Lecture 8 Flashcards
(115 cards)
1
Q
Prokaryotes have how many polymerase? Eukaryotes?
A
1, 3
2
Q
What is the relationship between consensus sequence and promotor stregnth
A
the closer to the Consensus Sequence, the stronger the promoter
3
Q
Determines how well genes are transcribed
A
consensus sequence
4
Q
In the initiation of bacterial transcription, the ____ binds and recognizes the -10 and -13 regions, which causes a….
A
sigma factor, closed complex
5
Q
Formation of an open complex in bacterial transcription is made by…
A
RNA poly opening up 2 DNA strands
6
Q
When RNA polymerase releases the sigma factor, what occurs
A
bacterial transcription
7
Q
What eukaryotic RNA polymerase transcribes 3/4 rRNAs
A
poly 1
8
Q
What eukaryotic RNA polymerase transcribes the majority of the RNA in eukaryotic cells
A
poly 1
9
Q
What eukaryotic RNA polymerase transcribes ribosomal RNA (rRNA) …except 5S rRNA
A
poly 1
10
Q
What eukaryotic RNA polymerase transcribes mRNA and snRNA and LINE-1 transposons
A
poly 2
11
Q
What eukaryotic RNA polymerase transcribes the most genes
A
poly 2
12
Q
Alu and LINE-1 have what feature?
A
internal promoters
13
Q
What eukaryotic RNA polymerase transcribes tRNA and 5SrRNA and Alu transposons
A
poly 3
14
Q
What eukaryotic rna polymerases are specialized
A
poly 1 and 3
15
Q
Bacterial and eukaryotic RNA polymerases have what in common?
A
similar general structure
16
Q
Euk. RNA poly 1 has what transcript?
A
45S transcript
17
Q
In Euk. RNA poly 1, the processing of rRNA in eukaryotes is that….
A
45S transcript gets put in ultracentrifuge, cleavage occurs, and left with 3 rRNAs
18
Q
In euk. RNA poly 3, when processing tRNA precursor into tRNA what occurs
A
base modification in tRNA, endonuclease cleaves and exonuclease cleaves
19
Q
What is a special feature of euk RNA poly 3?
A
RNase P
20
Q
is an “ribozyme” the catalytic activity resides in the RNA
A
RNase P (in rna poly 3)
21
Q
Amino acids are brought to the ribosome by…
A
tRNA
22
Q
Amino acids are brought to the ribosome by…
A
tRNA
23
Q
What is commonly found at a eukaryotic RNA pol II promotor
A
TATA box
24
Q
25 nucleotides upstream to initiation of transcription
A
TATA box
25
25 nucleotides upstream to initiation of transcription
TATA box
26
With RNA poly 2 in eukaryotes, TFIID binds to the...
TATA box
27
is a complex of proteins that includes the TATA binding protein (TBP)
and several TBP-associated factors (TAFs)
TFIID
28
Is TFIID found in bacteria?
No
29
TFIID recruit other proteins that....
tether to the RNA polymerase to the TATA box
30
Initiation of RNA poly 2 transcription needs help by....
TFIID
31
TFIID two roles with RNA poly 2 transcription
acts as a helicase to form open complex and phosphorylates CTD of RNA poly 2
32
releases the
RNA polymerase from the tether made up by
transcription factors and the tether falls apart
CTD phosphorylation
33
CTD phosphorylation causes a ___ and forms an ____
shape change and forms an open complex
34
The eukaryotic initiation of transcription is known as
basal transcription
35
Heat the DNA to break the hydrogen bonds
–> the two strands come apart (“denatured DNA”)
Then add mRNA and let it cool slowly
Hybridization of mRNA to DNA
36
In Hybridization of mRNA to DNA because DNA/RNA H bonds are stronger than DNA/DNA, you get an....
R loop
37
Where RNA binds to 1 DNA strand and single stranded DNA
R loop
38
A single “R Loop” was seen for...
most bacterial genes and some eukaryotic genes
39
An intro + mRNA equals...
mRNA bound to DNA with multiple R loops and intron loops
40
Discontinuous regions of DNA that are complementary to mRNA, spliced out
intron
41
Introns occur the most in what genes?
eukaryotic
42
Who discovered introns
Richard Roberts and Phil Sharp
43
introns occur in....
introns are spliced out when?
pre-mRNA
before mature mRNA leaves nucleus
44
Three different mechanisms for RNA splicing...
1. Group I intron splicing
2. Group II intron splicing
3. Spliceosome
45
What can self-splice?
Group 1 and 2 intro splicing
46
discovered by Tom Cech (Nobel Prize)
self-splicing
47
Group 1 intron splicing contains a _____ with what that cleaves?
Guanoside, 3' OH
48
Group 2 intron splicing contains a _____ with what that cleaves? This forms?
sugar from an A nucleotide, 2'OH, covalent closed loop
49
A lariat is an ____. Where is this found?
intron closed loop, group 2 intron splicing
50
Splicing by a spliceosome involves...
