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Fundamentals-Sarah > Replication, Transcription, Translation > Flashcards

Replication, Transcription, Translation Flashcards

1
Q

What are the major differences between DNA and RNA?

A

DNA–deoxyribose sugar, thymine

RNA-ribose sugar, uracil

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2
Q

what does dNMPs stand for?

A

Deoxynucleoside monophosphates

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3
Q

What are they four different DNA bases?

A

dAMP-deoxyadenosine
dGMP-deoxyguanosine
dCMP-deoxycytidine
dTMP-deoxythymidine

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4
Q

How do nucleotides link together?

A
  1. Base attaches to 1’ C of sugar by a glycosidic bond

2. Adjacent nucleotides connect by phosphodiester linkages formed between3’ and 5’ hydroxyls of pentose sugar

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5
Q

How does hydrogen bonding occur within the DNA double helix?

A

Purines hydrogen bond with pyrimidines

A with T and C with G

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6
Q

What does it mean that the two strands of DNA are antiparallel?

A

5’ end of one strand bonds with 3’ end of its complement strand

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7
Q

Where do the nitrogenous bases point? Why?

A

Inside the helix because they are hydrophobic

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8
Q

Where do the sugar phosphate backbones point?

A

Outside because they are hydrophilic

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9
Q

Explain the differences between A, B, and Z DNA

A

B DNA–predominates–double helix
A DNA–right handed hell that is shorter and wider (RNA structure)
Z DNA–left handed helix that’s longer and narrower

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10
Q

What is the function of a histone?

A

To help package DNA

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11
Q

Describe the structure of a histone

A

made of basic (arg and lys) amino acids

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12
Q

What does semiconservative replication mean?

A

the old strand serves as a template for the new strand for every round of replication

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13
Q

Why is DNA not conservative?

A

two entirely new strands were not made in the same round of replication

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14
Q

Describe the role of DNA polymerase

A

Carries out DNA synthesis and proof reads

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15
Q

what is the function of a sliding clamp

A

prevents DNA polymerase from falling off the template so that synthesis can happen more quickly

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16
Q

What is the function of helicase

A

to separate the double stranded DNA

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17
Q

What is the function of single stranded binding protein (ssBP)

A

prevents the DNA from reannealing once helicase has separated it

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18
Q

Once separated, superhelical stress occurs. What helps relieve this stress?

A

topoisomerases relieve stress ahead of the replication fork by cutting a strand and allowing it to unwind a little and reseal

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19
Q

Which way does DNA polymerase synthesize DNA

A

5’ to 3’

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20
Q

what is a primer?

A

short sequence of RNA already complementary to strand that will serve as a template

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21
Q

How does DNA polymerase begin

A

Recognizes primer and attacks 3’ hydroxyl

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22
Q

How does the final strand remove the RNA primer?

A

it is removed by the 5’ to 3’ exonuclease activity of DNA polymerase I

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23
Q

What are the gaps called on the lagging strand of DNA?

A

Okazaki fragments

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24
Q

What fills in the okazaki fragment gaps and removes the RNA primer?

A

DNA polymerase I

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25
Q

What is the function of ligase?

A

It seals the nicks left after DNA polymerase fills in the gaps on the lagging strand

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26
Q

What is the end replication problem?

A

Gaps that cannot be filled in at the end

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27
Q

How is the end replication problem solved?

A

Telomerase fixes it by extending the 3’ end of telomeres

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28
Q

Describe what telomerase does

A

an RNA dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material

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29
Q

How does smoking cause damage to DNA

A

oxidizes benzopyrene which then reacts with guanine residues forming bulky adducts

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30
Q

How does UV light cause damage to DNA?

A

causes formation of pyrimidine dimers which block replication and transcription

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31
Q

Nucleoside excision repair

A

acts on lesions causing large distortions like pyrimidine dimers

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32
Q

Base excision repair

A

acts on small lesions involving damage to one base

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33
Q

Mismatch repair pathway

A

fixes replication errors that escape proofreading

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34
Q

You always use undamaged strand as a template. This is the original strand. Once replicated, how can you tell which strand is the original?

A

Methylation of A bases (eventually new strand will have these too via addition by methylase)

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35
Q

Lynch Syndrome

A

impairs the mismatch repair pathway

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36
Q

Xerodermia pigmentosum

A

impairment of nucleotide excision repair

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37
Q

RNA polymerase

A

synthesizes mRNA 5’ to 3’

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38
Q

Promoter

A

RNA polymerase needs to recognize promoter to begin synthesis

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39
Q

Actions of RNA polymerase (4)

A

Search and bind promoters
Unwind DNA
Initiate polymerization
Detect termination signals

40
Q

What is the sense strand?

A

the coding strand

41
Q

What is the +1 base?

A

The first base of the official transcript of mRNA

42
Q

What value are points to the left of +1 give?

A

negative values (they are not transcribed)

43
Q

Cis acting elements of promoters

A

they are on the same molecule of DNA and near the gene they regulate

44
Q

Trans-acting elements

A

any protein that binds to the DNA to facilitate or inhibit binding of RNA polymerase

45
Q

operons in prokaryotes

A

several protein producing genes are linked together and are controlled by a single promoter

46
Q

how does RNA polymerase II bind in eukaryotes

A

proteins bind to TATA box

  1. TATA binding protein (TBP) binds
  2. Cofactors bind
  3. TFIIA and TFIIB interact with TBP
  4. TFIIF recruits polymerase
  5. TFIIE and TFIIH bind, cleaving ATP and transcription is initiated
47
Q

How does RNA polymerase nine in prokaryotes

A

sigma subunit recognizes promoter region–it will dissociate after initiation

48
Q

How does termination of transcription occur?

