FINAL EXAM FLASHCARDS
1
Q
who discovered the DNA double helix structure?
A
rosalind franklin & maurice wilkins
2
Q
who published the DNA secondary structure?
A
watson & crick
3
Q
what is DNA’s secondary structure?
A
- complementary base pairs
- complementary and anti-parallel strands
- 10 bp/turn
- 0.34 nm between stacked bases & 3.4 nm/turn
4
Q
what does DNA being semi-conservative mean?
A
that the strands separate to regenerate new DNA using the separated strands as a template
5
Q
what are the 3 ways DNA can split?
A
- conservatively
- dispersively
- semi-conservatively
6
Q
who discovered that DNA replication was semi-conservative?
A
meselson & stahl using their CsCl density gradient
7
Q
what are the modes of DNA replication?
A
- theta replication
- rolling circle replication
- linear chromosomal replication
8
Q
what is theta replication?
A
- occurs in prokaryotes circular DNA
- looks like theta before it splits into 2 circular DNA molecules
- BIDIRECTIONAL
9
Q
what is rolling circle replication?
A
- specialized (occurs in F factor & some viruses)
- produces multiple circular DNA molecules
- UNIDIRECTIONAL
10
Q
what is linear chromosome replication?
A
- occurs in eukaryotes
- chromosome has many origins which all form replication bubbles until they meet up (producing 2 linear DNA molecules)
- BIDIRECTIONAL
11
Q
what does DNA replication require?
A
- Mg 2+
- DNa polymerase
- A, G, C, T
- template DNA
- RNA primer
12
Q
what do RNA primers do?
A
provide the 3’ OH end to initiate DNA synthesis by DNA polymerase
13
Q
what end of a replicating DNA does nucleotides get added to?
A
3’ end of the new (synthesizing) strand
14
Q
what are DNA chains susceptible to?
A
DNA chains are susceptible to nuclease cleavage (results in phosphate group staying attached to 5’ carbon or the 3’ carbon
15
Q
which DNA polymerases are replicative?
A
DNA polymerase 1 & 3
16
Q
which DNA polymerases are for repairing?
A
DNA polymerases 2, 4, 5
17
Q
what does DNA polymerase 1 do?
A
removes RNA primers on lagging strand
- 5’ to 3’ polymerase/exonuclease activity (removal of RNA primers)
- 3’ to 5’ exonuclease (proofreading)
18
Q
what does DNA polymerase 3 do?
A
main replicative polymerase
- 5’ to 3’ polymerase activity
- cant remove RNA primers
- 3’ to 5’ exonuclease activity (proofreading)
19
Q
what is the beta clamp?
A
attaches to DNA and helps keep DNA polymerase 3 on the strand
20
Q
what is the name of the synthesis of DNA on the lagging strand?
A
discontinuous synthesis (due to okazaki fragments)
21
Q
what is the name of the synthesis of DNA on the leading strand?
A
continuous (no okazaki fragments)
22
Q
why is RNA more reactive than DNA?
A
because it has an OH group (not just H) on carbon 2 of ribose
23
Q
what is the tertiary structure of RNA?
A
tRNAs
24
Q
how are genes expressed in prokaryotes?
A
- transcription & translation are coupled (happen in same place)
- coding region is continuous
25
how are genes expressed in eukaryotes?
- coding region is non-continuous (contains introns & exons)
- transcription = nucleus
- translation = cytoplasm
26
how is RNA synthesized?
using the 3' to 5' DNA template strand (nucleotides are added to 3' end of RNA strand)
27
what are the differences between DNA replication and RNA synthesis?
- RNA only uses 1 strand to synthesize
- no primer needed for RNA synthesis
- uses A, G, U, C instead of A, G, T, C
- RNA is complementary to DNA template and identical to DNA non-template
28
what is the -35 sequence (for prokaryotic transcription)?
5' TTGACA 3' (on non-template strand)
29
what is the -10 sequence (for prokaryotic transcription)?
5' TATAAT 3' (on template strand)
| - aka. TATA box
30
where does prokaryotic transcription actually start on DNA?