Has the same structure as...
proteins, cannot self splice
Group 2 intron splicing
51
Components of a spliceosome
1. Bind to an intron sequence and precisely recognize
the intron-exon boundaries
– 2. Hold the pre-mRNA in the correct configuration
– 3. Catalyze the chemical reactions that remove introns
and covalently link exons
52
intron RNA is defined
by particular sequences within the intron
and at the intro-exon boundaries in....
splicesome splicing
53
What splicing requires less sequences
splicesome (self splicing need more sequences)
54
The consensus sequences in spliceosome splicing includes
5' donor site, 3' acceptor site and an internal adenine
55
a pre-mRNA with multiple
introns can be spliced in different ways
Alternative splicing
56
This will generate mature mRNAs with different
combinations of exons
alternative splicing
57
Different splicing choices occur in different cell types or
during different stages of development in....
alternative splicing
58
The biological advantage of alternative splicing is
that....
two (or more) polypeptides can be derived from
a single gene (allows organism to carry fewer genes in its genome)
59
The slower the life cycle of an organism, the...
more numerous and larger the introns
60
Bakerʼs yeast contains about
6,300 genes
61
Bacteria and yeast have how many introns
very few
62
Most mRNAs in ____ are spliced, what percent?
humans, 70%
63
what contains different alternatively spliced versions that vary in function to meet the needs of the cell type in which they are found
alpha-tropomyosin
64
Alternative splicing is or is not a random event, is it regulated?
is not
65
Alternative splicing involves what proteins? What is their role?
splicing factors, splice sites
66
Some splicing factors inhibit the ability of a
spliceosome to recognize a splice site. Example?
Exon skipping by a splicing repressor
67
A splicing repressor makes the what unrecognizable or masked
acceptor site
68
Some splicing factors enhance the ability of
a spliceosome to recognize a splice site. Example?
splicing enhancer, promotes the recognition of poorly recognized junctions
69
What process: Most mature mRNAs have a ____
covalently attached at their ___ end
Capping: 7-methyl guanosine, 5'
70
Capping occurs when?
as the pre-mRNA is being
synthesized by RNA pol II (when transcript is 20-25 bases long)
71
Capping contains what?
a rna (GTP) nucleotide attached to the 5' phosphate of rna in a phosphoate-to-phosphate linkage
72
During capping what is released
pyrophosphate
73
Capping is important why?
translation and stability of RNA
74
In capping what is added to the gene? What is removed?
Methyl, 2/3 phosphates
75
Most mature mRNAs have a string of adenine
nucleotides at their 3ʼ ends
polyA tail
76
It is added enzymatically after the gene is completely
transcribed
polyA tail
77
In tailing, what signal is transcribed? By what?
polyadenylation signal by endonuclease
78
important in the
stability of mRNA and the
translation of the polypeptide
polyA tail
79
Protein synthesis always begins with....
Met
80
Each amino acid is attached to....
tRNA
81
tRNA H bonds to what in mRNA in protein synthesis
3 bases (codon)
82
There is no tRNA that can base pair in a....
stop codon
83
The genetic code was determined by....
synthetic RNA
84
contents of cells that have been broken open
extracts
85
The genetic code was deciphered using....
Extracts
Degrade the DNA in the extracts by adding the DNase
Add synthetic RNA
Look to see the AA sequences of polypeptides that are made
86
A method to synthesize RNA
also helped crack the Genetic Code. What was created?
short RNAs (3 nucleotides) that had a defined sequence
87
Short RNAs with defined sequences that are linked together enzymatically to
copolymers
88
Brings in AA to ribosome
tRNA
89
An anticodon H bonds with...
3 bases in mRNA (codon)
90
Each AA has how many tRNAs
their own
91
AA have their own ____ that binds ATP
Aminoacyl-tRNA
synthetase
92
When ATP attaches to an AA, what is released and then bound to the AA
pyrophosphate released and AMP bound
93
What replaces the AMP bound to an AA
tRNA
94
When tRNA is attached to the AA, what is it called?
Charged tRNA
95
How many aminoacyl-tRNA synthetase for every amino acid
1
96
The macromolecular arena where translation (protein synthesis) takes place.
Ribosome
97
A ribosome has how many pockets, what are they?
3: A, P, E
98
Only occupied by tRNA with single AA attached
Aminoacyl site
99
Occupied by tRNA with chain of AA (not Met)
Peptidyl site
100
P site of ribosome in translation contains a...
AUG start codon
101
E site of ribosome in translation contains a...
UAG stop codon
102
In eukaryotes, transcription and translation occurs where?
transcription in nucleus, in cytoplasm
103
In bacteria, transcription and translation occurs where?
occurs at the same place in cytoplasm
104
A proteinʼs primary structure is its...
AA sequence
105
What structure within the cell will the protein adapt
3D
106
The folding of a protein begins during...
translation
107
The progression from the primary to the 3-D structure is dictated by...
the amino acid sequence within the polypeptide
108
The primary structure of a protein folds to
form regular, repeating shapes known as
secondary structures
109
alpha helix and beta sheet structures are stabilized by...
H bonds
110
Amino acids with non-polar R groups are...
hydrophobic
111
Amino acids with polar or charged R groups are
hydrophilic
112
The short regions of secondary structure in a protein
fold into a three-dimensional
tertiary structure
113
final conformation of proteins that are composed of a single polypeptide
tertiary structure
114
Proteins made up of two or more polypeptides have a
quaternary structure
115
Forces/interactions responsible for polypeptide folding and the aggregation
of polypeptides into proteins:
Hydrophobic/hydrophilic
Ionic interactions
Hydrogen bonds
Van der Waals interactions
