Midterm 3 Flashcards
(185 cards)
1
Q
What solves the end problem?
A
Telomerase
2
Q
What type of structure is telomerase?
A
ribonucleoprotein
3
Q
Can errors in DNA be eliminated?
A
no, but it can be reduced
4
Q
In human cells, how many times does DNA break spontaneously each day?
A
30,000,000
5
Q
How many bp are in our cells
A
6 billion base pairs per cell
6
Q
Chemical systems comply with what and are controlled by what?
A
thermodynamics and probability.
7
Q
What is the engineers triangle?
A
How fast, cheap, good something is, and you can only pick two.
8
Q
What is the cells place on the engineer traingle?
A
cells spend time and energy for accuracy
9
Q
What are some sources of DNA error?
A
- base mis incorporation
- chemical mutagenesis
- ionizing radiation
- genetic mutagenesis
- spontaneous lesions
10
Q
What are the kind of mutations?
A
- base substitutions
- insertions and deletions
- breaks in the backbone
11
Q
When must mutations arise?
A
-Replication
12
Q
When can descent occur?
A
-only with modificaton
13
Q
What are the ideas under descent of modification?
A
- Variation: not every individual in a population is the same.
- Heritability: these differences can be transmitted between generations.
14
Q
What is natural selection?
A
Differential survival: heritable differences increase or decrease the number of offspring that an organism has.
15
Q
As genomes get larger, what happens to the tolerance of mutation?
A
Lower rates of mutation are tolerated
16
Q
What are the three flavors of mutation reduction?
A
- Inherent accuracy (10^-3 - 10^-4)
- Proofreading . (10^-6-10^-7)
- Surveillance and repair . (10^-9-10^-10)
17
Q
What does an imino tautomer of adenine base pair to?
A
cytosine instead of thymine
18
Q
Which strand does DNA pol I proof read?
A
Nascent chain, 3’ end in the proofreading site, 3-5 exonuclease
19
Q
What are the two exonuclease activities of DNA Pol I?
A
5 ́–3 ́ exonuclease chews through primers & other debris
3 ́–5 ́ exonuclease proofreads for accuracy
20
Q
What are chemical mutagens?
A
DNA intercalating agents cause indels
21
Q
What are three chemical mutagens?
A
- Proflavin
- ethidium
- acridine orange
22
Q
What type of sequences are susceptible to slipped strand mispairing, which can cause indels?
A
Repetitive DNA sequences
23
Q
What is Huntington’s Disease?
A
Incurable, progressive neurodegenerative disease, usually fatal.
24
Q
How is Huntington’s Disease caused?
A
Expansion of triplet repeats. Usually normal people would have around 20 repeats, Huntington’s gives you 40, causing a protein structure to have too many of an amino acid. The mis-folded protein will aggregate and cause neuronal cell death.
25
What are the two types of mutations that can cause cancer?
Gain of function- in protooncogenes, promote cell division, is dominant
Loss of function- in antioncogenes, tumor repressor, is recessive.
Cancer is believed to need multiple mutational hits
26
With time, what happens to DNA repair machinery?
it becomes less efficient
27
How often doe sDNA damage occur?
- It is ongoing and cumulative
- Depurination (base loss): 20,000/cell/day -Deamination: 100/cell/day
- About 1/1000 of the genome in each human cell is damaged per year.
- If you live to age 80, that’s ~10% of the genome in each cell.
28
What can occur in DNA with radiation?
- UV crosslinking produces pyrimidine dimers
| - Leading cause in skin cancer, most common cancer
29
How are pyrimidine dimers in DNA repaired?
- Nucleotide excision repair
| - DNA photolyase (not in humans)
30
What is DNA photolyase?
a remarkable solar-powered enzyme that repairs cyclobutane thymine dimers
31
How does DNA photolyase fix dimers?
-MTHF photon antenna absorbs UV-A and gets as photo excited--MTHF transfers to photo excitation to FADH-- FADH transfers to dimer to break into monomers
32
What does MTHF stand for?
MTHF = methenyltetrahydrofolate
33
How are UV photoproducts recognized in NER?
System recognizes
| helix (backbone) distortions, not specific chemical groups or adducts.
34
What proteins are involved in NER?