5-9 base pairs down from the -10 sequence (either T or C)
| - this is aka. the +1 site
31
how many base pairs apart are the -35 and -10 sequences?
approx. 16-19 base pairs
32
what is upstream and downstream?
- upstream = anything before the +1 site (actual start of transcription)
- downstream = anything after the +1 site
33
what 3 RNA polymerases do eukaryotes have?
RNA polymerase 1, 2 and 3
34
what does RNA polymerase 1 do?
transcribes large rRNAs (structural/catalytic components of ribosomes)
35
what does RNA polymerase 2 do?
transcribes pre-mRNA, snRNAs (spliceosomes & tRNA/rRNA modification) and miRNAs (block complementary mRNA expression)
36
what does RNA polymerase 3 do?
transcribes tRNA, small rRNAs, certain snRNAs and miRNAs
37
where is the TATA box in eukaryotic transcription for RNA polymerase 2, and why?
at -25 sequence (because TFIIB recognition site is at -35)
38
what does the RNA polymerase 2 promoter consist of?
regulatory promoter (before -35) and core promoter (-35 to +30 - core promoter element)
39
who discovered RNA polymerase 2 structure/function?
Roger Kornberg
40
what is the inhibitor of RNA polymerase 2 called?
alpha amanitin (inhibits at both initiation & elongation)
41
what are the 3 main steps of transcription for both prokaryotes and eukaryotes?
1. initiation
2. elongation
3. termination
42
due to prokaryotes continuous coding region, how does that affect the mRNA/protein generated?
(amino acids -----> codons on mRNA -----> genes on DNA)
transcription translation
- no additional processing steps are required to form mRNA
43
what is the mRNA sequence that is only in prokaryotes?
the shine-dalgarno sequence = 5' UAAGGAGGU 3'
44
due to introns & exons in eukaryotes, how does that affect the mRNA/protein generated?
removal of introns (by RNA splicing) & additional RNA processing steps required to form mRNA
45
what are exons and introns?
- exons = protein coding segments
| - introns = non-coding segments
46
what are the 3 eukaryotic pre-mRNA processing steps?
1. addition of 5' cap
2. addition of 3' poly A tail
3. removal of introns
47
what is a spliceosome made of?
snRNPs U1, U2, U4/6 and U5
48
what is the 5' splice site on an intron?
"GU"
49
what is the branch site on an intron?
a single "A" in middle of intron
50
what is the 3' splice site on an intron?
"AG"
51
what is lariat formation?
linkage between the 5' phosphate of "G" (in 5' splice site) and the 2' OH of the "A" (branch site)
52
how can one gene code for many proteins?
different modes of splicing and multiple intron 3' cleavage sites produces different mRNAs from a single pre-mRNA
53
what are 3 types of RNA editing?
1. changing structures of individual bases
2. modification of mRNA by guide RNAs
- guide RNA adds nucleotides to mRNA that weren't encoded by DNA
3. insertion or deletion of uridine monophosphates
54
what is the function of tRNAs?
carries the anti-codon for the mRNA's codon, and the respective amino acid (attached to it's 3' end - ALWAYS ACC)
55
what is the function of rRNAs?
- key component of the ribosome (composed of large and small subunit)
56
what is the function of the ribosome?
RNA machine that forms peptide bonds between amino acids in protein synthesis
57
where does rRNA synthesis occur in eukaryotes and prokaryotes?
- eukaryotes = nucleolus
| - prokaryotes = has no nucleolus, so in cytoplasm
58
what are the eukaryotic ribosome subunits?
60S (large) subunit + 40S (small) subunit = 80S ribosome
59
what are the prokaryotic ribosome subunits?
