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Bio Chem 501 > Unit 2 > Flashcards

Unit 2 Flashcards

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1
Q

Nucleoside

A

Base connected to sugar

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2
Q

Nucleotide

A

Base + Sugar + Phosphate

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3
Q

Phosphodiester Bond

A

Btwn nucleotides
Form backbone of nucleic acids
Covalent

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4
Q

Glycosidic Bond

A

Connection btwn base and sugar
Covalent

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5
Q

Hydrogen Bond

A

Form base pairs
Non covalent

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6
Q

Watson Crick Franklin Pairing

A

Anti/Anti
C+G
A+T

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7
Q

Hoogsteen Pairing

A

Syn/Anti
Exotic RNA structures

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8
Q

Purines

A

A and G
2 rings

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9
Q

Pyrimidines

A

C, T, and U
1 ring

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10
Q

DNA vs RNA

A

DNA lacks 2’ OH group

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11
Q

Ester Linkage

A

Attach phosphate to nucleoside

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12
Q

A + T

A

2 x H-bonds

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13
Q

G + C

A

3 x H-bonds

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14
Q

Base stacking interactions

A

van der Waals (btwn base faces)

pi stacking

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15
Q

B form structure

A

Anti parallel
Right handed
Backbone on outside
Bases on inside

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16
Q

Major groove

A

Wide and deep

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17
Q

Minor groove

A

Shallow and narrow

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18
Q

RNA preferred conformer

A

C3’ endo

C2’ endo causes sterics

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19
Q

DNA preferred conformer

A

C2’ endo

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20
Q

T melting

A

Temp at which the helix is 1/2 double stranded and 1/2 single stranded

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21
Q

Negative supercoiling

A

Lk < 0
DNA = underwound

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22
Q

Positive supercoiling

A

Lk > 0
DNA = overwound

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23
Q

Topoisomerase

A

Change DNA topology

Resolve supercoiling that develops when genome is locally unwound

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24
Q

Nucleosome

A

DNA wrapped around a histone

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25
Q

Chromatin

A

Histones packaged into 30 nm fiber

Involves supercoiling

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26
Q

Heterochromatin proteins

A

Bind across methylated histones

Inaccessible

Transcription can’t occur

Marked by methylation

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27
Q

Euchromatin

A

Accessible

Transcription can occur

Marked by acetylation

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28
Q

Chem mechanism of nucleotide addition

A

Base activates 3’ OH
3’ OH does nucleophilic attach on 5’ phosphate

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29
Q

Synthesis direction

A

5’ to 3’

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30
Q

DNA Polymerase

A

Catalyze nucleotide addition
Requires stretch of primer

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31
Q

Polymerase and Mg2+

A

Mg2+ facilitates chemistry
- Activates 3’OH
- Stabilize - charge of phosphate
- Mg2+ binds to Asp

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32
Q

Primer

A

Short stretch of RNA annealed to template

Facilitates addition of complementary base pairs

Takes advantage of energy of base stacking

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33
Q

DNA Polymerase Mistakes (2)

A

Tautomerization

Wobbles

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34
Q

Wobbles

A

Normal bases that bind inappropriately

due to shift in position of nucleotides

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35
Q

Tautomerization

A

Change into form where positions of H-bond donor/acceptor changes

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36
Q

DNA Polymerase Activities

A

Add nucleotides via polymerase domain

Remove mismatches via exonuclease domain

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37
Q

Incorrect base detection

A

Destabilization of DNA structure

Adopt conformation that moves 3’ end into exonuclease site

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38
Q

Incorrect base correction

A

3’ end enters exonuclease site

Terminal nucleotide removed

Polymerase gets 2nd chance

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39
Q

DNA Pol III

A

Main replicative polymerase

Built for speed

Copies entire genome

Built for processivity

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40
Q

DNA Pol I

A

Odd jobs

Polymerizes small stretches as part of cleanup/repair

Built for accuracy

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41
Q

Start of replication

A

Origin of replication

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42
Q

Helicase

A

Melt and unwind DNA

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43
Q

Primase

A

Synthesize small RNA sequence as a primer for DNA Pol III

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44
Q

Leading strand

A

Continuous synthesis

Parent 3’ end on the bottom left

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45
Q

Lagging strand

A

Discontinuous synthesis

Parent 3’ end on the top right

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46
Q

Okazaki fragments

A

Fragments that make up discontinuous strand

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47
Q

Lagging strand activities

A

Primase adds primer

Pol III extends DNA until encounter of next fragment

Primase + Pol III make fragments

Pol I removes primer + replaces with DNA

Ligase seals fragments

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48
Q

Ligase

A

Seals nicked DNA fragments

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49
Q

How does Ligase work

A
  1. Ligase uses ATP to adenylate itself
  2. AMP transferred to 5’ phosphate of nicked strand
  3. Phosphate has good LG
  4. Base catalyzed 3’ OH attack seals strand
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50
Q

