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BIO130 > Lecture 5 > Flashcards

Lecture 5 Flashcards

1
Q

what is the molecular definition of a gene?

A

a specific sequence of DNA used to make RNA or protein

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2
Q

what are the two types of genes?

A
  1. protein-coding genes
  2. non-coding RNA genes
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3
Q

what are protein-coding genes?

A

genes that get transcribed into RNA then translated into proteins

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4
Q

what are non-coding RNA genes?

A

genes that are transcribed into RNA but remain so and are not translated into proteins

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4
Q

what is the amount of protein like when a small amount of RNA is transcribed?

A

a small amount of proteins are made

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5
Q

what is the amount of protein like when a lot of RNA is transcribed?

A

there are a lot of proteins

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6
Q

what does RNA polymerase make?

A

RNA

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7
Q

which direction does RNA polymerase add nucleotides?

A

in the 5’ to 3’ direction

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8
Q

what are the building blocks of ribonucleoside triphosphates?

A

ATP, UTP, CTP, GTP

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9
Q

What is ssDNA?

A

a single strand of DNA

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10
Q

does the coding strand use uracil or thymine?

A

uracil

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11
Q

what are RNA nucleotides linked by?

A

phosphodiester bonds

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12
Q

What is the DNA-RNA helix hybrid held together by in terms of bases?

A

through base pairing

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13
Q

what are the three main steps of the transcription cycle?

A
  1. initiation
  2. elongation
  3. termination
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14
Q

describe the initiation step of the transcription cycle.

A

sigma factors bind to RNA polymerase to help it locate the promoter sequence

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15
Q

describe the elongation step of the transcription cycle.

A

RNA polymerase moves along the DNA template strand adding nucleotides to the RNA strand

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16
Q

describe the termination step of the transcription cycle.

A

when RNA polymerase encounters a terminal signal on the DNA strand, RNA polymerase releases from the template strand

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17
Q

what is the promoter sequence?

A

the initial binding site

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18
Q

what is the promoter sequence also known as?

A

the TATA box

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19
Q

which DNA strand is transcribed?

A

the template strand

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20
Q

what is the RNA secondary structure?

A

the folding of an RNA strand due to interaction between nucleotides

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21
Q

what happens to nucleotides in the RNA secondary structure?

A

base pairs within the single-stranded RNA start pairing with each other

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22
Q

which step of the RNA transcription process is least efficient?

A

initiation step

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23
Q

what is the terminator sequence?

A

a certain sequence on DNA that ends the transcription process

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24
Q

which step of the RNA transcription process is most efficient?

A

elongation

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25
Q

what are the signals of termination?

A

hairpin structure followed by AT-rich region

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26
Q

How do these termination signals help to dissociate the RNA transcript from the polymerase?

A

Disrupts H-bonding of new mRNA
transcript with DNA template

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27
Q

which types of cell has more complicated gene expression?

A

eukaryotic cells

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28
Q

what is the job of rRNA?

A

make ribosomes

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28
Q

what is the job of snRNA?

A

splice pre mRNA

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29
Q

what is the job of snoRNAs?

A

process and chemical modify RNA

30
Q

which type of genes does RNA polymerase I transcribe?

A

rRNA genes

31
Q

which type of genes does RNA polymerase II transcribe?

A

all protein-coding genes, miRNA genes, genes for non-coding RNAs

32
Q

which type of genes does RNA polymerase III transcribe?

A

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

33
Q

how many subunits does bacterial RNA polymerase have?

A

5

34
Q

how many subunits does eukaryotic RNA polymerase II have?

A

12

35
Q

what is something RNA polymerase II has not found in bacterial or other
eukaryotic RNAPs?

A

has a special carboxyl-terminal domain
(CTD

36
Q

what are the proteins called that help RNA polymerase position at the promoter?

A

transcription factors

37
Q

why do Eukaryotic RNA polymerases need transcription factors?