A

RNA polymerase reaches terminal sequence with UUUU sequence following a hairpin

49
Q

What is Rho proteins involvement in transcription?

A

It travels along mRNA, catches the polymerase and terminates transcription

50
Q

Drug Rifampin

A

blocks initiation of transcription by blocking exit channel for RNA

51
Q

What is the differences between cistronic and polycistronic DNA

A

Cistronic–only one gene from transcript

Poly–multiple genes from a transcript

52
Q

Describe the functions of the three RNA polymerases in eukaryotes

A

I–makes rRNA
II–makes mRNA
III–makes tRNA

53
Q

List some of the promoters in eukaryotes

A

TATA box
TFIIB recognition element
Downstream promoter (DPE)
Motif ten element (MTE)

54
Q

What is the purpose of a guanine cap?

A

It seals the 5’ end of the primary transcript and decreases rate of degradation
Also serves as a site for ribosomal binding for translation

55
Q

How it the 5’ cap made?

A

Terminal triphosphate loses phosphate–diphosphate
Diphosphate attacks alpha phosphate of dGMP
Methyl group transferred to guanine ring

56
Q

What is the purpose of the poly A tail

A

added to the 3’ end and serves as a protein binding site that protects from degradation

57
Q

How is the poly A tail made?

A

Polyadensylation signal after stop codon
Enzyme binds signal and cleaves transcript about 10 nucleotides downstream
PolyA polymerase adds nucleotides

58
Q

Exons

A

Contain coding region of RNA

59
Q

Introns

A

Contain regions that do not code for proteins and must be spliced out

60
Q

Spliceosome

A

ensure that eons are spliced together with great accuracy

61
Q

How is protein synthesized? (From what end to what end)

A

Amino terminus to carboxy terminus

62
Q

Codons

A

3 base pairs read together–gives amino acid

63
Q

Degenerative code

A

almost all amino acids have more than one codon

64
Q

Unambiguous

A

each codon only specifies one amino acid

65
Q

Wobble position

A

Accurate base pairing is required only in the first 2 positions of an mRNA codon. the third position can wobble–still code for same amino acid

66
Q

Point mutation

A

single base pair change

67
Q

silent mutation

A

change that specifies for the same amino acid

68
Q

missense

A

change that specifies a different amino acid

69
Q

nonsense

A

change that leads to a stop codon

70
Q

Insertion/deletion

A

add or delete a base which causes an entire frameshift

71
Q

Amino-acyl tRNA

A

binds to mRNA using anitcodon–corresponding amino acid is attached at the 3’ end

72
Q

Aminoacyl-transferase

A

attaches the amino acid to the tRNA via an ester bond

73
Q

Initiation of Translation

A

Initiated by GTP hydrolysis; initiation factors (eIFs) help assemble 40S with initiator tRNA and are released when the mRNA and 60S assemble with complex

74
Q

Elongation

A
  1. Amino-acyl tRNA binds A site
  2. rRNA catalyzes peptide bond formation, transfers growing peptide to A site
  3. Ribosome advances 3 nucleotides towards 3’ end of mRNA, moving tRNA to P site
75
Q

Termination

A

Stop codon is recognized by release factor and completed polypeptide is released from ribosome

76
Q

What are some molecules that inhibit translation

A

Ricin–targets large subunit
Diptheria toxin–modifies His residue blocking translocation
Translation machinery is targeted by antibiotics

77
Q

Types of post translational modifications

A

Trimming–removal of C terminus or N termini pro peptides from zygomens to make mature proteins
Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination

78
Q

Spinal Muscular Atrophy (SMA)

A

Neuromuscular disease characterized by dysfunction and death of motor neurons

79
Q

What causes SMA

A

Mutation in both SMN 1 genes

Mutation C to T in SMN 2 (occurs in exon and is then not spliced correctly)

80
Q

What sequence is located at the 5’ splice site?

A

GU

81
Q

What sequence is located at the 3’ splice site

A

AG

82
Q

How does the spliceosome assemble

A
  1. U1 (5’ splice site) and U2 (branch site) bind
  2. U4-6 form complex
  3. U1 and U4 kicked out and left with catalytic complex
83
Q

Exonic splicing enhancers and intronic splicing enhancers

A

Work by binding proteins that will recruit U1 and U2 and direct splicing

84
Q

Exonic splicing silencers and intronic splicing silencers

A

bind proteins that interfere with identification of splice sites

85
Q

Why can’t SMN2 substitute for SMN1?

A

C-T mutation causes incorrect splicing because exon 7 is skipped (mutation in enhancer)

86
Q

What do insulator elements do?

A

Keep it so that one gene does not influence another

87
Q

Structure of Histones

A

tetramer of two dimers with 146 bp of DNA wrapped around

88
Q

Heterochromatic

A

proteins cannot access DNA and therefore the genes cannot be turned on

89
Q

Euchromatic

A

proteins can access the DNA so these genes can be turned on

90
Q

What charge do the amino terminal tails of histones have and why?

A

+ charge because of basic amino acids of lys and arg (interacts well with - charge DNA which causes compacting)

91
Q

effects of acetylation of histones

A

once acetylated, there is no positive charge on histone tail–DNA therefore does not want to compact

92
Q

How does acetylation of histones occur

A

Histone acetyl-transferase–transfers acetate from acetyl Co A to amino group on lysine

93
Q

effects of methylation of histones

A

NONE! don’t affect the charge at all!

94
Q

Bromo domain

A

recognized acetylated lysines

95
Q

Chromo domain

A

recognizes methylated histones

96
Q

What is the purpose of modifying chromatin?

A

To create a scaffold to attract different proteins to influence transcription

Fundamentals-Sarah (5 decks)

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