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Biochemistry > Genetics: Rep/Transcript/Translate/Modification > Flashcards

Genetics: Rep/Transcript/Translate/Modification Flashcards

1
Q

Direction of DNA Polymerases (2)

A

Read in 3’-5’ and synthesize in 5’-3’

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2
Q

DNA Gyrase

A

Topoisomerase II in proks that acts to relieve superhelical tension and decatenate replicated chromosomes

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3
Q

Mitotic Clock

A

In normal human somatic cells, linear chromosomes shorten w/ each cell division and once they reach a critical length they cannot divide and enter senesence

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4
Q

Telomerase (2)

A

Enzyme used to lengthen telomeres by repeated addition of ssDNA to 3’ end. Causes immortalization and can be reactivated by cancer

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5
Q

2.5 Processes of DNA Replication Initiation

A

Origin of Replication - DNA sequence/recognizing protein

DNA strand separation - Helicase loader, helicase, single-strand binding proteins

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6
Q

4 Steps of DNA Replication Strand Elongation

A

Primer
Elongation
Primer excision
Gap filling

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7
Q

DNA Ligase

A

Catalyzes 3’-5’ phosphodiester bond formation bw original DNA strand and gap-filled DNA strand

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8
Q

Prok/Euk Difference in Origin DNA Sequence

A

Proks have discreet, clear AT-rich regions

Euks have broad, less clear AT-rich regions

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9
Q

Prok/Euk Difference in DNA Polymerization

A

Proks have 3 different DNA pols w/ different functions

Euks have 1 DNA pol with many subunits

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10
Q

Prok/Euk difference in Primer Excision

A

Proks: Pol I does it
Euks: Have ribonuclease

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11
Q

Deamination

A

DNA damage in which exocyclic amino groups in pyrimidine rings (including those in purines) undergo spontaneous hydrolysis, generating a carbonyl and release of ammonia

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12
Q

Thymine Dimers

A

UV energy causes covalent cross linking bw adjacent thymines on same DNA strand

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13
Q

Psoralen (2)

A

Intercalates into dsDNA and upon UV irradation forms covalent links w thymine. Has two reactive sites so can crosslink thymines from opposite strands

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14
Q

Base Excision Repair 2 Repairs

A
  1. Deamination of adenine, guanine, and cytosine

2. Losses of single bases

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15
Q

Nucleotide Excision Repair 2 Repairs

A
  1. Intrastrand thymine dimers

2. Mismatches from errors in proofreading

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16
Q

DNA Repair of Double Strand Breaks (2)

A

Nonhomologous end joining (easy) and homologous recombination (complex)

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17
Q

4 Necessary Components for PCR

A

Template DNA
Primer DNA
dNTPs
Taq (temperature resistant) polymerase

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18
Q

Prokaryotic RNA Processing

A

tRNA and rRNA have modifications, mRNA has few little modification

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19
Q

Jobs of 3 Euk RNAPs

A

I: 18S, 5.8S, and 28S rRNA
II: mRNA precursors
III: tRNA and 5S rRNA

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20
Q

3 Euk Response Elements for RNA Transcription

A

Core promoter elements - TATA box at -25
Proximal Promoter Elements - CAAT box at -75
Distal Regulatory Sequences - enhancers or silences

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21
Q

3 Characteristics of Euk RNA Transcription

A

Nuclear membrane
Complex response elements
Complex mRNA processing

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22
Q

Euk RNA Transcription Initiation

A

GTFs bind TATA which assemble pre-initation complex/recruit RNA Pol

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23
Q

Serine Phosphorylation and Regulation of RNAPII (4)

A

S2/S5: PIC assembly
S2/S5P: Promoter clearance
S2P/S5: downstream elongation
S2/S5: termination, disengagement

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24
Q

Euk RNA Transcription Termination

A

Poly-A termination sequence transcribed and endonucleases cleave to terminate transcription

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25
Q

Lariats (2)

A

What introns are cast off as, formed by 2 transesterification reactions

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26
Q

Rifampin Mech and Use

A

Binds bacterial RNAP adjacent to P active site and prevents elongation of RNA
Used for TB treatment

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27
Q

Actinomycin D Mech and Use

A

Inhibits euk RNA transcription by binding DNA template at PIC
First antibiotic for cancer

