Unit 2 Flashcards

Question

Chromatin

Answer 1

Histones packaged into 30 nm fiber Involves supercoiling

Answer 2

Bind across methylated histones Inaccessible Transcription can't occur Marked by methylation

Answer 3

Accessible Transcription can occur Marked by acetylation

Answer 4

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

Answer 5

Catalyze nucleotide addition Requires stretch of primer

Answer 6

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

Answer 7

Short stretch of RNA annealed to template Facilitates addition of complementary base pairs Takes advantage of energy of base stacking

Answer 8

Tautomerization Wobbles

Answer 9

Normal bases that bind inappropriately due to shift in position of nucleotides

Answer 10

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

Answer 11

Add nucleotides via polymerase domain Remove mismatches via exonuclease domain

Answer 12

Destabilization of DNA structure Adopt conformation that moves 3' end into exonuclease site

Answer 13

3' end enters exonuclease site Terminal nucleotide removed Polymerase gets 2nd chance

Answer 14

Main replicative polymerase Built for speed Copies entire genome Built for processivity

Answer 15

Odd jobs Polymerizes small stretches as part of cleanup/repair Built for accuracy

Answer 16

Origin of replication

Answer 17

Melt and unwind DNA

Answer 18

Synthesize small RNA sequence as a primer for DNA Pol III

Answer 19

Continuous synthesis Parent 3' end on the bottom left

Answer 20

Discontinuous synthesis Parent 3' end on the top right

Answer 21

Fragments that make up discontinuous strand

Answer 22

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

Answer 23

Seals nicked DNA fragments

Answer 24

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

Answer 25

Keep ssDNA from reannealing

Answer 26

Sequence of repetitive sequences at the ends of chromosomes

Answer 27

Carries RNA fragment Template DNA synthesis at end of telomere on parental strand Prevent shortening of strands

Answer 28

Proofreading missed a mistake Modified base leads to incorrect pairing

Answer 29

Mark parental strand with methylation marks

Answer 30

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

Answer 31

Add methyl or ethyl groups to nucleobase

Answer 32

Replace amine with carbonyl group on nucleobase Thymine is immune

Answer 33

Loss of entire purine base from nucleotide

Answer 34

Adjacent Thymines and Cytosines become cross linked into dimers Distorted structure Misread by Polymerase

Answer 35

Direct repair

Answer 36

Base excision repair

Answer 37

Base excision repair

Answer 38

Nucleotide excision repair

Answer 39

Alkyl groups transferred to alkyltransferase Group is permanently attached to protein 1 Protein sacrificed per repair

Answer 40

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

Answer 41

Convert base into abasic site with glycosylase enzyme Repair site with base excision repair mechanism

Answer 42

Polymerase extend past abasic site Old part is displaced and cleaved Ligase seals the new strand

Answer 43

Old part removed by lyase Abasic site filled in by polymerase Ligase seals the strand

Answer 44

RNA is more susceptible to degradation

Answer 45

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

Answer 46

Enzyme that cleaves the phosphodiester backbone within a nucleotide chain

Answer 47

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

Answer 48

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

Answer 49

Very specific sequences used Highly controlled w/ predictable outcomes

Answer 50

2 sequential single strand breaks Holliday junction intermediate

Answer 51

Two double strand breaks introduced simultaneously No holliday junction

Answer 52

Mobile DNA elements that move around the genome Insertions may or may not occur Cause changes in gene expression of inserted into coding region

Answer 53

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

Answer 54

Cut/paste DNA transposon DNA sequence is excised and pasted elsewhere in the genome

Answer 55

Used to make RNA copy of coding strand

Answer 56

Strand of interest that you want to copy into RNA

Answer 57

Catalyzes RNA synthesis from DNA templates Doesn't need a primer Catalyzes own helicase activity

Answer 58

No exonuclase site Can backtrack to proofread Active site for polymerization acts as nuclease and cleave strands

Answer 59

Specifies where RNA polymerase will start transcription Specific sequences at defined distances from intended start site

Answer 60

In bacteria Recognizes specific sequence of DNA that defines a promoter Changing the sigma factor changes which sequences are transcribed

Answer 61

3 forms, each with own initiation specialty Regulated by other elements and sequences

Answer 62

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)

Answer 63

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

Answer 64

Repressor binds to operator;specific sequence that overlaps with promoter RNA pol is prevented from transcribing the lactose gene

Answer 65

Lactose binds repressor and blocks DNA binding Repressor converted to inactive form → does not bind RNA pol can bind and initiate transcription

Answer 66

Binds to CAP Increases when glucose decreases

Answer 67

Binds to promoter and stimulates RNA pol recruitment (activator)

Answer 68

Is needed to assemble RNA pol at promoter

Answer 69

Recruit coactivators Bind to enhancer elements

Answer 70

Block coactivator recruitment Block activator binding to DNA Recruit corepressors

Answer 71

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

Answer 72

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

Answer 73

Histone methylation compacts the genome Histone acetylation opens up the genome

Answer 74

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

Answer 75

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

Answer 76

Methyl mark does not interfere with base pairing Inhibits transcription New methylation marks added by de novo methyltransferases Permanently silence areas of genome

Answer 77

Contains info to make a specific protein sequence via translation

Answer 78

sequences removed from RNA transcript

Answer 79

sequences that remain in RNA transcript, are expressed

Answer 80

In the nucleus By the spliceosome

Answer 81

7 methyl guanosine cap Aids in formation of translation initiation complex Protect 5’ end from degradation Signals for export out of nucleus

Answer 82

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

Answer 83

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

Answer 84

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

Answer 85

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

Answer 86

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

Answer 87

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

Answer 88

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

Answer 89

Destruction and degradation of target mRNA Irreversible

Answer 90

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

Answer 91

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

Answer 92

Sanger sequencing Next generation/high throughput sequencing techniques

Answer 93

Plasmid based gene expression systems CRISPR/Cas9 genome modification

Answer 94

Going from mRNA to protein

Answer 95

Redundant Universal Triplet codons

Answer 96

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

Answer 97

Amino acid activated by adenylation of carboxyl group tRNA synthetase selects matching tRNA and transfers amino acid to tRNA 3’ OH

Answer 98

First 2 bases create coding specificity Third base does not make strong interaction Does not need to be a perfect match

Answer 99

Consecutive, non overlapping codon sequences translated into a polypeptide

Answer 100

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

Answer 101

Change mRNA sequence to a synonymous codon

Answer 102

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

Answer 103

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

Answer 104

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

Answer 105

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

Answer 106

Scanning mechanism Ribosome assembles initiation complex

Answer 107

Holds tRNA with next amino acid

Answer 108

Holds tRNA with growing peptide

Answer 109

Holds tRNA that will exit

Answer 110

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

Answer 111

Occurs in N to C direction

Answer 112

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

Answer 113

Translation and transcription coupled Physical connection between transcription and translation allows for clever regulatory strategies

Answer 114

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

Answer 115

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

Answer 116

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

Answer 117

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

Answer 118

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

Answer 119

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

Unit 2 Flashcards

(145 cards)