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Biol 130 > Transcription and Translation > Flashcards

Transcription and Translation Flashcards

1
Q

How is DNA used to synthesize the formation of a new RNA molecule

A

Template strand reads in 3’ to 5’ direction and builds the new RNA molecule in 5’ to 3’ direction

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2
Q

Which strand of DNA is the newly synthesized RNA molecule identical to (aside from U instead of T)

A

Non template (coding) strand

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3
Q

What is the first step of RNA synthesis

A

Sigma factor binds to RNA polymerase

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4
Q

What is the second step of RNA synthesis

A

Sigma factor binds to promoting region

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5
Q

What is the third step of RNA synthesis

A

Double helix of DNA is unwound, breaking apart the complementary strands

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6
Q

What is the fourth step of RNA synthesis

A

RNA synthesis begins

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7
Q

What is the fifth step of RNA synthesis

A

Sigma factor is released

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8
Q

How are RNA hairpins related to termination

A

Hairpins are formed by base pairings and break apart RNA transcript and RNA polymerase, so it terminates the synthesis

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9
Q

Where are promoters located in prokaryotic transcription

A

Non-template strand

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10
Q

What two things occur in eukaryotic but not prokaryotic transcription

A

Additon of 5’ cap (5’-7-methylguanosine cap) and 3’ poly-A tail

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11
Q

What happens in both eukaryotic and prokaryotic transcription

A

Recognition of TATA boxes by sigma factor

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12
Q

What component determines the correct amino acids are added to the peptide chains with reading of specific codons

A

The anticodon on a complementary tRNA strand (transfer RNA)

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13
Q

Post-transcriptional modifications on RNA strands

A

Additon of 5’ cap, 3’ poly-A tail, and removal of introns

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14
Q

How does termination take place

A

Stop codons are read - stop codons don’t have corresponding tRNA molecules

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15
Q

Chloramphenicol blocks peptidyl transferase in the ribosomes - what process would this molecule prevent

A

Peptide bond formation

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16
Q

What is possible in prokaryotes but not eukaryotes in relation to transcription

A

Concurrent transcription and translation

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17
Q

Increased expression of a gene, in terms of more protein production, could be acheived by what three possibilities

A
  1. increasing transcription of the gene
  2. inhibiting proteases that break down the protein it encodes
  3. increasing the half life of the mRNA transcript
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18
Q

What is prokaryotic RNA polymerase called

A

Holoenzyme

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19
Q

Holoenzyme is made up of what two components

A

Sigma factor and core enzyme

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20
Q

What is the role of sigma factor

A

RNA poly must be able to recognize the start of a gene and bind to DNA at this location

