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M2M > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

Name kinetic energy in living systems (4)

A

Radiant Energy Thermal Energy Mechanical Energy Electrical Energy

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2
Q

Name potential energy in living systems (4)

A

(1) Chemical Bonds
(2) Concentration Gradients
(3) Electrical Fields
(4) Redox Pairs

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3
Q

First law of Thermodynamics

A

Energy is neither created, nor destroyed. It can be converted but always conserved.

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4
Q

Second law of Thermodynamics

A

The entropy of the universe is always increasing

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5
Q

Gibb’s free energy equation (chemical)

A

ΔG = ΔH - TΔS

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6
Q

Gibb’s free energy equation (redox reaction)

A

ΔG = -nFΔE

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7
Q

Gibb’s free energy under non-standard conditions

A

ΔG = ΔG°’ + RT lnQ

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8
Q

Transcription

A

DNA -> RNA

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9
Q

Translation

A

RNA -> Protein

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10
Q

Building blocks of nucleic acids

A

Ribonucleotide 2’ deoxy-nucleotide

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11
Q

Universal energy currency of the cell

A

ATP

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12
Q

Nucleotide

A

Sugar-Base-Phosphate

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13
Q

Nucleoside

A

Sugar-Base

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14
Q

Relative Solubility of nucleotide components

A

Nucleotide > Nucleoside > Pyrimidine > Purine

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15
Q

Nucleotide linkages

A

Phosphodiester bonds 5’ - 3’

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16
Q

Reverse Transcriptase inhibitors

A

(1) ddI (dideoxyinosine)
(2) AZT (azideothymidine)

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17
Q

Chargaff’s Rule

A

%G = %C

%A = %T

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18
Q

B form DNA characteristics (6)

A

(1) Two strands in right-handed helix
(2) Anti-parallel arrangement
(3) Sugar-phosphate backbone is on outside of helix
(4) Bases are paired on the inside
(5) Geometry favors A-T and G-C pairs only
(6) Complementary of base pairing suggests a molecular mechanism for replication

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19
Q

Stabilization of DNA (Increased Tm) (3)

A

(1) Increased salt concentration
(2) Increased chain length
(3) Increased GC content

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20
Q

Major causes of Base-Change mutation (5)

A

(1) Deamination (A, C, G)
(2) Depurination/ Depyrimidination
(3) Oxidative damage (8-oxo-dG)
(4) UV induced covalent linkage (Thymidine dimers)
(5) Alkylating agents (O6-meG)

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21
Q

What recognizes the replication origin?

A

Origin binding proteins (Origin recognition complex)

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22
Q

What melts/unwinds DNA?

A

DNA helicase

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23
Q

What relaxes the torsional stress ahead of the replication fork?

A

Topoisomerase/gyrase

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24
Q

What protects unwound single-stranded DNA?

A

Single stranded binding proteins Replication Protein A

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25
Q

What synthesizes RNA primer?

A

Primase

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26
Q

What elongates DNA from the RNA primer?

A

DNA Pol III

DNA Pol δ & DNA Pol ε

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27
Q

What removes RNA primer and replaces with DNA?

A

DNA Pol I

DNA Pol α

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28
Q

What ligates DNA fragments?

A

DNA Ligase

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29
Q

What do origin binding proteins (origin recognition complexes) do?

A

Recognize origin of replication

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30
Q

What does DNA helicase do?

A

Unwinds DNA

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31
Q

What does topoisomerase/ gyrase do?

A

Relaxes torsional stress ahead of replication fork

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32
Q

What do single stranded binding proteins (replication protein A) do?

A

Protect unwound single-stranded DNA

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33
Q

What does primase do?

A

synthesizes RNA primers

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34
Q

What does DNA Pol III (DNA Pol δ & DNA Pol ε) do?

A

Elongates DNA from RNA primer

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35
Q

What does DNA Pol I (DNA Pol α) do?

A

Removes RNA primer and replaces with DNA

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36
Q

What does DNA ligase do?

A

Ligates DNA fragments

37
Q

Characteristics of replication origins (3)

A

(1) Unique DNA segments with multiple short repeats
(2) Recognized by multimeric origin-binding proteins
(3) Rich in A-T base pairs

38
Q

What contributes to the high processivity of DNA Pol III (DNA Pol δ)

A

β-subunit Proliferating Cell Nuclear Antigen

39
Q

What do the β-subunit (Proliferating Cell Nuclear Antigen) do?

A

Contribute to the processivity of DNA Pol III (DNA Pol δ)

40
Q

What elongates Telomeres (as a reverse transcriptase)?

A

Telomerase

41
Q

What does Telomerase do?

A

Elongates telomeres using a reverse transcriptase function

42
Q

Major causes of Structure-Change mutation (6)

A

(1) Insertion/Deletion of nucleotides
(2) Bulky chemical adducts
(3) Replication errors
(4) Intra/inter-strand crosslinks
(5) DNA Strand breaks
(6) Stalled DNA replication forks

43
Q

Types of DNA Repair (4)

A

(1) Direct Reversal
(2) Excision
(3) Tolerance/Bypass
(4) Strand Break repair

44
Q

Types of Direct Reversal (3)

A

(1) Single-stranded DNA Break by DNA LIGASE
(2) UV-caused base damage by PHOTOLYASE
(3) Base alkylation by O6-meG METHYLTRANSFERASE

45
Q

Types of Excision Repair (3)

A

(1) Damage that doesn’t distort DNA - BASE EXCISION REPAIR
(2) Damage that distorts DNA - NUCLEOTIDE EXCISION REPAIR
(3) Misincorporated nucleotides during DNA Replication - MISMATCH REPAIR

46
Q

Types of Strand Break Repair (2)

A

(1) Single-strand break repair (SSBR)
(2) Double-strand break repair (DSBR)