-UvrABC endonuclease (ABC excinuclease), UvrD, Pol I, ligase . (total of 16 proteins involved in humans)
35
What is Xeroderma Pigmentosum?
- genetic diseases of excision repair.
- In humans NER utilizes 16 different proteins. Mutations in many of these cause XP.
- characterized by sun sensitivity (sever sun burns) . 25 % of affected have neurological manifestations
36
What are the steps to mismatch repair?
- MutS recognizes DNA damage and dimerizes
- MutL is recruited
- ATP is used, the complex acts like a motor and moves in opposite directions creating a spool
- Mut H is recruited, using UvrD and exonuclease to remove strand with error
37
How can DNA mismatch repair tell which DNA strand is the parent strand?
-Hemi methylation of the parent strand
38
What are some alkylating agents?
- Nitrogen mustard
- ethylnitrosourea
- MNNG
39
What are some alkylation products?
- O6-methylguanine (pairs with C or T)
| - O6alkylgunaine
40
How are common alkylation products repaired?
-MGMT:
| Removes alkylmoiety by transferring onto its cys residue, not an enzyme can only be used once
41
What DNA modifications are produced through normal metabolism?
-oxidizers, over 100 DNA oxidative modifications
42
What are some powerful oxidizers?
- cytosine to Uracil
| - adenine to hypoxanthine (binds to cytosine)
43
What is the process of base excision repair?
1. The defective or incorrect base is removed by DNA glycosylase. (several DNA glycosylases recognize different bases.
2. Backbone cleaved at AP site by endonuclease.
3. DNA polymerase removes the naked sugar/phosphate and fills in the gap which is then sealed by DNA ligase
44
What is an AP site?
abasic (apurinic or apyrimidinic),
| OH is left when DNA glycosylase acts on base
45
Why does DNA have Thymine?
-Do not have uracil in DNA because cytosine deanimates into Uracil, uses base excision to remove it. So thymine is used for an indicator of Uracil damage.
46
What catalyzes base excision?
-Uracil-DNA glycosylase
47
What is the mechanism of Uracil-DNA glycosylase?
-hydrolysis, base flipping, distorts DNA backbone
48
Why is RNA an intermediate?
Regulation, and maybe the history.
- RNA is catalytic, it could function as genome and replicase.
- RNA is used for amplification, ribosomes as factories, and mRNA as messages to factories
49
What came first, RNA or DNA?
RNA
50
What is the DNA coding strand?
-sense strand
51
What is the DNA template strand?
-antisense strand, base pairs with nascent RNA
52
What is RNAP?
RNA polymerase, can initiate without primers
53
What is used in the active site of RNAP?
- 2 Mg2+
| - catalytic site is conserved
54
How do transcription machinery know where to initiate?
-promoters, Cis-acting DNA
55
How many DNA-dependent RNA polymerases does Eukaryotes have?
- 3-Pol I, II, III
| - discovered at UW from sea urchins from the sound
56
How is the Pre-initiation complex formed?
-From RNAP II and General transcription factors
57
What is the TATA-binding site (TBP)?
- key subunit of TFIID
- TBP introduces a 45 degree bend to the double helix, locally untwisting DNA
- Universal GTF, required for RNAP I, II, III
58
What are enhancer sequences?
- regulate activity of core promoters in Eukaryotes
- a few hundred bases upstream from start site.
- each gene has different array of enhancer sites
- specific sequences bind different transcription factors, modular control
59
Core promoters are regulated by?
Enhancer sequences
60
How do enhancer sequences regulate core promoters?
- activator protein binds to enhancer sequences
| - activator proteins interact with mediator proteins (large complex) in order to regulate transcription
61
Mediators are required for all ---- promoters.
RNA II promotors.
62
What is heterochromatin and euchromatin?
regions of repressed (condensed) and activated (dispersed) transcription.
63
How many different proteins make up histones?
4 different proteins form and octamer.
64
How is transcription initiation regulated by DNA accessibility?
- chromatin structure is changed
- motors use ATP hydrolysis to move nucleosomes around to expose sites
- resemble helicases, but lack the ability to unwind DNA.
65
How is the structure and activity of chromatin controlled?
- post translational modifications
- Writers add marks to chromatin
- erasers removes marks
- marks can be placed on DNA or histones
66
How are biological readouts produced from the marks placed on chromatin?
