG
68
The AUG codon codes for:
Methionine
69
In bacteria, the start codon is preceded by a:
Ribosome binding site (AKA Shine-Dalgarno sequence)
Complementary to a section of one rRNA in the small ribosomal subunit
70
The interaction between the small subunit of the ribosome and the mRNA is mediated by:
Initiation factors
71
Translation in bacteria is initiated by:
Modified Methionine, f-Met
72
Elongation is:
The process where the polypeptide chain is grown and more amino acids are linked to it
73
List the substeps of elongation
1. Incoming aminoacyl tRNA (A site filled)
2. Peptide bond formation (between 1st amino and 2nd amino)
3. Translocation (A-site tRNA moved to P-site, P-site tRNA moved to E site)
4. Process repeats over and over
74
Termination phase of translation
Starts when A site encounters a stop codon
75
A stop codon causes _______ to enter the site
a protein called release factor
76
True or False: Release factors resemble tRNAs in size and shape but do not carry an amino acid
True
77
Most proteins go through a series of processing steps called ___________.
Post-translational modification
78
______________ speed up protein folding
Molecular chaperones
79
Folding of a protein determines:
The protein's shape and therefore its function
80
Adding or removing a phosphate group from a protein has this effect:
Switching the protein from an inactive state to an active state or vice versa
Add phosphate = Activate
Remove phosphate = Deactivate
81
Protein synthesis overview steps:
1. Transcription (pre-mRNA)
2. RNA processing (mature mRNA)
3. Translation (mRNA -> protein)
4. Post-translational modification (folding, activation, etc.)
82
RNA Polymerase reads the DNA template from the ___ to ___ direction
3' to 5'
This is so that it can print the primary transcript in the 5' to 3' direction
83
Pre-mRNA is the product of ________ and has to go through ________ before maturing into mRNA
Transcription (for transcribed RNA that is destined to be mRNA)
RNA processing
84
A poly(A) tail is:
A long series of Adenosine bases repeated over and over again (70-100 A bases)
85
The 5' cap on mRNA is made of:
Modified guanine
86
True or False: Primary transcript goes through RNA processing in prokaryotes
False
87
Downstream is in the ____ direction as RNA polymerase reads, and Upstream is in the _____ direction as RNA polymerase reads
Same, Opposite
Think of floating down a river, everything in front of you is downstream, and everything behind you is upstream.
88
Primary transcript is:
The RNA transcript that is produced by RNA polymerase
Primary transcript can end up as mRNA, tRNA, or rRNA
89
True or False: In prokaryotes, Ribosomes directly attach to primary transcript and begin translation as the primary transcript is being produced
True
90
Primary transcript has to be _____ before maturing into mRNA
Processed
This is done by adding a 5' cap and a poly(A) tail [added to 3' end] to the primary transcript
91
Molecular chaperones have this function:
Speed up and facilitate protein folding process
92
Describe the differences between the template strand and the non-template (coding) strand
The template strand is the strand that the RNA polymerase is attached to and reading
The non-template(coding) strand is the DNA strand that will be matching (except for T/U) to the primary transcript (hence the name coding strand)
93
Briefly describe the wobble hypothesis
Explains how there are 61 different codons but only 40 tRNA types
First two bases in a codon match, third one will be different. The two matching bonds on the anti-codon can make up for this and will still bond to the technically incorrect codon on the mRNA transcript, hence 40 tRNAs can work to translate 61 codons
94
What is the function of the 5' and 3' UCRs (uncoded regions)
- Stabilize the mRNA
- Regulate translation
- Essential to protein function (textbook doesn't list how, just know that they are essential somehow)
95
List the two main bacterial transcription promoters
- 10 box [TATAAT]
| - 35 box [TTGACA]
96
List the two main RNA (primary transcript) processing steps in prokaryotes
Trick question! There is none (extremly rarely) any primary transcript processing in prokaryotes
97
List the two main RNA (primary transcript) processing steps in Eukaryotes
- Splicing
| - 5' cap and poly(A) tail addition
98
Aminoacyl tRNA (AKA: charged tRNA/acyl tRNA) carries a(n) _____ to the ribosome for the elongation process
Amino acid
99
tRNA bonds _______ to its corresponding amino acid
covalently
100
Ribosomes translate from the ____ direction to the ___ direction
5' to 3'
101
Multiple ribosomes that are attached to the primary transcript produced by RNA polymerase in prokaryotes are referred to as:
Polyribosome
Numbered in order that they were attached
102
Ribosomes are composed of:
rRNA and proteins
103
List the 3 post-translational modifications made to proteins
1. Proteolysis
2. Glycosylation
3. Phosphorylation
104
Proteolysis is a post-translational processing modification process where:
The polypeptide is cut up into smaller polypeptides, which can either fold on their own to become unique proteins or can come together to form a single protein
105
Glycosylation is a post-translational processing modification where:
Sugar groups are added to the polypeptide (ex. glucose, sucrose, fructose)
106
Phosphorylation is a post-translational processing modification where:
Phosphate groups are added to the polypeptide
107
The poly(A) tail is added onto an mRNA sequence at the end of ______ (process)
Transcription
The poly(A) tail is transcribed from a repeating series (70-100 repetitions or potentially more) of T bases in the template strand of DNA.
108
The poly(A) tail signals to ____ transcription
Stop
The poly(A) tail acts as both protection for the mRNA AND as a signal to end transcription (in Eukaryotes only)
109
The 5' cap of mRNA signals to ________
Begin translation
The 5' cap has the function of both protecting the mRNA AND signaling to the translation machinery (collection of things involved in transcription, ex. Ribosome) that the mRNA strand is ready to be translated
110
The 5' UTR and 3' UTR have these functions:
- Stabilize mRNA
| - Regulate translation of the mRNA
111
Hairpins produced after transcription in prokaryotes have this function:
Causes RNA to have the right base pair coding so that it will fold to create a hairpin shape
112
Initiation factors of translation have what function:
Guide small subunit of ribosome to the mRNA sequence to be translated
113
The large subunit of a ribosome binds to the small subunit when:
The small subunit encounters an AUG start codon
114
f-Met (modified methionine) is used in ________ to ______
Prokaryotes, Initiate translation
115
True or False: f-Met (modified methionine) is used in translation in eukaryotic cells
False
116
Autosomes are:
Chromosomes that are not X or Y chromosomes
117
Elongation factors are:
Factors that help the ribosome translocate