Single stranded binding proteins

A

Keep ssDNA from reannealing

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51
Q

Telomere

A

Sequence of repetitive sequences at the ends of chromosomes

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52
Q

Telomerase

A

Carries RNA fragment

Template DNA synthesis at end of telomere on parental strand

Prevent shortening of strands

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53
Q

Main pathways to mutation

A

Proofreading missed a mistake

Modified base leads to incorrect pairing

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54
Q

Distinguish parent from daughter strand for repair

A

Mark parental strand with methylation marks

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55
Q

Mismatch Repair Pathway

A

Mismatch detected b MutL-MutS

DNA threaded through complex until encounter of MutH

Complex cleaves unmodified daughter strand

Nuclease and helicases degrade unmethylated strand

Gap filled in by DNA Pol III
Sealed by ligase

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56
Q

Alkylation

A

Add methyl or ethyl groups to nucleobase

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57
Q

Deamination

A

Replace amine with carbonyl group on nucleobase

Thymine is immune

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58
Q

Depurination

A

Loss of entire purine base from nucleotide

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59
Q

UV light induced dimerization

A

Adjacent Thymines and Cytosines become cross linked into dimers

Distorted structure
Misread by Polymerase

60
Q

Repair of Alkylation

A

Direct repair

61
Q

Repair of Deamination

A

Base excision repair

62
Q

Repair of Depurination

A

Base excision repair

63
Q

Repair of dimerization

A

Nucleotide excision repair

64
Q

Direct repair pathway

A

Alkyl groups transferred to alkyltransferase

Group is permanently attached to protein

1 Protein sacrificed per repair

65
Q

Base excision repair (Depurination)

A

AP nuclease recognizes abasic site
Nicks at site of damage

Free 3’ OH provides template for DNA polymerase to extend

Long or short patch pathway

Ligase seals strands

66
Q

Base Excision repair (Deamination)

A

Convert base into abasic site with glycosylase enzyme

Repair site with base excision repair mechanism

67
Q

Long patch

A

Polymerase extend past abasic site

Old part is displaced and cleaved

Ligase seals the new strand

68
Q

Short patch

A

Old part removed by lyase

Abasic site filled in by polymerase

Ligase seals the strand

69
Q

Why is the genome DNA

A

RNA is more susceptible to degradation

70
Q

Exonuclease

A

Enzyme that cleaves nucleotides one at a time from the end of a nucleic acid

71
Q

Endonucelase

A

Enzyme that cleaves the phosphodiester backbone within a nucleotide chain

72
Q

DNA Recombination

A

Process in which pieces of DNA are broken and reassembled to create new fragments

73
Q

Homologous Recombination

A

Occurs between any 2 homologous sequences

Leads to exchange of DNA material

Material in between the homologous sequences doesn’t need to be the same

74
Q

Sequence Specific Recombination

A

Very specific sequences used
Highly controlled w/ predictable outcomes

75
Q

Tyrosine Recombinase

A

2 sequential single strand breaks
Holliday junction intermediate

76
Q

Serine Recombinase

A

Two double strand breaks introduced simultaneously
No holliday junction

77
Q

Transponsons

A

Mobile DNA elements that move around the genome

Insertions may or may not occur

Cause changes in gene expression of inserted into coding region

78
Q

Class 1 Transponsons

A

Copy/paste

Sequence copied to an RNA intermediate that is used to make a second DNA copy for insertion