- reader proteins specifically bind to the histone modification
- chromatin condensation or de-condensation
- transcription activator binding
67
What are some enzymes that write and erase chromatin marks?
```
writes:
-DNA methytransferases (DNMTs)
-histone acetyltransferases (HATs)
-histone methyltransferases (HMTs)
Erases:
-histone deacetylases (HDACs)
-lysine demethylases (LSDs)
```
All these occur on tail of histones, bunch of different reactions
Also histone kinsases and ubiquitin ligases
68
What is a covalent modification of DNA?
Methylation:
- DNA methytransferses use DNA (CpG) and SAM
- the methyl on the DNA does not affect base pairing, but prevents transcription factors from binding, shutting of transcription
- in mammals -60-90 percent will be methylated
69
What are some modifications of histones?
- phosphrylation (Ser, Thr)
- acetylation (Lys)
- methylation (Arg, Lys)
- ubiquitination
70
What happens when histones are phosphorylated versus acetylation?
-Phosphorylation adds a negative charge, acetylation neutralizes it with a positive charge, making DNA not as bound tightly and easier to open up.
71
What are major target sites for regulatory modifications of histones?
N-terminal tails:
- H3
- H4
- H2A
- H2B
72
In the methylation of histone, what substrate is the methyl donor?
-SAM
73
What can be found in active genes?
-heavy acetylation
74
What are primed genes?
-inactive genes in an activatable state. have less-heavily acetylated histones.
75
What are silenced genes?
Heterochromatin- not heavily acetylated, but are heavily methylated on DNA and on histones
76
What do HATs do?
- acetylate lysines, especially on the N-terminal tails of histones
- many different proteins, including remodeling factors, bind to acetylated lysines and other modified residues on histones.
77
What has to occur to allow the polymerase RNAP II to leave the promotor?
-phosphorylation of the C-terminal domain (CTD). It is the floppy intrinsically disordered part of the enzyme made of 53 repeats of the sequence YSPTSPS (hydrophilic).
78
What happens to histones during transcriptional elongation?
-they are acetylated, displaced, and repositioned during transcriptional elongation.
79
What are the order of events that start transcriptional elongation?
- PIC assembled, CTD of RNAP II phosphorylated multiple times
- Elongator complex binds
- Elongator contains a histone acetyltransferase that helps displace nucleosomes
80
What are the trail of breadcrumbs left as genes are transcribed by RNAP II?
-acetylation marks
81
What are three ways eukaryotic mRNA are processed?
- 5' cap addition
- 3' polyadenylation
- splicing, to remove introns
-occurs during elongation
82
What si the 5' end of nascent mRNA capped with?
-7-methylgaunosine
83
How doe s the capping enzyme cap mRNA?
1. hydrolysis removes 5 ́ γ-Pi from pre-mRNA.
2. Gunaylation of pre-mRNA through 5' to 5' triphosphate bridge (PPi released)
3. methylation of the guanosine base at position N7. Methyl donor is SAM.
(only in eukaryotes only, during elongation, binds to CTP of RNA II.
84
What occurs when the 3' end of nascent mRNA is polyadenylated?
- Cleavage signal is cleaved by a specific endonuclease
| - using ATP a tail of A's is added by poly (A) ppolymerase
85
Why are a bunch of A's added to end of mRNA?
-it is not exactly known why, but a possibility may be due to making it more stable, making able to transport out of the nuclease.
86
What happens when mRNA is spliced?
-introns removed, exons remain. Occurs after capping and after polyadenylation
87
Why do bacteria not have introns?
-bacteria economized, they got rid of their introns.
88
What is alpha-tropomyosin pre-mRNA?
- it is a pre-mRNA that encodes structural protein.
| - By certain splicing it can create different types of structural proteins in muscles.
89
What part of the mRNA are invariant?
- two nt's at the beginning and end of introns
| - key for lariat mechanism
90
What is the lariat mechanism of mRNA?
- It is when the intron in pre-mRNA
- One of the invariant ends will forma a lariat with one of the other base's OH (2,5)
- the intron lariat is excised and the spliced exons will form a splice junction.
91
What is a splicesome?
- carries out mRNA splicing, composed of snRNPs (small nuclear ribonucleoproteins)
- almost the same size as a ribosome
- RNA acts as enzymes
92
What is the U7-snRNP?
splicesome controlling the processing of the 3' end of mRNA encoding histone proteins.
