molecular bio 3 Flashcards
(123 cards)
1
Q
non-template strand synonyms
A
sense, coding
2
Q
template
A
antisense, noncoding
3
Q
Is the template strand always the same across a linear chromosome?
A
No
4
Q
What determines which strand is template?
A
Which side the promoter is on
5
Q
Upstream
A
before the start of transcription (i.e. promoter)
6
Q
Downstream
A
after start of transcription
7
Q
What does the promoter control?
A
access of RNA polymerase to gene
8
Q
Transcription begins at
A
+1 nucleotide
9
Q
Termination region
A
regulates end of transcription
10
Q
RNA polymerase in prokaryotes
A
5 subunit core enzyme + sigma subunit, which binds to the promoter
11
Q
Apo
A
Incomplete enzyme; RNA polymerase
12
Q
Holo
A
Complete enzyme; RNA polymerase + sigma factor in prokaryotes
13
Q
Different sigma subunits
A
To bind to different promoters
14
Q
Ribonucleotide
A
Sugar and the base and the phospahte
15
Q
Chromatin - prokaryotes vs eukaryotes
A
Prokaryotes don’t have it
16
Q
NFR
A
Nucleosome free regions; contain promoters; nucleases could cleave these portions if not G4
17
Q
G4
A
Protect NFR from nucleases; DNA quadruplex
18
Q
Consensus sequence
A
Typical sequence for that area (most frequent)
19
Q
-10 sequence, -35 sequence
A
-10 = Pribnow box; almost all prokaryotes have these
-35 = 6-bp region
20
Q
5’ and 3’ UTR
A
Untranslated region on each side
21
Q
Function of UTRs
A
Regulate translation
22
Q
Start codon
A
AUG - Met
23
Q
How many stop codons are there?
A
3; UAA, UAG, UGA
24
Q
Promoter includes
A
Consensus sequences and nucleotides between
25
Closed promoter complex > open promoter complex
Holoenzyme brings helicase to open the strands
26
Acetylation vs methylation of histones
Acetyl allows for transcription, methylation represses
27
What happens to histones at the start of transcription?
Acetylation
28
What continually opens DNA ahead of RNA pol?
Helicase
29
Termination in bacteria
Intrinsic termination most common
30
Intrinsic termination
2 inverted repeats with a poly A tail; the mRNA will have a stem loop; the stem loop breaks the structure off
31
Rho-dependent
rho helicase recognizes 50 nucelotidies rich in cystosines; Rho moves after binding to Rut site with ATP; separates RNA from DNA
32
RNA pol I
eukaryotic; rRNA
33
RNA pol II
eukaryotic; mRNA; main polymerase
34
RNA pol III
eukaryotic; transcribes tRNA
35
Which has more subunits: RNA polymerases in eukaryotes or prokaryotes?
eukaryotes have 6-11 additional subunits on polymerases
36
How far are eukaryotic promoters from transcription start?
they can be multiple kB away from transcription start
37
How might promoters be identified?
Can be id'd by what TFs bind to, mutations that affect transcription
38
Promoter elements in eukaryotes (RNA pol II)
-25, -80, -90 consesnus boxes; TATA box closest, CAAT, GC-rich box
39
Promoters
some have different combos of the consensus sequences at different places; harder to id promoter sequences in eukaryotes
40
TFs bind to
promoters and recruits polymerase
41
TFIIH
Helicase will unwind the DNA; necessary
42
General transcription factors
I.e. TFIIH
43
Are more TFs recruited after polymerase is recruited?
Yes to stabilize and get things ready
44
What happens before the polymerase starts moving?
Complex is released
45
Do sequences between consensus regions matter?
Mutations outside of the consensus region have non-significant effects on transcription
46
Enhancers and silencers
lead to differential expression of genes
47
Enhancers
bind activator proteins + coactivator proteins bind to those and poly and TF complex (multiple kb away)
48
Silencer sequences
repressor proteins are tfs! repressors induce bends in the dna; keep it repressed but ready to go when the stimulus happens
49
What is the availability of a TF is determined by?
signal transduction
50
Nucleolus
Structure within nucleus where rRNA is made and ribosomal machinery is assembled
51
Core element for Pol I
-45 to + 20; bound by initiation factor
52
Upstream control element
-100 to -150; pol I
53
Pol III
TATA box and a couple other consensus sequences (OCT and PSE promoter-specific)
54
Pol III internal promoter
Located downstream of +1
55
Pol II
all upstream; TATA, CAAT GC
56
Pol I
rRNA core element slightly downstream, upstream control element
57
TF1
associate to Pol I
58
2 ways termination ends in prokaryotes
Rho-dependent, rho-independent (intrinsic)
59
Eukaryotic RNA polymerases terminate
differently from each other;
Pol I - termination factor
Pol II - polyadenylation signal, then cleaved, exonucleases eat remaining RNA
Pol III - termination signal
60
Eukaryote vs prokaryote transcripts
Eukaryote separation of transcription and translation, eukaryotic transcripts have introns, and are more stable (so that they can be transported)
61
Initial eukaryotic gene mRNA
pre-mRNA
62
opposite of pre-mRNA
mature mRNA
63
Modifications to pre-mRNA
5' capping, 3' polyadenylation (put a lot of As), intron splicing
64
5' capping
Adds a guanine to the 5' end and methylates (on 7th nitrogen) it connected by triphosphate (2 separate enzymes, first one guanylyl transferase, second methylase)
65
What might happen when the guanine cap is methylated?