A

because of complex chromosomal structures

38
Q

what is the transcription factors role similar to?

A

sigma subunit

39
Q

where are the base pairs in the TATA box?

A

30 base pairs upstream

40
Q

what is the first step of transcription?

A

TBP binds to the TATA box

41
Q

what is the job of the TATA box?

A

position RNAP II

42
Q

what is the purpose of TBP attaching to the promoter?

A

aids the attachment of a more complex protein TFIID

43
Q

what is the job of TFIIH?

A

Helicase activity & Phosphorylation of C-Terminal Domain (CTD) of RNAP II

44
Q

where does the activator protein bind?

A

on the enhancer

44
Q

what happens to the DNA when TBP binds to the promoter?

A

distortion of the DNA

45
Q

what is the job of “other transcription factors”

A

help to orient and bind RNA polymerase II to the DNA

46
Q

what is the purpose of the helicase activity of TFIIH?

A

helps pry open the DNA double helix to expose one template strand

47
Q

what does the helicase activity of RNA polymerase II use to pry apart
DNA strands?

A

ATP

48
Q

where does the helicase activity of RNA polymerase II pry apart
DNA strands?

A

transcription start site

49
Q

what is the purpose of TFIIH phosphorylating C‐terminal domain of
RNA polymerase II?

A

to initiate the transcription process

50
Q

where is the C-terminal domain located?

A

the tail of RNAP II

51
Q

what is the Carboxyl
terminal domain made of?

A

repeat of 7 amino acids

52
Q

how many repeats does the yeast enzyme have?

A

26

53
Q

what is the Carboxyl terminal domain essential for?

A

viability

53
Q

how many repeats does the human enzyme have?

A

52

54
Q

what is RNA capping?

A

modified guanine nucleotide added to the 5’ end of the mRNA

55
Q

what is polyadenylation?

A

sequence of adenine called the poly-A tail added to the 3’ ends of the mRNA

56
Q

what is the overview of mRNA processing?

A

 Addition of a 5’ cap
 Removal of introns
(splicing)
 Processing and
polyadenylation of
3’ tail

57
Q

what does Phosphorylation of C‐ terminal tail of RNA polymerase II results in?

A

RNA processing
proteins

Additional phosphorylation of
CTD, including Ser 2

58
Q

what is the purpose of 5’ pre-mRNA capping?

A

helps protect RNA from
exonucleases

58
Q

when is the 5’ pre-mRNA capping completed?

A

before mRNA fully is transcribed

59
Q

what are the introns and exons like in eukaryotes compared to prokaryotes?

A

there are more

60
Q

what are the two steps to remove introns from pre-mRNA?

A
  1. branch point A attacks the 5’ splice site
  2. 3’ end of one exon reacts with the 5’ end of another exon to release intron
61
Q

what is the hydroxyl group in RNA necessary for the formation of?

A

lariat structure

62
Q

Can pre mRNA splice themselves?

A

no

63
Q

what are spliceosomes composed of?

A

small nuclear protein or snRNAs

64
Q

what is the job of spliceosomes?

A

remove introns from the pre mRNA

65
Q

what happens after splicing is complete?

A

the exon junction complex is added

66
Q

is the poly-A tail encoded in the genome?

A

no

66
Q

what are examples of abnormal splicing?

A
  1. normal adult B-globin RNA transcript
  2. a single nucleotide changes that destroys a normal splice site causing exon skipping
  3. a single nucleotide change that destroys a normal splice site activating a cryptic splice site
  4. a single nucleotide change creates a new splice site causing new exons to be incorporated
67
Q

how does mRNA know there needs to be processing at the 3’ end?

A

the genome has specific sequences that signal

68
Q

what is the purpose of consensus sequences?

A

signals where the 3’ end should be cut and where the poly tail should be added

69
Q

what do cleavage and poly-A tail refer to?

A

the 3’ end was cut off and the poly-A tail was added

BIO130 (6 decks)

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