RNA intermediate

RNA transponson

79
Q

Class 2 Transponsons

A

Cut/paste

DNA transposon

DNA sequence is excised and pasted elsewhere in the genome

80
Q

Template Strand

A

Used to make RNA copy of coding strand

81
Q

Coding Strand

A

Strand of interest that you want to copy into RNA

82
Q

RNA Polymerase

A

Catalyzes RNA synthesis from DNA templates

Doesn’t need a primer

Catalyzes own helicase activity

83
Q

RNA Pol Proofreading

A

No exonuclase site

Can backtrack to proofread

Active site for polymerization acts as nuclease and cleave strands

84
Q

Promoter

A

Specifies where RNA polymerase will start transcription

Specific sequences at defined distances from intended start site

85
Q

Sigma factor

A

In bacteria

Recognizes specific sequence of DNA that defines a promoter

Changing the sigma factor changes which sequences are transcribed

86
Q

RNA pol in eukaryotes

A

3 forms, each with own initiation specialty

Regulated by other elements and sequences

87
Q

Rho dependent termination

A

RNA pol transcribes through a stretch of DNA that produces a binding site for Rho factor

Rho factor = helicase
Moves towards 3’ end
Climbs RNA until it reaches RNA/DNA anneal point
Rho unwinds RNA/DNA hybrid → terminates transcription
Helicases unwind DNA hybrids (peel off RNA from DNA)

88
Q

Rho independent termination

A

RNA polymerase transcribes through a stretch of DNA that makes

  • A G/C rich region that adopts a hairpin structure (form base pairs with itself)
  • A U rich segment downstream of hairpin
  • Hairpin causes RNA pol to stall

U rich region has weak base pairing interaction with template strand

Stall + weak interaction cause RNA pol to fall off

89
Q

Lac Operon

If lactose is absent

A

Repressor binds to operator;specific sequence that overlaps with promoter

RNA pol is prevented from transcribing the lactose gene

90
Q

Lac Operon

If lactose is present

A

Lactose binds repressor and blocks DNA binding

Repressor converted to inactive form → does not bind

RNA pol can bind and initiate transcription

91
Q

cAMP

A

Binds to CAP

Increases when glucose decreases

92
Q

CAP

A

Binds to promoter and stimulates RNA pol recruitment (activator)

93
Q

Basal machinery

A

Is needed to assemble RNA pol at promoter

94
Q

Eukaryotic

Activators

A

Recruit coactivators
Bind to enhancer elements

95
Q

Eukaryotic

Repressors

A

Block coactivator recruitment
Block activator binding to DNA
Recruit corepressors

96
Q

How side chains read DNA

A

Hydrogen bonds form between specific amino acids and nucleotide bases

Based on patterns of donors and acceptors

Proteins can read bases without having to melt DNA

Use the major groove to read DNA

97
Q

Epigenetics

A

Changes to gene expression not caused by change in DNA sequence itself

98
Q

Chromatin Modification

A

Histone methylation compacts the genome

Histone acetylation opens up the genome

99
Q

Histone acetylation

A

Acetylated on lysine residues by HATs
Removed by HDACs
Associated with active gene expression
Reduces affinity of histones for DNA
Remove positive charge on lysine
Directly recruit activators

100
Q

Histone methylation

A

Methylated on lysines by histone methyltransferases
Removed by histone demethylases
Associated with inactive gene expression

101
Q

5 methyl cysteine

A

Methyl mark does not interfere with base pairing

Inhibits transcription

New methylation marks added by de novo methyltransferases

Permanently silence areas of genome

102
Q

mRNA

A

Contains info to make a specific protein sequence via translation

103
Q

Intron

A

sequences removed from RNA transcript

104
Q

Exon

A

sequences that remain in RNA transcript, are expressed

105
Q

Splicing is performed

A

In the nucleus
By the spliceosome

106
Q

5’ cap

A

7 methyl guanosine cap

Aids in formation of translation initiation complex

Protect 5’ end from degradation

Signals for export out of nucleus

107
Q

3’ Poly A tail

A

Poly tail added by PAP
Signal sequence recruits enzyme to add tail
Stabilize mRNA
Promote translation
Signal to export out of nucleus

108
Q

Reason for RNA modification

A

Many ways to splice mRNA
Can get different flavors or proteins from 1 mRNA strand
Processing is proof that your cells produced the mRNA

109
Q

Spliceosome

A

Complex machine of proteins and snRNAS (non coding)
Ribonucleoprotein (RNP)

110
Q

Splicing steps

A

2’ OH from ribose within intron cleaves backbone at 5’ splice site

Free 3’ OH of the 5’ first exon attacks phosphate connecting intron to second exon
Release lariat

111
Q

Group 1 introns

A

Use free guanosine nucleotide to initiate cleavage

3’ OH on guanosine attack phosphate at 5’ splice site
3’ OH of exon attacks phosphodiester attack at 3’ exon
Release linear fragment as the intron