Other bases get methylated
66
What is the linkage between the 5' cap and the mRNA sequence?
Triphosphate linkage
67
3' Polyadenlyation
Replaces 3' end with poly A (endonuclease snips the end, another enzyme adds (polyadenylate polymerase))
68
AAUAAA
Gets recognized for polyadenylation; cleaved off
69
Number of BP of telomeres
~ 2,000 bp
70
Number of BP of polyA tails
20 to 200 bp
71
Do RNA polymerases have any proofreading capabilities?
no
72
Does polyadenylation happen inside or outside the nucleus?
Inside
73
Does splicing happen inside or outside the nucleus?
Inside
74
What does polyadenylation do?
Helps recognition of mRNA by ribosome, prevents degredation of mRNA
75
Histone genes don't have polyA tails. Why?
Made so highly
76
Do exons or introns get translated?
Exons
77
How is it determined which introns will be taken out in alternative splicing?
Proteins that bind to CREs (cis regulatory elements within pre-mRNA)
78
Explain how a frameshift mutation could occur by a point mutation in the intron
Splice site alteration
79
R-looping
DNA is bound to mRNA, DNA loops out where the introns have been spliced
80
5' splice sites
contains a consensus sequence with GU at 5'
81
3' splice site
11 nucleotide consensus with a pyrimidine rich region and AG at the 3' end
82
Spliceosome
Made of multiple snRNPs (small nuclear ribonucleoproteins) that perform splicing
83
mRNA editing
Substitution, addition, or deletion, prevalent in bacteria
84
Are all 3 mRNA processing processes carried out at the same time?
Yes
85
How many ribosomes in a cell?
Thousands
86
Highest amount of RNAs?
rRNA
87
Meaning of 70S
70 Svedberg units, a unit of measurement for how fast molecules settle in a centrifuge
88
Eukaryotes rRNA genes
Tandem repeats to make a lot
89
Is tRNA always in the translation machinery? What do they do?
Yes; they contain anti-codons
90
How many main subunits are there in a ribosome?
2; large and small
91
ITS
Internal transcribed sequence; analogous to introns in rRNA
92
Do NTS get transcribed?
No (nontranscribed sequences)
93
RNA Pol II
Good processivity, pauses for processes to take place like capping
94
Promoter clearance
Polymerase becomes detached from promoter region and moves for transcription
95
Mushroom poisons
inhibit kinases that work on the C-terminal domain on a polymerase that makes promoter clearance happen by recruiting elongation factors when phosphorlated
96
Elongation factors
suppress pausing
97
Kinases phosphorylate CTD so that
promoter clearance happens
98
+ strand
can be directly made into protein
99
- strand
needs to be copied before making protein (reverse transcribed, then make a copy!)
100
HPV
dna does not get integrated for a while (remains as episome)
101
Retrovirus
RNA > DNA > integration > RNA > protein
102
Enzyme that can make DNA from RNA
Reverse transcriptase
103
cDNA
DNA resultant from RT of mRNA
104
Does cDNA contain introns?
No
105
Does RNA polymerase have proofreading activity?
No
106
Does an RT have a nuclease portion?
Yes
107
Do all viruses integrate into human genomes?
No
108
What enzyme allows viral DNA to become part of the human genome?
Integrase
109
Polycistronic genes
multiple proteins/ gene
110
Do viruses have polycistronic genes?
Yes
111
Lytic virus
Leaves and breaks the cell
112
Non-lytic virus
Cell does not break
113
Do we have receptors that bind to spike proteins? Why?
Yes, they are for some other ligands in our cells
114
DNA better than RNA because
Deamination (which can make C > U)
115
RNAse H
Cleave duplex-form or RNA (RNA:DNA, RNA:RNA) (chew up the RNA) (is it in eukaryotes besides being brought by viruses?)
116
RNA bound to DNA
Transcription, RNA primers in okazaki fragments
117
RNAse H
As reverse transcriptase makes DNA from RNA, the RNA gets chewed by this enzyme
118
Is RNA transcriptase fast? Good at proofreading?
No, no
119
What is used as a primer in RT?
tRNA
120
Is trna brought in virus?
Yes
121
What structure is better for integration of viral DNA? What makes that?
Hairpins, complementary/ inverted repeats
122
Is it typical for multiple integrations to happen?
Yeah
123
Where do viruses prefer to integrate DNA?
Prefers to integrate to DNA wrapped around histone