50S (large) subunit + 30S (small) subunit = 70S ribosome
60
who discovered "one gene, one colinear polypeptide"?
beadle & tatum
| - yanofsky discovered that nucleotide triplets corresponded to amino acid sequence in a protein
61
why is the genetic code a triplet code?
because 4 bases ^ (3 codons) = 64 (more than enough to encode all amino acids)
- single and double codons = 4 and 16 (not enough for 20 amino acids)
62
who discovered that the genetic code is triplet?
crick & colleagues (generated "crick's wobble hypothesis")
63
what feature of the triplet code explains degeneracy?(more than 1 codon for an amino acid)
the 3rd codon position is a "wobble" codon
64
what is crick's wobble hypothesis?
that base pairing only really occurs between the first 2 codons
65
how does the amino acid get linked to the tRNA?
using the aminoacyl tRNA synthetase (there is one for each amino acid, therefore 20)
66
what are the 3 main steps in prokaryotic & eukaryotic translation (protein synthesis)?
1. initiation
2. elongation
3. termination
67
what are the 3 sites in the ribosome?
```
A = aminoacyl site (tRNA binds to mRNA)
P = peptidyl site (formation of peptide bonds between AA)
E = exit site (where empty tRNA leaves)
```
68
how does the aminoacyl tRNA synthetase work?
1. AA reacts w/ ATP, producing AMP + PPi (AMP binds to COO- on AA)
2. tRNA binds to COO- of amino acid kicking off AMP
69
who discovered the ribosome structure & how it operates during protein synthesis?
ramakrisham, steitz and yonath
70
what is quality control of RNA and proteins?
eliminating mRNAs with errors
71
what are the 3 types of eliminations of mRNAs (for quality control of RNA/proteins)?
1. mRNAs with nonsense mutations
2. mRNAs where ribosome can't complete translation
3. chemically damaged mRNAs
72
what are the types of mutations?
- point mutations (base substitutions, frameshift mutations, and tautomeric shifts)
- expanding nucleotide repeats
73
what is a pyrimidine?
T & C
74
what is a purine?
A & G
75
what are the base substitutions?
1. transition = pyrimidine to pyrimidine OR purine to purine
| 2. transversion = pyrimidine to purine (vice versa)
76
how many base substitutions are there?
12
77
what is a frameshift mutation?
inserting/deleting ONLY 1 or 2 base pairs (alters entire reading frame downstream of mutation)
78
what is a tautomeric shift?
movement of H atoms from one position on a purine/pyrimidine to another
- generates rare AC and GT base pairing
79
what are expanding nucleotide repeats?
- dynamic mutation caused by errors in replication
| - repeating triplet codons causes part of strand to be replicated twice
80
what is a forward mutation?
changes wild-type phenotype to mutant
81
what is a reverse mutation?
changes a mutation back to wild-type phenotype
82
what is a missense mutation?
base substitution = amino acid changes
83
what is a nonsense mutation?
base substitution = amino acid changes to stop codon
84
what is a silent mutation?
base substitution = amino acid unaffected
85
what is a neutral mutation?
missense where AA change has no effect on protein
86
what is a loss of function mutation?
mutation that causes complete/partial loss of normal protein function
87
what is a gain of function mutation?
mutation that produces a protein that isn't normally present
88
what is a conditional mutation?
only produced under certain conditions (ex. temp)
89
what is a lethal mutation?
mutation that results in premature cell death
90
what is a suppressor mutation?
second site mutation in a gene that hides or restores a first mutation back to normal (ex. amino acid changes, but is then restored)
91
what are the 2 types of suppressor mutations?
1. intragenic = in same gene
| 2. intergenic = in separate genes
92
what are the rates for spontaneous gene mutations? (hint: they're infrequent)
- prokaryotes = 10^-8 to 10^-10 per nucleotide pair/generation
- eukaryotes = 10^-7 to 10^-9 per nucleotide pair/generation
93
what factors can mutations come from?
- internal factors = spontaneous
| - external factors = induced (ex. radiation/chemicals)
94
how is DNA usually damaged?
by internal factors such as hydrolysis, oxidation, or alkylation
95
in what ways does spontaneous DNA damage occur?
1. DNA replication errors
2. DNA replication pausing
3. endogenous chemical reactions
96
what are examples of DNA replication errors?
