Test 2 Notes Study Guide Flashcards
(93 cards)
1
Q
What are the three major components required for transcription?
A
- DNA template
- The ribonucleotide-triphosphates required to build the new RNA molecule.
- The transcription apparatus: proteins necessary from catalyzing the synthesis of RNA, and RNA polymerase
2
Q
How do RNAs relate to the template strand?
A
RNAs are complementary and antiparallel to the template strand
3
Q
What is the name of the 5’->3’ strand?
A
sense/coding strand
4
Q
What is the name of the 3’-5’ strand?
A
antisense/noncoding strand
5
Q
What is the difference between the template stand and the non template strand?
A
The template strand is complementary and antiparallel to RNA.
6
Q
What does a transcription unit (gene) include?
A
A promotor, an RNA coding region, and a terminator.
7
Q
What is the promotor?
A
A DNA sequence that RNA pol recognizes and binds
8
Q
What is the transcription start site?
A
where the 1st nucleotide is laid
9
Q
What is the function of RNA polymerase?
A
- synthesizes RNA in a 5’-3’ direction
- unwinds and rewinds DNA
10
Q
Why are the consensus sequences AT rich?
A
because AT only has 2 hydrogen bonds so it is easier to break.
11
Q
Where are the consensus sequences on the bacterial promotors?
A
-35 and -10 (pribnow box)
12
Q
What does a consensus sequence consist of?
A
the most commonly encountered bases at each position in a group of related sequences.
13
Q
What does the transcription apparatus consist of?
A
Core polymerase and holoenzyme
14
Q
What is the core polymerase?
A
made-up of five subunits and actually transcribes/ builds RNA
15
Q
What is a holoenzyme?
A
made up of the core polymerase and sigma factor
16
Q
What does the sigma factor do?
A
recognizes -10 and -35 consensus sequences and binds to promotor sequence and recruits pol
17
Q
What are the steps of transcription initiation?
A
- sigma factor binds promotor; -10 and -35 consensus sequence
- sigma attracts core pol
- Holoenzyme is at promotor
- Holoenzyme melts promotor + opens transcription bubble
- RNA pol adds 1+ nucleotide complementary to ssDNA
- sigma factor leaves
18
Q
What happens during transcription elongation?
A
RNA pol extends seq 5’->3’ until termination sequence in DNA ; RNA pol unwinds and rewinds DNA
19
Q
What are the two types of transcriptions termination?
A
1) Rho-dependent termination
2)Rho-independent termination
20
Q
What happens during Rho dependent termination?
A
- Rho finds rut site on RNA
- goes up till it reaches polymerase and stops it
*works like helices but doesn’t have to unwind so it goes faster
21
Q
What happens during Rho-independent termination?
A
1) inverted repeats in RNA bind to each other and cause hair pin loop
2) weak AU base pairs is enough to destabilize pol and pol lets go
22
Q
What does the concept of collinearity suggest?
A
that a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein
23
Q
What are the ends of mRNA called?
A
5’ UTR and 3’UTR
24
Q
What part of prokaryotic mRNA tells the ribosome to bind there?
A
Shine dalgarno sequence
25
What tells the ribosome to start and stop translation?
stop and start codons
26
What recruits the ribosome in prokaryotes?
shine-dalgarno sequence
27
What recruits the ribosome in eukaryotes?
5' cap
28
What interrupts the coding sequences of many eukaryotic genes?
noncoding introns
29
When are intron removed?
RNA processing
30
What makes up the 5' cap?
a single nucleotide with a 7-methylguanine attached to the pre-mRNA by a unique 5'-5' bond
31
What are the functions of the 5' cap?
- protection
- required to get out of the nuclear. pre/export
- recruit ribosome
32
What does the AAAAAA tail do?
bind ribosome
33
What are the steps of splicing?
1. spliceosome binds consensus sequences at intron/exon boundaries
2. mRNA is cut at 5' end of intron
3. 5' end of intron attaches branch point A (lariat)
4. 3' end of intron cut
5. exons joined, lariat (intron) free to be degraded
34
What does a spliceosome consist of?
five RNA molecules and 300 proteins
35
What is the branch point?
the adenine "A", ~ 18-40 nucleotides upstream of 3' splicing site
36
What are the steps of pre-mRNA processing?
1) the addition of the 5' cap
2) the addition of the poly(A) tail
3) splicing removes the introns
37
What is alternative splicing.
alternative splicing enables exons to be spliced together in different combinations to yield mRNAs that encode different proteins
- multiple 3' cleavage sites allow pre-mRNA to be cleaved and polyadenylated at different sites
38
What is the function of 3'cleavage and addition of poly(A) tail
- increases stability of mRNA
- aids in export of mRNA form nuclease
- facilitates binding of ribosome to mRNA
-
39
What is the function of RNA splicing?
- removes noncoding intron from pre-mRNA
- facilitates export of mRNA to cytoplasm
- allows for multiple proteins to be produced through alternative splicing
40
What is the structure of tRNA?
- made of rare modified RNA nucleotide bases (ribothymin, pseudourine)
- common secondary structure: clover leaf structure
- contains anticodon
41
What is the function of tRNA?
delivers amino acids to ribosome
42
What is RNA interference?
limits the invasion of foreign genes and censors the expression of their own genes
43
What do microRNAs do and where are they made?
Function: inhibits translation of mRNA
Made: body
44
What is the function of small interfering RNAs and where are they made?