93
What is special about Group I introns?
- they splice themselves (autocatalytic)
| - one of the first examples of RNA catalysis.
94
What is the relation to mRNA processing and transcription?
-they are coupled together.
95
What is the most abundant macromolecule in a cell?
-proteins
96
What are a vast majority of enzymes?
-they are proteins
97
-90 percent of a cell's energy can be directed towards...?
-protein synthesis
98
In E. Coli, what makes up 25 % of its dry mass?
-ribosomes, 1000 new ribosomes made per E. coli per minute.
99
What do many important abx like to target?
-protein synthesis
100
How cant he amplification of gene expression be regulated?
-by regulation of transcription and translation.
101
What is the genetic code?
-a set of rules by which a linear sequence of nucleotides specifies the linear sequence of a polypeptide.
102
How many reading frames are in DNA or RNA strand when reading in one direction?
-three possible reading frames.
-in double strand there are 6
=+2 change equivalent to moving -1
103
What happens to the reading frame when there is a + nt insertion?
- 1 shift in the reading frame.
104
How is a reading frame restored when there is a +1 insertion?
- deletion of 1 nt will restore it.
| - or insert 2 nt
105
Which amino acids have the most codons that code for them?
- Arg, Leu, ser
| - these guys are most abundant in proteins, used a lot so have more codes for them
106
Which AA have the least amount of codons
-Met, Trp
107
What is the adaptor hypothesis?
Crick believed each amino acid was bound to a specific adaptor that would base pair to to the right codon based on the bases. An enzyme would catalyze all of this. He was hypothesizing tRNA. Believed there was 20.
108
What are the arms of tRNA?
- D arm
- anticodon arm
- extra arm
- T C arm
The differences in these arms and how tRNA folds differentiates all the tRNA.
109
What is the the secondary structure of RNA?
-double helices similar to A-DNA.
110
What is the wobble effect?
It is where the third nt in the codon does not have to base pair with the right base. Like how in alanine tRNA will recognize any A/C/U at the third position. In that case the third codon is Inosine.
111
what are the wobble rules?
2- U (A,G) . G (C, U)
| 3. I (AUC)
112
What is inosine?
Deanimated adenosine, hypxanthine base. Promotes wobble base pairing.
113
How are codons assigned to tRNA?
By tRNA synthetases - aaRS (aminoacyl tRNA synthetase)
114
What must occur before tRNA can be used in order for a tRNA with an amino acid can be formed?
-The amino acid must be charged by ATP using tRNA synthetase, then added to tRNA, creating a charged tRNA (aminoacylated tRNA).
115
When the aa is activated, what does it form?
-a mixed anhydride, aminoacyl-AMP
116
In the formation of an anhydride, what does each class of tRNA synthetase do?
- Class I- adds amino acyl-amp to 2' of the adenine on the end of tRNA
- Class II- adds to the 3' end
117
What is the difference in the steps of Class I and Class II aminoacyl-tRNA synthetases?
Class II has an extra transesterification step.
118
What are the three sources of error in translation?
1. aaRS uses wrong amino acid as substrate
2. aaRS selects wrong tRNA as substrate
3. Ribosome selects wrong aa-tRNA for codon
119
Why is it hard to achieve specificity in an aaRS?
-Very similar aa, and not a big difference in free energy. At equilibrium at every 100.
120
Aminoacyl-tRNA synthetase adds amino acid to what end of tRNA?
-3' end
121
How are tRNAs proofread?
When they are being synthesized, if the wrong amino acid is added there is an editing site that ill remove it.
ATP and time are consumed in a futile cycle to increase accuracy.
122
aaRS can proof read what two compouns?
- adenylated amino acid
| - aminoacyl tRNA
123
What are the three stages of polymer synthesis?
- initiation
- elongation
- termination
124
What subunits makes up prokaryotic ribosomes?
- 50S : 5S rRNA, 23S rRNA
| - 30S: 16S RNA
125
What subunits make up eukaryotic ribosome subunits?
- 60S: 5SrRNA, 28SrRNA
| - 40S: 18S rRNA
126
Folding in in Eukaryotic and Prokaryotic organism are fairly..?
complex and conserved
127
Where si the conserved region in ribosomes?
around the polypeptide tunnel exit.
