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Central dogma/DNA replication > DNA replication > Flashcards

DNA replication Flashcards

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1
Q

B-DNA

A
  • “normal” DNA
  • Right handed
  • Pitch: 35 A (10.4 bp)
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2
Q

A-DNA

A
  • Right handed
  • shorter/wider than B-DNA
  • Pitch: 25.3 A
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3
Q

Z-DNA

A
  • Left handed
  • Tall, narrow
  • Pitch: 45.6 A
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4
Q

Supercoiling

A
  • DNA in the cell must be organized
    • Allows for packing of large DNA molecules within the cells
    • Allows for access of proteins to read the information in DNA sequence
  • Many circular DNA are supercoiled
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5
Q

L

A
  • linking number
  • number of times strands go around each other; number of times plane is crossed
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6
Q

T

A
  • twist
  • number of turns of double helix
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7
Q

W

A
  • writhe
  • number of times the double helix wraps around itself
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8
Q

L,T,W association in closed system

A
  • L=T+W
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9
Q

Relaxed DNA

A
  • W =0
  • L=T=# of bp divided by 10.4
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10
Q

(negatively) supercoiled DNA

A
  • W ≠ 0 ⇒ compacted DNA
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11
Q

How to change linking # of circular or closed DNA

A
  • Cut, twist, reattach
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12
Q

Function of topoisomerases

A
  • change the linking number
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13
Q

Type I topoisomerases

A
  • Add negative supercoils
  • Cleave 1 strand
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14
Q

Type II topoisomerases

A
  • Remove negative supercoils
  • Cleave 2 strands
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15
Q

OriC

A
  • In E coli: one origin of replication/chromosome
  • 245 bp
  • highly conserved sequence elements
  • Binding site for initiator protein: DnaA
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16
Q

ARS

A
  • In eukaryotes
  • Approx. 400 well defined origins
  • Entire genome replicated 1X/cycle
    • Regulation due to cyclin proteins and cyclin-dependent kinases (CDKs)
    • Cyclins are ubiquinated for proteolytic destruction at the end of the M (mitosis) phase
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17
Q

OriC and ARS similarities

A
  • A,T rich
  • easy to “melt” DNA into single strands
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18
Q

Helicase

A
  • Melts double stranded DNA
  • Use ATP
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19
Q

Primase

A
  • Make RNA primers
  • RNA primers are added first to replicating strand; later removed
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20
Q

DNA polymerase I

A
  • Replaces RNA primer with DNA
  • 5’ to 3’ exonuclease activity
  • Not ideal for replication
  • Slow, low processivity
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21
Q

DNA polymerase III

A
  • Principal replication polymerase
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22
Q

Ligase

A
  • Seals “knicks”
  • Puts Okazaki fragments together
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23
Q

Telomerase

A
  • replicates telomeres
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24
Q

Topoisomerase I

A
  • Behind replication fork (on 2 daughter DNA)
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25
Q

Topoisomerase II

A
  • Ahead of replication fork (on parent DNA)
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26
Q

Leading strand synthesis

A
  • Replicated continuously
  • DNA polymerase 𝛅
  • DNA polym III in prokaryotes
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27
Q

Lagging strand synthesis (what and proteins)

A
  • Generated in small steps
    • Okazaki fragments
  • Priamse: makes 15 bp RNA primer for each okazaki fragment
  • DNA polym. III
    • Does all leading strand synthesis
    • Makes DNA from from 1 primer to the next on lagging strand
  • DNA polym. I
    • Replaces RNA in primer with DNA
  • Ligase
    • Seals knicks
  • Single stranded binding proteins
    • Stabilize single stranded DNA
    • Prevent strands from sticking back together
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28
Q

Subunits

A
  • 20 individual peptides combined
    • In pol III: 10 types of subunits
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29
Q

Homotetramer

A
  • 4 identical subunits
  • “Same” “four”
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30
Q

Heteropentamer

A
  • 2 or more different monomers
  • “Different” “five”
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31
Q

Holoenzyme

A
  • does most DNA synthesis activity
  • proofreading capabilities that correct replication mistakes by means of exonuclease activity working 3’→5’
  • high processivity (i.e. the number of nucleotides added per binding event)
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32
Q

Central structure

A
  • hold 2 holoenzymes together and allows them to move together
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33
Q

a subunit

A
  • catalytic subunit
  • Has a groove for DNA to slide along and active site where nucleotides are added
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34
Q

e subunit

A
  • proofreading subunit
  • Just behind a; removes incorrect nucleotides
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35
Q

b subunit

A
  • processivity subunit/beta-clamp
  • Forms “donut” around DNA to prevent pol III from falling off
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36
Q

What is crossing over?

A
  • The exchange of genetic material between homologous chromosomes that results in recombinant chromosomes during sexual reproduction
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37
Q

When does crossing over occur?

