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BIO130 > Lecture 5 > Flashcards

Lecture 5 Flashcards

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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
which step of the RNA transcription process is most efficient?
elongation
25
what are the signals of termination?
hairpin structure followed by AT-rich region
26
How do these termination signals help to dissociate the RNA transcript from the polymerase?
Disrupts H-bonding of new mRNA transcript with DNA template
27
which types of cell has more complicated gene expression?
eukaryotic cells
28
what is the job of rRNA?
make ribosomes
28
what is the job of snRNA?
splice pre mRNA
29
what is the job of snoRNAs?
process and chemical modify RNA
30
which type of genes does RNA polymerase I transcribe?
rRNA genes
31
which type of genes does RNA polymerase II transcribe?
all protein-coding genes, miRNA genes, genes for non-coding RNAs
32
which type of genes does RNA polymerase III transcribe?
tRNA genes, 5S rRNA genes, genes for many other small RNAs
33
how many subunits does bacterial RNA polymerase have?
5
34
how many subunits does eukaryotic RNA polymerase II have?
12
35
what is something RNA polymerase II has not found in bacterial or other eukaryotic RNAPs?
has a special carboxyl-terminal domain (CTD
36
what are the proteins called that help RNA polymerase position at the promoter?
transcription factors
37
why do Eukaryotic RNA polymerases need transcription factors?
because of complex chromosomal structures
38
what is the transcription factors role similar to?
sigma subunit
39
where are the base pairs in the TATA box?
30 base pairs upstream
40
what is the first step of transcription?
TBP binds to the TATA box
41
what is the job of the TATA box?
position RNAP II
42
what is the purpose of TBP attaching to the promoter?
aids the attachment of a more complex protein TFIID
43
what is the job of TFIIH?
Helicase activity & Phosphorylation of C-Terminal Domain (CTD) of RNAP II
44
where does the activator protein bind?
on the enhancer
44
what happens to the DNA when TBP binds to the promoter?
distortion of the DNA
45
what is the job of "other transcription factors"
help to orient and bind RNA polymerase II to the DNA
46
what is the purpose of the helicase activity of TFIIH?
helps pry open the DNA double helix to expose one template strand
47
what does the helicase activity of RNA polymerase II use to pry apart DNA strands?
ATP
48
where does the helicase activity of RNA polymerase II pry apart DNA strands?
transcription start site
49
what is the purpose of TFIIH phosphorylating C‐terminal domain of RNA polymerase II?
to initiate the transcription process
50
where is the C-terminal domain located?
the tail of RNAP II
51
what is the Carboxyl terminal domain made of?
repeat of 7 amino acids
52
how many repeats does the yeast enzyme have?
26
53
what is the Carboxyl terminal domain essential for?
viability
53
how many repeats does the human enzyme have?
52
54
what is RNA capping?
modified guanine nucleotide added to the 5' end of the mRNA
55
what is polyadenylation?
sequence of adenine called the poly-A tail added to the 3' ends of the mRNA
56
what is the overview of mRNA processing?
 Addition of a 5’ cap  Removal of introns (splicing)  Processing and polyadenylation of 3’ tail
57
what does Phosphorylation of C‐ terminal tail of RNA polymerase II results in?
RNA processing proteins Additional phosphorylation of CTD, including Ser 2
58
what is the purpose of 5' pre-mRNA capping?
helps protect RNA from exonucleases
58
when is the 5' pre-mRNA capping completed?
before mRNA fully is transcribed
59
what are the introns and exons like in eukaryotes compared to prokaryotes?
there are more
60
what are the two steps to remove introns from pre-mRNA?
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
what is the hydroxyl group in RNA necessary for the formation of?
lariat structure
62
Can pre mRNA splice themselves?
no
63
what are spliceosomes composed of?
small nuclear protein or snRNAs
64
what is the job of spliceosomes?
remove introns from the pre mRNA
65
what happens after splicing is complete?
the exon junction complex is added
66
is the poly-A tail encoded in the genome?
no
66
what are examples of abnormal splicing?
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
how does mRNA know there needs to be processing at the 3' end?
the genome has specific sequences that signal
68
what is the purpose of consensus sequences?
signals where the 3' end should be cut and where the poly tail should be added
69
what do cleavage and poly-A tail refer to?
the 3' end was cut off and the poly-A tail was added

BIO130 (6 decks)

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