47
Q

Types of Double-Strand Break Repair (2)

A

(1) Homologous Recombination (HR)
(2) Nonhomologous End Joining (NHEJ)

48
Q

Types of Excision Repair (3)

A

(1) Base Excision Repair
(2) Nucleotide Excision Repair
(3) Mismatch Repair

49
Q

Base Excision Repair

A

Repairs base damages that do not distort DNA. Uses base specific glycosylases to remove damaged base

50
Q

Nucleotide Excision Repair

A

Repairs base damages that distort DNA Removes oligonucleotide that contains damaged base

51
Q

Mismatch Repair

A

Removes misincorporated nucleotides during DNA replication Distinguishes between template strand and new strand

52
Q

Common Steps to Excision Repair Mechanisms

A

(1) Recognition of damaged/mismatched nucleotide
(2) Cutting of phosphodiester backbone (endonuclease)
(3) Removal of DNA fragment (nuclease)
(4) Synthesis of missing nucleotides (DNA polymerase)
(5) Sealing of nick in phosphodeister backbone (DNA ligase)

53
Q

What does Endonuclease do?

A

Cuts phosphodiester backbone

54
Q

What does Nuclease do?

A

Removes damaged DNA fragments

55
Q

What does DNA polymerase do?

A

synthesizes nucleotides

56
Q

What does DNA ligase do?

A

Ligates phosphodiester backbone nicks

57
Q

Steps in Base Excision Repair

A

(1) Modified base recognized by specific DNA GLYCOSYLASE
(2) AP site-specific endonuclease (APE1) cleaves sugar-phosphate backbone
(3) Gap filled in by DNA Pol
(4) Nick sealed by DNA ligase

58
Q

Steps in Nucleotide Excision Repair

A

(1) Recognition and binding of damaged site by multi-protein complex
(2) Local unwinding of DNA duplex by helicases (TFIIH) to form ~25base bubble
(3) Incision of damaged strand by two endonucleases ~30base
(4) Gap filled by DNA Pol 5. Nick sealed by DNA ligase

59
Q

Two ways NER machinery recognizes damage

A

(1) Global Genome NER - recognizes damage anywhere in genome
(2) Transcription-Coupled NER - recognizes damage within transcribed region

60
Q

How does MMR recognize which strand to repair?

A

Lagging strand marked by transient 5’ DNA ends of Okazaki fragments Leading strand marked by transient ribonucleotides processed into nicks?

61
Q

When is DNA damage tolerance/ bypass employed?

A

When there is too much damage for normal repair machineries to handle

62
Q

What do bypass DNA pol lack?

A

3’-5’ exonuclease activity

63
Q

Characteristics of Non-homologous end-joining

A

No homology needed Inaccurate, resulting in deletion/insertion

64
Q

Characteristics of Homologous end-joining

A

Extended sequence homology needed Accurate

65
Q

Three main classes of RNA

A

(1) Structural (rRNA, tRNA, snRNA, snoRNA)
(2) Regulatory (miRNA, siRNA)
(3) Information Containing (mRNA)

66
Q

Why is RNA more easily hydrolized than DNA?

A

Due to nucleophilic attack by 2’ OH on phosphodiester bond.

67
Q

What is Puromycin?

A

A nucleotide analogue that mimics tRNA which terminates translation

68
Q

What is the segment of DNA which gets transcribed into RNA?

A

Transcription Unit

69
Q

What are two features of Transcription

A

(1) Unidirectional
(2) Completely processive

70
Q

What is the product of transcription called?

A

Primary Transcript

71
Q

What is a Transcription Unit?

A

The segment of DNA which gets transcribed into RNA

72
Q

What is a Primary Transcript?

A

The product of transcription

73
Q

Which strand complements the RNA transcript?

A

DNA Template Strand

74
Q

Which strand codes the RNA transcript?

A

DNA Non-Template Strand (Coding Strand)

75
Q

What are the three steps of Transcription Initiation?

A

(1) Polymerase binds to promotor sequence in duplex DNA
(2) Polymerase melts duplex DNA near transcription start site forming transcription bubble
(3) Polymerase catalyzes phosphodiester linkage of two initial rNTPs.

76
Q

What happens in RNA Transcription Elongation?

A

RNA Pol advances 3’ - 5’ down template strand, melting duplex DNA and adding rNTPs.

77
Q

What happens at RNA Transcriptino Termination?

A

At transcription stop site, polymerase releases completed RNA and dissociates from DNA.

78
Q

What are the functions of C-terminal domains in RNA Pol II?

A

Binding of proteins that regulate elongation and processing of RNA transcript.

79
Q

What directs RNA Pol to the start of genes?

A

Promoters

80
Q

What helps direct assembly of pre-initiation complexes at the promoter?

A

TATA-Box Binding Proteins

81
Q

What does TFIIH do?

A

Functions in Transcription and DNA Repair

82
Q

What are the three steps in RNA modification?

A

(1) Capping
(2) Splicing
(3) Polyadenylation

83
Q

What caps RNA?

A

RNA Pol II

84
Q

What are the steps for the 5’ capping?

A

(1) Triphosphatase
(2) Guanylyltransferase
(3) Guanine 7 methyl transferase

85
Q

How are introns recognized by spliceosomes

A

(1) 5’: GU
(2) 3’: AG
(3) Branchpoint: A

86
Q

How does splicing proceed?

A

(1) Attack by the 2’ OH of branch point A - Forms lariate intermediate
(2) Attack by the 3’ OH of exon 1

87
Q

How can different proteins be encoded for by a single gene?

A

Alternative splicing

88
Q

What are the steps in 3’ polyadenylation?

A

(1) Cleavage
(2) Polyadenylation (poly-A binding protein)

M2M (4 decks)

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