A
  • Prophase I (meiosis)
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38
Q

Quartenary stucture of pre-recombinase

A
  • homotetramer
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39
Q

How does Cre recombinase work?

A
  • catalyzes site specific recombination between 2 DNA recognition sites
  • cyclic recombination
  • @ LoxP sites (8 bp sequence with 34 bp palindromic sequences on either side)
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40
Q

What do tyrosine resiudes do in cre recombinase?

A
  • nucleophilic attack on phosphate bonds of DNA
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41
Q

How is cre recombinase similar to topoisomerase I?

A
  • forms covalent bonds between hydrogen bonds and tyrosine residues (how it controls strand breaks and combine DNA)
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42
Q

What is a mutation?

A
  • alteration in DNA structure that produce permanent changes in the genetic information encoded therein
43
Q

When do mutations take place?

A
  • during cell division (replication)
  • environmental factors
    • UV
    • chemical
    • viruses
44
Q

DNA damage vs mutation

A
  • mutation: affects nucleotide sequence (can’t be fixed)
  • Damage: damage to bonds, etc; abnormalities in DNA
    • can be fixed
45
Q

3 causes/types of DNA damage and the mutations they cause

A
  • UV light
    • pyrimidine dimers
  • Chemical damage
    • point mutation
  • Intercalating agents (insertion of molecule between DNA planes)
    • frameshift mutation
46
Q

3 steps of DNA repair

A
  1. Abnormal DNA is recognized
  2. abnormal DNA is removed (upstream and downstream)
  3. normal DNA is synthesized
47
Q

3 enzymes of DNA repair

A
  1. polymerase III
  2. Ligase
48
Q

What is an Ames test?

A
  • Indicates mutagenic potential of a compound
  • Add compound to plate of salmonella
    • see if it grows in His free medium
  • Colonies (+test) indicates the compound mutated the salmonella, restored ability to synthesize His
49
Q

Use of liver cells in Ames test

A
  • Can treat the compound with liver cells to turn it into a mutagen, to see if the body processes it into a mutagen
50
Q

RNA polymerase: quartenary structure in prokaryotes

A
  • 5 subunits (pentamer)
  • a: (2) assembly and binding to UP (upstream promoter) elements
  • B: main catalytic subunit
  • B’: responsible for DNA binding
  • o: directs enzyme to promoter
  • w: protect polymerase from denaturation
51
Q

What does RNA polymerase I transcribe in eukaryotes?

A
  • pre rRNA (turns into rRNA)
52
Q

What does RNA polymerase II transcribe in eukaryotes?

A
  • pre mRNA
  • some snRNAs
53
Q

What does RNA polymerase III transcribe in eukaryotes?

A
  • pre tRNAs
  • 5S rRNA
  • some snRNAs
54
Q

Initiation

A

RNA polymerase binds to promoter on DNA (by transcription factors in eukaryotes)

55
Q

Elongation

A
  • Elongation factors enhance activity of RNA polymerase
  • RNA polymerase reads template strand
  • Goes in 3’ to 5’ direction
56
Q

Termination

A
  • In bacteria: stops due to hairpin loop
  • In eukaryotes:cleavage of the new transcript followed by template-independent addition of adenines at its new 3’ end, in a process called polyadenylation
  • Pol II released
57
Q

Template strand

A
  • Non-coding
  • template for RNA polymerase
  • Antisense
58
Q

Coding strand

A
  • Non-template strand
  • has same sequence as RNA transcript
  • Sense
59
Q

Promoter

A

region of DNA that initiates transcription of a particular gene

60
Q

+1

A
  • 1 bp away from promoter
  • On coding strand
61
Q

Why different sigma subunits in prokaryotes

A
  • bind different promoters
  • transcribe unique set of genes
62
Q

What do transcription factors do?

A

proteins that bind DNA and regulate gene expression by promoting or suppressing transcription

63
Q

How are transcription factors named?

A
  • by what they do
64
Q

RNA Pol vs DNA Pol

A
  • One produces RNA, one produces DNA
  • RNA poly does not require primer
  • DNA faster than RNA pol
    *
65
Q

Protein dependent termination

A
  • C/A rich sequence called rut site
  • process continues until termination site reached
  • rho protein is a helicase, binds to rut site
66
Q

Protein independent termination

A
  • 3 U’s near 3’ end of transcript
  • self-complementary regions in transcript form hairpin 15-20 before 3’ end
    • makes RNA poly pause, then dissociate
  • C/G rich
67
Q

