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Genetics > Chapter 8-test 2 > Flashcards

Chapter 8-test 2 Flashcards

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1
Q

In RNA, the pyrimidines are

A

C and U. the purines are A and G.

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2
Q

thymine compared to uracil

A

thymine has a methyl group.

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3
Q

rna polymerase

A

adds from 3’ end to create phosphodiester bond bw 5’C of one nucleotide and 3’C of other nucleotide, eliminating two phosphates (pyrophosphate).

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4
Q

messenger rna (mrna)

A

is produced by protein-producing genes and is a short-lived intermediary between DNA and protein
• only type of RNA that undergoes translation
• Transcription of mRNA followed by posttranscriptional processing
-may be polycistronic (encoding 2 or more polypeptides) in bacteria and archaea.

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5
Q

funcitonal rna

A

dont encode proteins, but perform functional roles in cell

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6
Q

Ribosomal RNA (rRNA)

A

combines with numerous proteins to form ribosomes, helps for small and large ribosomal subunits.

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7
Q

transfer rna (tRNA)

A

encoded in many forms and carries amino acids to ribosome for construction of proteins.

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8
Q

Telomerase RNA

A

provides a template for synthesis of repetitive DNA telomere sequences

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9
Q

Small nuclear RNA (snRNA)

A

various types is found in the nucleus of eukaryotes and plays a role in mRNA processing and removes introns.

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10
Q

Micro RNA (miRNA) and small interfering RNA (siRNA)

A

active in plant and animal cells and are involved in posttranscriptional regulation of mRNA. can attack other rna molecules, destroy them.

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11
Q

transcription

A

synthesis of a single-stranded RNA molecule by RNA polymerase

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12
Q

four stages of transcription in bacteria

A
  1. Promoter recognition
  2. Transcription initiation
  3. transcript elongation
  4. transcription termination
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13
Q

coding strand (or nontemplate strand)

A

complementary to the template strand

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14
Q

promotor

A

double-stranded DNA sequence that is the RNA polymerase binding site; promoters also bind other transcription proteins

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15
Q

The promoter is immediately

A

upstream (5’) to the start of transcription, referred to as the +1 nucleotide

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16
Q

The coding region of the gene

A

contains info needed to synthesize the protein product

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17
Q

• The termination region is located immediately

A

downstream (3’) to the coding segment of the gene

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18
Q

bacterial holoenzyme

A

complex between the core polymerase and the sigma subunit.

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19
Q

Consensus sequences are written on

A

coding strand

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20
Q

Pribnow box sequence

A

at -10 position. (or -10 consensus sequence) 5’-TATAAT-3’

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21
Q

-35 consensus sequence

A

At -35 is a 6-bp region. 5’-TTGACA3’

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22
Q

RNA polymerase binds to -10 and -35 sequences and

A

occupies the space between and around them

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23
Q

transcription initiation

step 1: closed promoter complex

A

First, the holoenzyme makes a loose attachment to the promoter sequence, then binds tightly. bind to -10 and -35

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24
Q

transcription initiation

step 2: open promoter complex

A

Then, the holoenzyme unwinds about 18 bp of DNA around the -10 position to form open promoter complex.