Function: triggers degradation of other RNA molecules
Made: scientists
45
What do ds RNAs prevent?
translation
46
What is the one gene, one enzyme hypothesis?
genes function by encoding enzymes and each gene encodes a separate enzyme
47
What is a protein?
a long polymer of amino acids joined by peptide bonds
48
Describe primary organization.
sequence/chain of amino acids, n'-c' (Shoe string)
49
Describe secondary organization.
back bone atoms bond
- alpha helix: shoelace around finger
- beta sheet: ribbon candy
both are held by hydrogen bonds
50
Describe tertiary organization?
folding of secondary into 3D globular shapes
*side chains make bonds (r-groups)
51
Describe quaternary organization?
two or more products interact to be functional
52
What is a codon?
a triplet RNA code
- 64 possible codons
53
What is a sense codon?
codons that encode amino acids
54
What is the initiation codon?
AUG
55
What are the termination codons?
UAA, UAG, UGA
56
What is the degenerate code? (wobble)
amino acid may be specified by more than one codon
57
What are synonymous codons?
codons that specify the same AA
58
What are isoaccepting tRNAs?
different tRNAs that accept the same amino acid but have different anticodons
59
What is wobble?
When the tRNA and mRNA pair in a antiparallel fashion, odd base pairing occurs in wobble be there is more than 1 option for an amino acid
60
What is the reading frame?
three ways in which the sequence can be read in groups of three. Each different way of reading encodes a different amino acid sequence
61
What is non overlapping?
a single nucleotide may not be included in more than one codon.
62
What is the universality of the code?
the code is near universal with some exceptions
63
What determines the specificity between an AA and its tRNA
Each individual aminoacyl-synthetase in a cell.
64
How do amino acids attach to the 3' end of tRNAs?
The carboxyl group of the amino acid attaches to the hydroxyl group of the 2' or 3' carbon atom of the final nucleotide at the 3' and of the tRNA in which the case is always adenine
65
Why is the cap and poly(A)tail are important for Eukaryotic translation initiation?
proteins that attach to the 3' poly(A)tail interact with cap binding proteins to attract and bind ribosome
66
In elongation, the creation of peptide bonds between AA is catalyzed by?
rRNA
67
What is polyribosomes in proks and euks?
multiple ribosomes per mRNA strand
68
What do the release factor bound to the termination codon cause the release of?
- the polypeptide from the last tRNA
- the tRNA from the ribosome
- the mRNA from the ribosome
69
What are the steps of prokaryotic translation initiation?
1. IF-3 bound to small subunit (so large subunit can't attach)
2. small subunit + IF 3 bind at shine dalgarno sequence on mRNA
3. F-met +RNA+IF2+GTP +IF1(stabilizes base pairing) base pari the anti codon of the tRNA to start codon (AUG)
4. GTP hydrolyzes; GDP and IFs disassociate
5. Large subunit binds -> F-met tRNA is in the p-site
70
What are the steps of prokaryotic translation elongation?
1. Fmet tRNA in p site
2. EF-Tu w/ GTP bind next tRNA and bring it to A-site
3. GTP hydrolyzed to GDP and EF-Tu disassociates (Efts recycles EFtu +GTP)
4. Peptide bond between Met-AA2 catalyzed by ribosome (rRNA)(2OH-)
5. Ribosome translocates 1 codon w/ EF-G +GTP; Fmet tRNA in E site
6. uncharged tRNA exits
71
What are the steps on prokaryotic translation termination.
1. ribosome reaches stop codon and there is no tRNA to pair with stop codon in the a-site
2. RF1 attaches to the a-site and RF3 forms a complex with GTP and binds to the ribosome
3. The polypeptide is released from the tRNA in the p site
4. GTP associated with RF3 is hydrolyzed to GDP
5. The tRNA, mRNA and release factors are released from the ribosome.
72
What are structural genes?
genes that encode proteins
73
What do regulatory genes encode?
encoding products that interact with other sequences and affect the transcription and translation of these sequences
74
What are regulatory elements?
DNA sequences that aren't transcribed but play a role in regulating other nucleotide sequences
75
What is cleavage of proteins?
chopping in half/ piece cut off
76
What is glycolysation?
adding a sugar to a protein (makes it slippery so cells can slide past each other)
77
What is phosphorylation?
adds phosphate group change protein charge
78
What is lipidization?
adds lipid to protein (binds it to lipid membrane)
79
What is ubiquitination?
ubiquitin protein is added to protein which tags it for destruction and it gets sent to proteosome
80
What are the 6 levels that gene expression can be controlled?
1. chromatin packaging
2. transcription
3. mRNA processing
4. mRNA stability
5. translation
6. post-translational modification
81
What is an example of chromatin packaging modification?
heterochromatin vs. euchromatin
82
example of transcription regulation
RNA pol, promotor, enhancer
, GTF, TF, silencer
83
example of mRNA processing regulation
spliceosome alt splicing, no cap
tail (alt poly(a) site)
84
example of mRNA stability regulation
short half life cycle, siRNA
85
example of translational regulation
miRNA, ribosome can't bind, ribosome function, aa availibility
86
Why is transcription a particularly important level of gene regulation in both bacteria and eukaryotes
bacteria-respond to environment
eukaryotes- specialized cell project
87
What is TBP?
TATA binding protein: protein that recognizes Eukaryote promoter (works like sigma)
88
What does each promoter respond to in euks?
a unique combination of transcription factors
89
What is an enhancer?
DNA sequence stimulating transcription a distance away from promoter
90
How does the binding of transcription factors to enhancers affect transcription at genes that are thousands of base pairs away?
can loop up the chromosome so transcription factors touch polymerase
91
What type of RNA makes up a spliceosome?
snRNA
92
What all is required for eukaryotic transcription?
TBP, Transcription Factors, Mediator, Coactivator, enhancer sequence, RNA polymerase.
93
What makes up the basal transcription factor?
RNA Pol, TATA binding protein, general transcription factors, TATA sequence