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21
Q

Where is the promoter region located

A

Directly upstream of the start of a gene

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22
Q

What sequence does sigma factor recognize

A

Promoter sequence

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23
Q

What strand are promoter sequences on, and how long are they

A

Non-template strand, 40-50 base pairs long

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24
Q

What are the two key regions of promoters

A

-10 box; 10 bases upstream of the start site
-35 box; 35 bases upstream

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25
Where does transcription start on a promoter region
+1
26
How are the numbers -35, -10, +1 signifigant to transcription
The sigma factor identifies the promoter sequence at -35 and -10 sites, and begins transcription at +1
27
How does initiation of transcription occur in bacteria
Sigma is present to unwind the helix and allow transcription to begin
28
How does elongation of transcription occur in bacteria
Sigma releases and transcription continues
29
How does termination of transcription occur in bacteria
Polymerase reaches the termination signal in the DNA template strand, which codes for RNA that folds back on itself and creates a hairpin structure to disrupt the transcription process
30
Which strand is used as the template
Depends on the gene
31
What is a histone
Related to DNA packaging - structural support proteins for chromosomes (DNA, and the chromosomes as a whole, wraps around histones) and are tightly packed
32
How many types of polymerase are used in prokaryotic cells, and how many are used in eukaryotic
Prokaryotic; 1 Eukaryotic: 3 (I, II, & III)
33
Why are promoters of eukaryotic cells more complex
RNA poly II recognizes promoters by TATA box (repeating T and A bases) 30 pairs upstream
34
What other than RNA poly must assemble at promoter
General transcription factors: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH - composed of ~30 proteins
35
What else must RNA do before exiting nucleus in eukaryotic cells
Go through processing
36
What is different about eukaryotic gene sequences
Genes can be spaced out, with hundreds of thousands of unpaired bases between them which allows for complex regulation of gene transcription by regulatory sequences scattered through genome
37
Higher order of DNA structure (compared to prokaryotes)
DNA molecules combine with proteins to create higher order of structure and allow for compact packaging and strict gene regulation
38
RNA poly I
most rRNA genes
39
RNA poly II
protein-coding genes, miRNA genes, plus genes for some small RNAs (like those in spliceosomes)
40
RNA poly III
tRNA genes, 5S rRNA gene, genes for many other small RNAs
41
How does initiation occur in eukaryotic cells
TATA box is recognized at subunit TFIID (one of the general transcription factors), TFIID distorts helix and allows for other general transcription factors to pile and form the 'transcription initiation complex' TFIIH pries appart the double helix into seperate strands at the start point
42
What is TATA box regognized by
TATA binding proteing (TBPs)
43
What is the transcription initiation complex
A pile of general transcription factors, initiated by TFIID distorting the helix structure
44
TBPs
Subunit of TFIID recognizes the TATA box and starts transcription - causes kinks and unwinding of the helix
45
What processes must be done before transcripts can be exported from the nucleus
Capping, splicing, and polyadenylation
46
Where are the enzymes that carry out capping, splicing, and polyadenylation
RNA poly II
47
What are the coding regions of eukaryotic cells
Exons
48
What are the non-coding regions of eukaryotic cells
Introns
49
Are introns and exons both transcribed as part of the gene
Yes
50
How are introns removed after being transcribed
Splicing - occurs after capping while still being transcribed
51
How are introns recognized
Has a few sequences at/near the start/end of its strand that signify removal
52
What does the term "lariat" mean
Branched structure of introns
53
How are introns removed
- The A site on the branched intron attacks the 5' splice side opposite to it, and cuts the sugar-phosphate backbone - The cut end forms a covalent bond with the sugar group - The lariat structure is deteioriated
54
What RNA complexes carry out splicing
Spliceosomes
55
What are spliceosomes made up of
Consists of 5 small nuclear ribonucleic particles (snRNPs - otherwise known as "snurps") RNA + 100 proteins - catalytic activity provided by the RNA component - "ribozymes"
55
What are spliceosomes made up of
Consists of 5 small nuclear ribonucleic particles (snRNPs - otherwise known as "snurps") RNA + 100 proteins - catalytic activity provided by the RNA component - "ribozymes"
56
What are the advantages of RNA splicing
- can create different protein types from the same gene / same primary RNA transcript depending on cell type, stage development, gender, etc.
57
Disadvantages of RNA splicing
- more work due to more steps - more oppertunity for error: mutations of splice cites can result in loss of exons with inclusion of introns, or shift in location of the splice
58
What makes RNA "mature" and ready to leave nucleus
- 5' cap, removal of introns, and 3' poly-A tail - exon junction complex binds to properly spliced mRNAs
59
What is the exon junction complex
Group of proteins that bind to mRNAs and allow them to leave the nucleus into the cytoplasm
60
What is the genetic code
Different 3-base combinations that code for different amino acids to form proteins
61
What is a codon
One singular 3-base combination
62
How many stop codons are there
3
63
Genetic code exceptions in mitochondria
Mitochondria in animal cells use the codon UGA to encode tryptophan rather than stop - has implications for transferring of mitochondrial genes to nuclear genome - cytosolic protein-synthesizing machinery reading a mitochondrial gene will always stop when it should be inserting a tryptophan ONLY in eukaryotic mitochondria - plant mitochondria uses the stop codon as normal
64
How can loss/gain of bases impact a protein
Deletions, additions, or shifts can shift the reading frame, and can cause disasterous genetic mutations
65
What is tRNA
An 'adapter' molecule that holds amino acids to interact with specific codons on mRNA transcript
66
How do tRNA and amino acids combine
tRNA + amino acid (with the help of aminoacyl tRNA synthetase) = aminoacyl tRNA - each amino acid has its own aminoacyl tRNA synthetase enzyme
67
What location is the amino acid bound to on tRNA
The 3' end
68
What is the anticodon loop
Adjacent from the 3' end amino acid on the tRNA molecule, the anticodon loop holds the anticodon that matches the codon on the mRNA strand
69
What is the wobble hypothesis
The anticodon of tRNAs can still bind to a codon whose third position requires a non-standard base pairing
70
How many aminoacyl-tRNA synthetases are there
20 - each must regonize its amino acid plus all anticodons that recognize that amino acid - combined action of tRNA and synthetases ensure each amino acid is matched with its correct codon
71
What are the 2 subunits of ribosomes
Small and large subunit
72
When does translation begin
When the anticodon of a 'charged' tRNA molecule binds to the codon on the mRNA transcript
73
What is the A-site
Acceptor site for aminoacyl tRNA (the binding site of the remaining tRNA molecules)
74
What is the P-site
Where peptide bond forms and adds amino acid to growing peptide chain (the binding site for the first tRNA molecule)
75
What is the E-site
Where tRNAs no longer bound to amino acid exit the ribosome
76
What codon does translation begin with
AUG
77
What amino acid (matching AUG) is always loaded onto the initial tRNA molecule
MET
78
Initiator tRNA binds to which site
P-site
79
Is the ribosome an enzyme or a ribozyme
The A, P, and E sites are all mainly rRNAs, and the catalytic site where peptide bond is formed between P and A sites in large subunit are formed entirely by RNA, therefore it is a ribozyme
80
What is a ribozyme
RNA molecule with a well defined tertiary shape that allows it to catalyze chemical reactions
81
What are polysomes
Proteins are made up of polyribosomes (polysomes)
82
When do proteins fold
Long before termination, while translating - no energy is required, it is spontaneous, and assisted by proteins called molecular chaperones
83
Post-Translational Modifications
- Glycosylation (addition of carbohydrate) - Addition of lipid - Phosphorylation - Ubiquitination - Methylation, hydroxylation, acetylation - Proteolysis - cleavage of peptide bonds - and more *There are more than 30 types of PTMs

Biol 130 (5 decks)

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