RNA Processing steps

A
  • Splicing out introns, leaving exons (pro/euk; mRNA)
  • Addition of 5’ cap (euk mRNA)
  • Addition of 3’ polyA tail (euk mRNA)
  • Clevage
  • Base modification
  • RNA editing
68
Q

rRNA processing

A
  • in pro/euk
  • created from longer pre-rRNA by cleavage/methylation
69
Q

tRNA processing

A
  • formed from pre-tRNA by cleavage, base modification, splicing
70
Q

Consensus sequence for polyadenylation

A
  • @ -10 and -30
  • betweem -40 and -60
71
Q

snRNA

A
  • snRNP (small nuclear ribonuclear proteins) RNAs
  • Part of spliceosome
72
Q

Spliceosome

A
  • U1 and U2 snRNPs bind intron’s ends (at 5’ and 3’ ends)
  • U2-6 bind along with other proteins to splice intron
73
Q

Tetrahymena

A

self splicing group I intron

74
Q

Two ways a cell can control which genes are expressed

A
  • Increase the affinity of the promotor for RNA polymerase
  • Make promotor physically more accessible → controlling DNA structure
75
Q

How do activators/repressors regulate transcription

A
  • bind promoter/release from promoter to allow or prevent transcription of genes
76
Q

Operon

A
  • functioning unit of DNA containing cluster of genes under the control of one promoter
  • Found in prokaryotes
77
Q

Chromatin

A
  • Tightly wound complex of DNA and histones to allow for control of DNA/gene expression
  • Remodeling only happens in eukaryotes
78
Q

What are histones?

A
  • proteins found in nuclei that package and order the DNA into structural units called nucleosomes
79
Q

Histone structure

A
  • core: 2(H2A, H2B, H3, H4)
  • H1: links nucleosomes to create chromatin
80
Q

Histone modifications

A
  • methylation
  • acetylation
  • Affect charge (DNA binding) or sturcture/condensation to activate or repress transcription
81
Q

Enhancer

A
  • region of DNA bound by proteins that activate transcription of a gene
82
Q

Silencer

A

DNA sequence capable of binding repressors

83
Q

Location of silencer/repressor

A
  • Can be anywhere, but usually upstream of target gene
84
Q

Location of activator/enhancer

A
  • could be up or downstream of gene
  • do not act on promoter region
85
Q
A

tRNA

86
Q

What do aminoacyl-tRNA synthetases do?

A
  • enzyme that attaches the appropriate amino acid onto its tRNA
  • By esterification of a specific cognate amino acid
87
Q

How do aminoacyl-tRNA synthetases determine genetic code?

A
  • Adds charged a.a. onto growing polypeptie chain
  • tRNA reads genetic code and adds new a.a according to genetic code
88
Q

Second genetic code

A
  • matching each a.a with correct tRNA (must be specific for each other) can be viewed as second genetic code
  • the “code” is in the molecular recognition of a specific tRNA molecule by a specific synthetase
89
Q

Wobble

A
  • pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules
  • allows some base pairs to bind more than one codon (3rd bp of codon)
90
Q

Ribosome structure

A

small and large subunits

91
Q

Ribosome small subunit

A
  • decoding center which monitors the complementarity of mRNA and tRNA
  • has APE sites for adding polypeptides
92
Q

Ribosome large subunit

A
  • contains active site (creates peptide bonds when proteins are synthesized)
93
Q

The directions in which mRNA is translated and proteins are synthesized

A
  • 5’ to 3’
  • N to C terminus
94
Q

3 steps of translation

A
  • Initiation
  • Elongation
  • Termination
95
Q

Initiation (translation)

A
  • mRNA and aminoacylated tRNA bind to ribosome
  • IF-1, IF-2, IF-3 (initiation factors)
  • FMet (forylmethothionine)
  • GTP
96
Q

Elongation (translation)

A
  • Cycles of aminoacyl-tRNA binding and peptide bond formation…until a STOP codon is reached
  • EF-TU (elongation factor Tu)
  • GTP
97
Q

Termination (translation)

A
  • mRNA and protein dissociate, ribosome recycled
  • RF-1, RF-2, RF-3 (release factors)
98
Q

Prokaryotes (translation)

A
  • Shine-Dalgarno sequence
  • Must be located for initiation
99
Q

Eukaryotes (translation)

A
  • Scanning
  • mRNA loops through ribosome
  • Binds 5’ cap
100
Q

MET vs FMET

A
  • FMET binds P site along with initiating AUG
  • MET in eukaryotes
  • FMET in prokaryotes
101
Q

EF-Tu

A
  • Aminoacyl tRNA binds to a complex of elongation factor Tu that also carries GTP
102
Q

EF-G

A
  • translocase
  • prokaryotic elongation factor with GTPase
  • catalyze the coordinated movement of tRNA and mRNA through the ribosome
  • Moves tRNA along to next site
103
Q

3 stop codons

A
  • UAA
  • UGA
  • UAG
  • Recognized by termination (release) factors/ribosome

Central dogma/DNA replication (1 decks)

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