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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
Q

Where does transcription start on a promoter region

A

+1

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26
Q

How are the numbers -35, -10, +1 signifigant to transcription

A

The sigma factor identifies the promoter sequence at -35 and -10 sites, and begins transcription at +1

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27
Q

How does initiation of transcription occur in bacteria

A

Sigma is present to unwind the helix and allow transcription to begin

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28
Q

How does elongation of transcription occur in bacteria

A

Sigma releases and transcription continues

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29
Q

How does termination of transcription occur in bacteria

A

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

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30
Q

Which strand is used as the template

A

Depends on the gene

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31
Q

What is a histone

A

Related to DNA packaging - structural support proteins for chromosomes (DNA, and the chromosomes as a whole, wraps around histones) and are tightly packed

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32
Q

How many types of polymerase are used in prokaryotic cells, and how many are used in eukaryotic

A

Prokaryotic; 1
Eukaryotic: 3 (I, II, & III)

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33
Q

Why are promoters of eukaryotic cells more complex

A

RNA poly II recognizes promoters by TATA box (repeating T and A bases) 30 pairs upstream

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34
Q

What other than RNA poly must assemble at promoter

A

General transcription factors: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH - composed of ~30 proteins

35
Q

What else must RNA do before exiting nucleus in eukaryotic cells

A

Go through processing

36
Q

What is different about eukaryotic gene sequences

A

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
Q

Higher order of DNA structure (compared to prokaryotes)

A

DNA molecules combine with proteins to create higher order of structure and allow for compact packaging and strict gene regulation

38
Q

RNA poly I

A

most rRNA genes

39
Q

RNA poly II

A

protein-coding genes, miRNA genes, plus genes for some small RNAs (like those in spliceosomes)

40
Q

RNA poly III

A

tRNA genes, 5S rRNA gene, genes for many other small RNAs

41
Q

How does initiation occur in eukaryotic cells

A

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
Q

What is TATA box regognized by

A

TATA binding proteing (TBPs)

43
Q

What is the transcription initiation complex

A

A pile of general transcription factors, initiated by TFIID distorting the helix structure

44
Q

TBPs

A

Subunit of TFIID recognizes the TATA box and starts transcription - causes kinks and unwinding of the helix

45
Q

What processes must be done before transcripts can be exported from the nucleus

A

Capping, splicing, and polyadenylation

46
Q

Where are the enzymes that carry out capping, splicing, and polyadenylation

A

RNA poly II

47
Q

What are the coding regions of eukaryotic cells

A

Exons

48
Q

What are the non-coding regions of eukaryotic cells

A

Introns

49
Q

Are introns and exons both transcribed as part of the gene

A

Yes

50
Q

How are introns removed after being transcribed

A

Splicing - occurs after capping while still being transcribed

51
Q

How are introns recognized

A

Has a few sequences at/near the start/end of its strand that signify removal

52
Q

What does the term “lariat” mean

A

Branched structure of introns

53
Q

How are introns removed

A
  • 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
Q

What RNA complexes carry out splicing

A

Spliceosomes

55
Q

What are spliceosomes made up of

A

Consists of 5 small nuclear ribonucleic particles (snRNPs - otherwise known as “snurps”) RNA + 100 proteins
- catalytic activity provided by the RNA component
- “ribozymes”

55
Q

What are spliceosomes made up of

A

Consists of 5 small nuclear ribonucleic particles (snRNPs - otherwise known as “snurps”) RNA + 100 proteins
- catalytic activity provided by the RNA component
- “ribozymes”

56
Q

What are the advantages of RNA splicing

A
  • can create different protein types from the same gene / same primary RNA transcript depending on cell type, stage development, gender, etc.
57
Q

Disadvantages of RNA splicing

A
  • 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
Q

What makes RNA “mature” and ready to leave nucleus

A
  • 5’ cap, removal of introns, and 3’ poly-A tail
  • exon junction complex binds to properly spliced mRNAs
59
Q

What is the exon junction complex

A

Group of proteins that bind to mRNAs and allow them to leave the nucleus into the cytoplasm

60
Q

What is the genetic code

A

Different 3-base combinations that code for different amino acids to form proteins

61
Q

What is a codon

A

One singular 3-base combination

62
Q

How many stop codons are there

A

3

63
Q

Genetic code exceptions in mitochondria

A

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
Q

How can loss/gain of bases impact a protein

A

Deletions, additions, or shifts can shift the reading frame, and can cause disasterous genetic mutations

65
Q

What is tRNA

A

An ‘adapter’ molecule that holds amino acids to interact with specific codons on mRNA transcript

66
Q

How do tRNA and amino acids combine

A

tRNA + amino acid (with the help of aminoacyl tRNA synthetase) = aminoacyl tRNA
- each amino acid has its own aminoacyl tRNA synthetase enzyme

67
Q

What location is the amino acid bound to on tRNA

A

The 3’ end

68
Q

What is the anticodon loop

A

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
Q

What is the wobble hypothesis

A

The anticodon of tRNAs can still bind to a codon whose third position requires a non-standard base pairing

70
Q

How many aminoacyl-tRNA synthetases are there

A

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
Q

What are the 2 subunits of ribosomes

A

Small and large subunit

72
Q

When does translation begin

A

When the anticodon of a ‘charged’ tRNA molecule binds to the codon on the mRNA transcript

73
Q

What is the A-site

A

Acceptor site for aminoacyl tRNA (the binding site of the remaining tRNA molecules)

74
Q

What is the P-site

A

Where peptide bond forms and adds amino acid to growing peptide chain (the binding site for the first tRNA molecule)

75
Q

What is the E-site

A

Where tRNAs no longer bound to amino acid exit the ribosome

76
Q

What codon does translation begin with

A

AUG

77
Q

What amino acid (matching AUG) is always loaded onto the initial tRNA molecule

A

MET

78
Q

Initiator tRNA binds to which site

A

P-site

79
Q

Is the ribosome an enzyme or a ribozyme

A

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
Q

What is a ribozyme

A

RNA molecule with a well defined tertiary shape that allows it to catalyze chemical reactions

81
Q

What are polysomes

A

Proteins are made up of polyribosomes (polysomes)

82
Q

When do proteins fold

A

Long before termination, while translating
- no energy is required, it is spontaneous, and assisted by proteins called molecular chaperones

83
Q

Post-Translational Modifications

A
  • 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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