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25
transcription initiation step 3
the holoenzyme goes downstream( past +1 site) is intact until first 8-10 rna nucleotides have joined. then sigma subunit dissociates.
26
Considerable sequence variation exists among promoters
alternative sigma subunits recognize diff consensus | sequences, allowing for holoenzyme bind to alternative promoters
27
transcription initiation step 4
core enzyme synthesizes until it reaches termination sequences. 18 bp of dna is unwound ahead of the core enzyme.
28
transcription initiation step 5
rna transcript is released, and core enzyme dissociates from dna.
29
reading mRNA strand
go off coding strand, replace T with U.
30
terminators
bacterial genes have sequences on their 3' ends that ensure RNA polymerase does not transcribe more than it should.
31
difference bw bacterial and eukaryotic transcription
Eukaryotes have three RNA polymerases (instead of 1) that transcribe different genes
32
Eukaryotic genes carry
introns and exons, and require processing to remove introns
33
Eukaryote DNA is associated with proteins to form
chromatin; the chromatin composition of a gene affects its transcription. chromatin is important in gene regulation.
34
RNA polymerase I (RNA pol I)
transcribes ribosomal RNA
35
RNA polymerase II (RNA pol II)
transcribes mRNAs and small nuclear RNA
36
RNA polymerase III (RNA pol III)
transcribes tRNA, one small nuclear RNA gene, and one ribosomal RNA gene
37
RNA pol II and RNA pol III
transcribe miRNA and siRNA
38
rna pol II composed of
a dozen or more subunits, compared to bacterial rna polymerase, which has five subunits.
39
TATA box, or the Goldberg–Hogness box
-25 position. 5'-TATAAA-3'
40
CAAT box
-80 position
41
GC-rich box
5'-GGGCGG-3'. around -90 position.
42
The TATA box is most common, whereas
the CAAT box and GCrich box are more variable
43
Consensus sequence elements are important
for binding of transcription factors.
44
Eukaryotic promoters display a high degree of
variability in type, number, and location of consensus sequence elements
45
transcription factors (TFs)
RNA pol II binds to promoter consensus sequences in eukaryotes with the aid of proteins called tf.
46
TFs bind to
regulatory sequences and interact directly, or indirectly, with RNA polymerase; those interacting with pol II are called TFII factors
47
eukaryotic transcription
* The assembled TFIID bound to the TATA box forms the initial committed complex * Next, TFIIA, TFIIB, TFIIF, and RNA pol II join the complex, followed by TFIIE and TFIIH to form the preinitiation complex (PIC) * TFs of the PIC are commonly referred to as general transcription factors
48
not all rnas
get translated
49
dNTP's are for | NTP's are for
dna | rna
50
rna polymerase can always
start from scratch. they dont need primer.
51
what rna will be produced form the dna template 3-actagtgatta-5?
5-ugaucacuaau-3 | change A to U. change T to A.
52
which of the following is most commmon in bacteria?(eukaryotes dont do this)
transcription termination.
53
which of the following is the earliest step in eukaryotic transcription?
chromatin remodeling.
54
what is a gene?
coding region of a gene that gets transcribed into rna and any other regulatory sequence.
55
5'-UGAUCACUAAU-3' 5’-TGATCACTAAT-3' 3'-ACTAGTGATTA-5 which is template which is coding?
top-coding (U --> T) everything else stays the same | bottom-template (3-->5) U-->A, G-->C, A-->T
56
5’-UGCAAUCGUA-3' 5’-TACGATTCGA-3' 3’-ATGCTAACGT-5' which is template which is coding?
top-template (3-->5) U-->A, G-->C, A-->T bottom-coding (U-->T) everything else stays the same flip it.
57
Promoters alone may not be sufficient to initiate eukaryotic transcription
the ones that initiate are enhancer sequences and silencer sequences
58
Enhancer sequences location
-increase the level of transcription of specific genes • They bind proteins that interact with the proteins that are bound to gene promoters (together the promoters and enhancers drive gene expression) -upstream or downstream of the gene. far away.
59
protein bridge Enhancer sequences
- bind activator proteins and associated coactivators to form “protein bridge."links transcription complex at the promoter to activator(coactivator complex at enhancer) - bridge bends DNA so proteins at both locations are brought close together for them to interact - increases RNA pol II efficiency
60
silencer sequences