- tautomeric shifts
- transition mutations induced by wobbling
- strand slippage in repeated sequences
97
what are examples of DNA replication pausing?
stalling at a nick (due to ROS, etc)
98
what are examples of endogenous chemical reactions?
- depurination = loss of purine through hydrolysis (leaves AP site - can lead to transition/transversion mutations)
- deamination = loss of NH2 (cause transition mutations)
- oxidation = ROS damage to DNA (causes transversion mutations)
- alkylation = adds methyl groups to bases (causes transition mutations)
99
who discovered induced mutations (DNA damage)?
hermann muller discovered you can induce mutations in fruit flies using x-rays
100
what are the chemical agents that can induce mutations in ALL DNA?
- alkylating agents
- nitrous acid
- hydroxylamine
101
how do alkylating agents induce mutations?
add methyl/ethyl groups to DNA bases (can cause transition, transversion, frameshift, and chromosomal mutations)
- examples = mustard gas, EMS, EES
102
how does nitrous acid induce mutations?
removes NH2 groups from the bases A, G, and C (causes transition mutations)
103
how does hydroxylamine induce mutations?
adds OH group to C causing it to pair with A (transition mutation)
104
what are the chemicals that can induce mutations in ONLY replicating DNA?
- base analogs = 5-BU, resembles T & 2-AP, resembles A/G (causes transition mutations)
- acridine dyes = causes frameshift mutations during DNA replication by inserting in between DNA bases (ex. proflavin or acridine orange)
105
what are the mutations induced by radiation?
- UV causes thymine dimers to form (blocks DNA replication & causes DNA breaks)
- Xray induces mutations through ionization (causes nicks & double strand breaks)
106
what are the 6 DNA repair mechanisms?
1. direct reversal of DNA damage
2. base excision repair
3. nucleotide excision repair
4. mismatch repair
5. recombination
6. translesion DNA polymerases
107
what is direct reversal of DNA damage?
- direct repair of thymine dimers by photolyase (only in prokaryotes)
- enzymes removing alkyl groups from DNA bases
- repairing nicks in DNA with ligase
108
what does base excision repair do?
specifically recognizes & repairs damaged DNA bases (found in prokaryotes & eukaryotes)
109
what does nucleotide excision repair do?
removes thymine dimers (entire strand & re-synthesizes) and bulky DNA damage
110
what does mismatch repair do?
recognizes mismatched bases in new strand by identifying hemi-methylated GATC sequence
- defects in mismatch repair results mutation accumulation
111
what does recombination do?
repairs spontaneous/induced double strand breaks
- homologous = occurs after DNA replication (damaged sister chromatid can be fixed by the other)
- non-homologous = uses proteins to repair double strand breaks
112
what do translesion DNA polymerases do?
replicate through DNA damage (bypassing lesion) so normal replication can occur
- error prone
113
what are transposable elements?
- jumping genes (40% of human genome)
- major source of mutations
- can carry antibiotic resistance genes
114
what are the 3 types of transposable elements?
1. cut and paste
2. replicative transposons
3. retrotransposons
115
what are cut and paste transposons?
1. IS elements
| 2. composite transposons
116
what are IS elements composed of?
- gene that encodes a transposase
- terminal inverted repeats (at both ends)
- target site duplication (after repeats, at both ends)
117
how do IS elements work as cut and paste transposons?
1. staggered cuts are made in DNA so that a transposable element can insert itself
2. due to staggered cuts, the gaps filled in by DNA pol. create direct repeats
- can mobilize anti-biotic resistant DNA during homologous recombination
118
how do composite transposons work?
created when 2 IS elements near each other (separated by a gene) trap a segment of anti-biotic resistant DNA
119
what is an example of replicative transposons (hint: found in bacteria)?
Ex. Tn3 which can carry anti-biotic resistant genes
1. Tn3 is replicated to form co-integrate structure
2. recombination of co-integrate structure separates into 2 separate DNAs (each with a copy of Tn3)
120
who discovered transposons?
Barbara McClintock when studying chromosome breakage in corn (discovered cut and paste Ds and Ac transposable elements)
121
what are retroviruses & retrotransposons?
use reverse transcriptase to copy retroviral RNA into DNA
| - ex. of retrovirus = HIV/AIDS
122
what are retroviruses made of?