128
How do you tell which direction polysomes are translating?
you look at how long each peptide is, the longer it is the farther along it is.
129
What is faster, ribosome or a polymerase?
polymerase
130
What are the three stages of translation?
Initiation: the ribosome is placed on the start codon Elongation: mRNA-templated polypeptide polymerization Termination: the polypeptide and mRNA are released
131
In bacterial initiation, ribosome subunits bind to what part of the mRNA to begin translation?
-Ribosome binding site or the Shine Dalgarno Sequence.
132
In eukaryotes, how do the ribosome subunits initiate translation?
They bind the the 7-metylguanine cap and scan to fine an AUG start sequence to begin going 5-3.
133
What are the three binding sites for tRNAs in ribosomes?
A-amino acyl tRNA site .
P-peptidyl-tRNA site .
E- exit site
134
What are the functions of each of the sites
A- tRNA selection
P-peptidyl transferase
E-Translocation of the uncharged tRNA to exit
135
In ribosomes, how are the aa transferred onto the chain?
- The formed chain is placed onto the newly incoming aa-tRNA in the P site.
136
What are all the ingredients of initiating bacterial translation?
- mRNA
- fMEt
- IF1, IF2, IF3
- GTP an Mg2+
- small (30s) subunit
137
What is the difference between the start codon of bacteria and eukaryotes?
-Bacteria use fMet while eukaryotes use normal Met. Fmet is kind of a danger signal in animal immune system, they recognize it as foreign.
138
What are mechanisms of all the IF factors?
IF1 binds to the A site of the 30s subunit. IF3 binds as well. Afterwords IF2 with a GTP attached to it will bind to fMet tRNA and the 30S subunit. IF2 drives the initiation.
139
How is the elongation state started in bacteria translation?
- Initiation factors fall off
- large 50s subunit binds
- fMEt-tRNA and AUG codon are in P site
- A and E sites empty
140
What is a consequence of Eukaryotic translation initiation method?
-They only have one start site so they monocistronic while prokaryotes are polycistronic.
141
If prokaryotes are polycistronic, how does the polyprotein become individual proteins?
-site specific proteases.
142
In initiation of Eukaryote translation, what part of the ribosome (40S) binds to the mRNA?
-The EIF-4 complex binds to the 5'-cap and the poly A tail.
143
What is the hybrid state in the elongation cycle of translation?
-When the tRNAs are trying to translocate between sites, they enter a hybrid state where they are in two sites at once. In this step all sites are occupied.
144
What is the selection/accommodation step in elongation of peptides?
It is the step of proof reading. The tRNA is bent and not fully in the ribosome. EF-Tu and GTP is bound to the aa and will fall off once the aa is recognized.
145
What are the functions of EF--Tu protein.
Binds to GTP, it will help with proofreading in ribosomes. Forms the bent formation complex with tRNA and the ribosome.
146
What abx blocks the 30s aa-tRNA-EF-Tu complex?
tetracycline
147
What type of formation does aa-tRNA-EF-Tu complex adopt.
-The bent conformation
148
What increases the accuracy of translation?
The slow hydrolysis of GTP on EF-Tu. It increases accuracy but it is very slow.
149
What is different about the N terminus of aa in bacteria that are waiting to be incorporated into a peptide?
The N terminus is in a formyl form.
150
What is purimycin?
-mimics aminoacylted tRNA, but terminates the chain.
151
What did fragment reaction reveal?
Peptidyl transferase enzyme is RNA, not protein.
152
What does EF-G do?
Acts like a motor to help translocation and uses GTP to do it.
153
What was determined from Noller result?
Ribosome is ribozyme (RNA rather than protein in the peptidyl transferase site). They used K and SDS to attempt to deactivate protein, but the organism tested was found to have 80 percent activity of ribosomes, pointing to the fact that ribosome is a rna.
154
What are 4 abx that bind to the PTC (peptidyl transferase site) of ribosomes?
- tetracycline
- puromycin
- chloramphenicol
- macrolides
155
How does tetracycline work?
-bind to the 30S A site, inhibits entry of aa-tRNA
156
What does chloramphenicol do?
-bind in PTC, inhibiting peptidyl transferase activity and blocks the exit tunnel.
157
What do macrolides do?
bind to PTC, block the exit tunnel.