DNA elements repress transcription of their target genes • Silencers bind proteins that causes bends in DNA • bends reduce transcription of target gene by shielding DNA from transcription activation by RNA pol II
61
The level of chromatin compaction affects this chromatin based regulation is called
- accessibility of RNA pol II and its transcription factors to target DNA sequences. there are different chromatin states in diff cell types. - epigenetic process
62
The chromatin changes are referred to as
“chromatin modification” and “chromatin remodeling”
63
eukaryotes do have termination
just not mrna.
64
bacteria have two terminations | intrinsic and rho dependent termination
- hairpins are signal for rna polymerase to fall off. | - rut sequence. signal for rho protein to bind there. makes polymerase fall off.
65
Eukaryotic transcripts are more stable than bacterial and archaeal transcripts
eukaryotic transcripts have -have introns - transcription and translation are separated in time and location
66
pre-mRNA
initial eukaryotic gene mRNA
67
mature mRNA
fully processed mRNA
68
modification steps include
1. 5' capping 2. 3' polyadenylation 3. Intron splicing
69
Capping 5' mRNA
After the first 20-30 NT of mRNA are made, guanylyl transferase adds a “flipped” G to 5' end of pre-mRNA. linked 5'to5' triphosphate linkage. then methylates. beginning with the second, it will be 5'-3' so on.
70
Functions of the 5' Cap
1. Protection mRNA 2. Facilitating nuclear export 3. Facilitating intron splicing 4. Guides ribosomes to the 5’ end of mRNA
71
Steps of Polyadenylation
1. Cleavage near the polyadenylation signal sequence (5'-AAUAAA-3'), downstream of stop codon 2. removes segment of 3' end, replaces it w/ 20-200 A’s (poly A tail)
72
Functions of Polyadenylation
1. Protecting mRNA 2. facilitates nuclear export 3. Guides ribosomes to the 5’ end of mRNA • Some eukaryotic transcripts (e.g., the histone genes) do not undergo polyadenylation
73
Exons become part of
mature mRNA and encode protein segments while introns are intervening segments that are removed from premRNA
74
most common type of intron
Pre-mRNA transcript introns. removed by a spliceosome complex. Other types of introns are removed by self-splicing or diff enzymatic process
75
Intron splicing
requires great precision to remove intron nucleotides | -errors: lead to incorrect protein sequences
76
5' splice site
at 5' intron end and has consensus sequence with a nearly invariant GU dinucleotide
77
3' splice site
at 3' intron end has an 11-nucleotide consensus with a pyrimidine-rich region and a nearly invariant AG
78
in addition to 5' and 3' splice site, a third consensus region, called the branch site
"branch point adenine." 20 to 40 nucleotides upstream of the 3' splice site (they need all three sequences {3', 5' spice site, and branch site} for intron removal)
79
spliceosome
Introns are removed from pre-mRNA by snRNA
80
lariat intron structure
5' splice site is cleaved first. 5' intron end binds to the branch point adenine. Then the 3' splice site is cleaved and the exon ends are ligated together
81
common for large eukaryotic genomes to express
more proteins than there are genes in the genome. ex) human cells produce over 100,000 distinct polypeptides but contain ~22,000 genes
82
alternative pre-mRNA splicing
Pre-mRNA can be spliced in alternative patterns in different cell types
83
alternative polyadenylation
Alternative localizations of polyadenylation can produce different mature mRNAs
84
Alternative intron splicing
mature mRNAs with different combinations of exons = different polypeptides
85
Approximately 70% of human genes
undergo alternative splicing | • It is less common in other animals and rare in plants
86
Alternative Processing
used when more than one sequence upstream of a gene can initiate transcription
87
Why would bacteria “want” to terminate transcription?
reduce risk unwanted translation.
88
Why wouldn’t eukaryotes “want” that too?
reduce redundant transcription.
89
Why would mRNAs need to be “protected”? | Protected from what?
against exonucleases.
90
They found that E. coli infected with bacteriophage
T2 used existing bacterial ribosomes and a messenger molecule to encode phage proteins. (rna that synthesized phage proteins were called mRNA).
91
How do eukaryotic cells “know” how to | splice introns out of a pre-mRNA?
Based on specific splice donor and acceptor sequences
92
Many eukaryotic genes contain multiple ____, except… origins of replications introns and exons +1 sites poly a tails
origins of replication

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