112
Q

Group 2 Intron

A

Use adenosine to initiate cleavage
2’ OH of adenosine attacks 5’ splice site
3’ OH of 5’ exon does attack of backbone at 3’ exon
Release lariat as the intron

113
Q

MicroRNA

A

22 nucleotide genome encoded RNAs
Regulate gene expression
Base pairing used to locate miRNA targets

114
Q

miRNA perfect match

A

Destruction and degradation of target mRNA
Irreversible

115
Q

miRNA imperfect match

A

Repression but not destruction
RNA stored in P-body structures
Reversible

116
Q

Techniques for making synthetic DNA

A

Chemical synthesis of short oligonucleotides
PCR to amplify DNA fragments
Assembly of DNA fragments and cloning of synthetic genes

117
Q

Techniques for reading out sequence of DNAs

A

Sanger sequencing
Next generation/high throughput sequencing techniques

118
Q

Modifying the biology of living systems using synthetic DNA

A

Plasmid based gene expression systems

CRISPR/Cas9 genome modification

119
Q

Translation

A

Going from mRNA to protein

120
Q

Genetic code

A

Redundant
Universal
Triplet codons

121
Q

tRNA

A

Adapter molecule that links triple codon to its associated amino acid

Amino acid held by 3’ end

Use WCF base pairing to read codons in mRNA

122
Q

Addition of amino acid to tRNA

A

Amino acid activated by adenylation of carboxyl group

tRNA synthetase selects matching tRNA and transfers amino acid to tRNA 3’ OH

123
Q

Wobble base pairs

A

First 2 bases create coding specificity

Third base does not make strong interaction

Does not need to be a perfect match

124
Q

Reading frame

A

Consecutive, non overlapping codon sequences translated into a polypeptide

125
Q

Missense mutation

A

Change mRNA sequence from a codon for 1 amino acid to a codon for a different amino acid

126
Q

Silent mutation

A

Change mRNA sequence to a synonymous codon

127
Q

Nonsense mutation

A

Change mRNA sequence form a codon for an amino acid to a stop codon

Terminate translation

128
Q

Frameshift mutation

A

Disrupt normal reading frame by inserting or deleting nucleotides that are not in multiples of 3

Give entirely different sequence

129
Q

Ribosome

A

Initiates synthesis at start codon
Forms peptide bonds between amino acids to make a polypeptide
Terminates synthesis at the stop codon

130
Q

Prokaryote translation iniation

A

Base pairing between ribosome RNA and mRNA at shine dalgarno positions ribosome at intended start codon

131
Q

Eukaryote translation initation

A

Scanning mechanism
Ribosome assembles initiation complex

132
Q

A site

A

Holds tRNA with next amino acid

133
Q

P site

A

Holds tRNA with growing peptide

134
Q

E site

A

Holds tRNA that will exit

135
Q

Translation condensation rxn

A

A site N amine attacks P site ester linkage to the C end

136
Q

Translation direction

A

Occurs in N to C direction

137
Q

Translation termination

A

Release factor (protein) recognizes stop codon and promotes peptide release + translation termination

138
Q

Prokaryote translation regulation

A

Translation and transcription coupled

Physical connection between transcription and translation allows for clever regulatory strategies

139
Q

Eukaryotes translation regulation

A

Block interaction between 5’ cap and capping protein
Decapp enzymes
Binding proteins can prevent formation of initiation complex
Enzymes trim or remove poly A tail

140
Q

Oligonucleotides

A

Chemically synthesized
10-80 nucleotides
Chemical synthesis is fast, easy, cheap
Solid state

141
Q

PCR

A

Amplify sequence of interest
Use pair of primers
Copied DNA spans btwn priming sites

142
Q

Gibson assembly

A

Makes uses of cocktail of enzymes
Mimic recombination reaction
Produce free overhangs

143
Q

Sanger method

A

Exploit nucleotide structure to read DNA sequence
Incorporate di-deoxynucleotide into DNA
No 2’ OH or 3’ OH

144
Q

CRISPR/Cas9

A

Endonuclease that is programmed by RNA sequence that tells it what to cut

Use WCF base pairing between guide RNA and dsDNA to locate target

Test dsDNA makes protein/DNA interaction with a short sequence (PAM)

Extensive base pairing leads to cleavage

145
Q
A

Bio Chem 501 (4 decks)

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