158
What occurs at termination?
at the stop codon a RF binds, causing the polypeptide to hydrolyze (water acts as the nucleophile) in the P site, then the Ribosome complex dissociates. EF-G helps the subunits and the complex dissociates.
159
What are the release factors similar to in structure?
They are similar to tRNA.
160
What are the 5 main stages of protein synthesis?
1. activation
2. initiation
3. elongation
4. termination
5. folding and post translational processing .
161
What steps in the formation of a peptide bond requires energy?
- aminoacylation
- aaRS proof reading
- initiation (IF-2)
- elongation (EF-Tu)
- translocation (EF-G)
- termination (unkown)
- Ribosome scaniing
162
What are the essential components of activation of tRNA?
- 20 amino acids
- 20 aminoacyl-tRNA synthetase
- ATP
- Mg2+
163
What are the essential components of initiation?
- mRNA
- F-met
- Initiation codon of in mRNA
- 30S and 50s
- initiation factors
- GTP
- Mg2+
164
What are the essential components of Elongation?
- Functional 70s ribosome
- aminoacyl-tRNAs specified by codons
- Elongation factors
- GTP
- Mg 2+
165
What are the essential components for termination release?
- Termination codon inmRNA
| - Release factors .
166
What are the essential components for folding and post translational processing?
-specific enzymes, cofactors, proteases, signals, folding protein, etc.
167
What happens to proteins after they are made?
-N-terminus for the growing peptide will worm through the exit tunnel in the large subunit.
168
What are the four possible target for protein signals?
- ER
- Mitochondrial matrix
- Peroxisome
- Nucleus
169
If a protein is meant to be in the mitochondrial matrix, what type of signal would the protein need?
- - multiple N-terminal signal that is a amphipathic helix.
- - once in the signal will be cleaved
170
If a protein is meant to sent to the ER, what type of signaling will the protein need?
- the protein will need t be on the N-terminal or internal
- -the signal will be about 6-12 hydrophobic aa followed by 1 or more positive aa.
- some signals get cleaved and some don't depending
171
What type of protein signal would a protein need if it was going to be sent to the peroxisome?
-C-terminal signal that is a S-K-L that will not get cleaved .
172
If a protein is needed to be sent to the nucleus, what type of protein signal will it need?
- it will need and internal signal 1 cluster of 5 basic aa's or 2 clusters with a few basic aa's
173
Why are NLS located internally and not cleaved?
- possibly due to the protein needing to be able to shuttle back and forth past the nucleus.
- possibly because during mitosis the nuclear envelop dissolves and the proteins need a way to get back in.
174
What is cotranslational protein translocation?
-When a protein is being translated it is also channeled into the lumen of the ER at the same time by a protein conducting channel. The ribosome docks onto a protein translocase.
175
What is pre protein translocase (Sec 61 complex)?
-a Protein-conducting channel with an aqueous pore that spans the ER membrane. It is also an integral membrane protein so it needs another translocase to but it into the ER.
176
What are the three functions of SRP?
- Recognizes the signal sequence emerging from the ribosome exit tunnel.
- Pause translocation
- Direct ribosome and nascent polypeptide preprotein translocase channel on the ER membrane .
177
What is the SRP cycle?
- Ribosome starts translation, a signal sequence produced
- SRP bind and pauses translation
- SRP Receptor binds to SRP, hydrolyzing GTP and falls off
- Translation can resume
178
Why is the region around the ribosome exit tunnel highly conserved?
-it has to interact with SRP and the preprotein translocase
179
What is SRP made of?
It is a ribonucleoprotein.
| Made of RNA and some Protein
180
What cleaves the signal from a peptide?
-signal peptidase
181
Once cleaved, what happens to the signal peptide?
-Preprotein allows the signal to laterally escape from the alpha subunit into transmembrane segments into the membrane.
182
What is the pulse chase experiment?
-A guy named Palade wanted to identify the traffic of protein and did an experiment to track the pathway of a protein.
183
What pathway is vital and important for a large amount of proteins?
-The secretory pathway.
184
What are all the ribonucleoproteins we have covered so far?
- Telomerase
- Ribosome
- SRP
- Splicesome
185
What is the purpose of the each of the Eukaryotic RNA polymerases?
I- rRNA for ribosome
II-mRNA for protein
III-tRNA