- gene that encodes reverse transcriptase/integrase (copies RNA into DNA)
- terminal inverted repeats & target site duplication
123
what are retrotransposons made of?
- gene that encodes reverse transcriptase/endonuclease
- contains poly A tail
- has no terminal inverted repeats
124
what is a long interspersed nuclear element (LINE) made of?
ex. L1 element
- contains promoter, 2 reading frames (one encodes nucleic acid binding protein, other encodes protein with endonuclease/reverse transcriptase)
125
what is a short interspersed nuclear element (SINE)?
- only the Alu element can move around
- do not encode proteins
- reverse transcriptase required is provided by a LINE
126
what are the major transposable elements in humans?
LINEs and SINEs account for 33% of transposons in genome
127
what are the minor transposable elements in humans?
- defective retroviruses
| - cut and paste transposon related elements
128
what are the genetic/evolutionary significances of transposons?
1. they're mutagens
2. they can mobilize foreign genes (ex. anti-biotic resistant genes)
3. they can change genome organization
129
what are the 3 types of changes in genome organization (homologous recombination) by transposons?
1. transposable elements in same direction will form a loop when crossing over = deletion
2. transposable elements in opposite direction will form a bend = inversion
3. unequal exchange between transposable elements = one chromosome has a deletion, other chromosome has a duplication
130
what is an example of an induced gene?
when lactose is present & glucose is absent, gene expression for lac operon is induced (enzymes involved in breakdown are often inducible)
131
what is an example of a repressed gene?
when tryptophan is present, genes that make tryptophan are repressed
132
what does an operon consist of?
promoter, operator, and series of structural genes
| - also a regulator protein, which helps control gene expression
133
what is a negative inducible operon?
the lac operon
- no lactose = regulator protein is active and is able to bind to operator to stop transcription
- lactose = regulator protein is inactivated by lactose and is unable to bind to operator (transcription occurs)
134
what is a negative repressible operon?
the trp operon
- no tryptophan = regulator protein is inactive and is unable to bind to operator (transcription occurs)
- tryptophan = regulator protein is activated by tryptophan and binds to operator to stop transcription
135
what is positive control of gene expression?
an "activator" - type of regulatory protein (binds to DNA to assist RNA polymerase with transcription)
136
when are the lac operon genes expressed?
ONLY when lactose is present, and glucose is ABSENT
137
who discovered the lac operon of E. coli?
jacob & monod
138
how does the lac operon have ON and OFF characteristics?
- ON in the presence of allolactose (lac repressor is inactivated by allolactose so transcription of Z, Y, and A genes occurs)
- OFF in the absence of allolactose (lac repressor is active because no allolactose so it binds to lac operator, halting transcription of Z, Y, and A genes)
139
what are the main mutations in the lac operon? (hint: constitutive expression)
I- or Oc results in Z, Y, and A genes always being transcribed (constitutive expression) because I- can't bind to operator and Oc blocks repressor from binding (I gene)
- Oc only works if its connected in cis
- I+ is dominant to I-
140
what are other mutations in lac operon? (hint: no transcription)
- lacIs = lacI repressor always bound to operator (no transcription)
- lac P mutation = RNA polymerase can't bind (no transcription)
141
how does the cAMP/CAP complex (regulated by glucose) regulate the lac operon?
- high glucose = low cAMP (cAMP/CAP complex not formed = no binding to lac promoter, no promotion of RNA polymerase binding - no transcription)
- low glucose = high cAMP (cAMP/CAP complex formed = binding to lac promoter, promotion of RNA polymerase binding - transcription occurs)
142
why is cAMP/CAP complex formed or not formed at certain glucose levels?
- cAMP/CAP not formed when glucose is high because it has sufficient glucose (doesn't need to produce enzymes to break down lactose)
- cAMP/CAP formed when glucose is low because it doesn't have sufficient glucose (needs to produce enzymes to break down lactose for energy)