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28
Q

Difference in P/E Promoters

A

Proks are -10/-35

Euks have CREs (-25), PREs (-75), and DREs

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29
Q

Difference in P/E RNA Polymerases

A

Prok: core-RNAP does everything
Euk: 3 RNAPs

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30
Q

Difference in P/E Promoter Recognition

A

Prok: sigma factor
Euk: GTFs and Mediator

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31
Q

Rho-Independent Transcription Termination (3)

A

In proks
GC-rich hairpin folds in on itself
Poly-U sequence is weak and dissociates from complex

32
Q

Rho-Dependent Transcription Termination (2)

A

In proks

Rho helicase recognizes poly-C sequence upstream of termination site and dislodges everything

33
Q

Transcription Bubble (2)

A

Core-RNAP moving through/separating dsDNA. Maintains RNA-DNA hybrid

34
Q

Difference bw core-RNAP and holo-RNAP (2)

A

In proks

Sigma factor required to join core-RNAP to form holo-RNAP and initiate promoter contact

35
Q

Closed vs. Open Complex (2)

A

Closed complex from -35 to -10 in proks as holo-RNAP translocates along. Opens once gets to -10 TATA box and opens up dsDNA

36
Q

Difference in Prok/Euk Transcription Promoter Clearance

A

Prok: Polymerization clears >10 nt, sigma released
Euk: Clears >23 nt, TFs/Mediator released

37
Q

Difference in Prok/Euk Transcription Termination

A

Prok: GC rich inverted repeat + poly-U sequence or C-rich rho helicase recognition sequence
Euk: Poly-A termination sequence

38
Q

Difference in P/E mRNA Processing

A

P: Not much
E: 5’capping, poly-A tail, splicing, export from nuc to cyt

39
Q

2 Steps of aa-tRNA formation

A

Activated by reacting w/ ATP to form aa-AMP

AA transferred to 3’CCA of tRNA to form aa-tRNA w/ expulsion of AMP

40
Q

Shine-Dalgarno Sequence (2)

A

Slightly upstream of start codon in Proks

Base pairs w/ 30S 16S rRNA and guides “AUG” start codon into P site on ribosome

41
Q

Transformylase (3)

A

In proks
Only recognizes Met-tRNAf and catalyzes transfer of formyl group to amino groupof Met to make it fMet-tRNAf, which will be only tRNA to go into P site

42
Q

IF1 Role

A

Binds 30S A-site in proks which blocks binding of f-Met-tRNA there and guides it to P

43
Q

IF2 role (3)

A

In proks
As IF2-GTP, Binds fMet-tRNA and loads it into P-site. Interacts with GTPase activating region (GAR) on 30S and conformational change allows binding of 50S to form 70S initiation complex

44
Q

Delivery of aa-tRNA to A site in Proks (3)

A

EF-Tu-GTP binds aa-tRNA and loads, GAR stimulates GTPase to release, then EF-Ts act as GEF to reset

45
Q

Prok Peptide Bond Formation

A

Peptidyl transferase center (PTC, a ribozye) moves peptide from P site to new AA at A site

46
Q

Prok Translocation During Peptide Elongation

A

EF-G-GTP binds near A site, hydrolyzes, causes 30S and 50S to “ratchet”, moving deacylated tRNA from P-E and peptidyl tRNA from A-P

47
Q

Fate of N-terminal f-Met

A

Removed before translation completed

48
Q

5 Prokaryotic Translation Inhibitor Antibiotics

A 
Streptomycin
Tetracycline
Chloramphenicol
Erythromycin
Puromycin
49
Q

2 Eukaryotic Translation Inhibitor Antibiotics

A

Cyclohexamide

Puromycin

50
Q

2 Eukaryotic Protein Toxins

A

Diphtheria toxin

Ricin

51
Q

43S Pre-Initiation Complex (6)

A

In euks
eIFs bind small 40S ribosomal sub
Factors that block premature assocation w/ 60S, block “A-site”, and function as GAP
eIF2-GTP loads Met-tRNAi into P-site

52
Q

48S Initiation Complex (4)

A

In euks
Cap binding complex (CBC) binds to mRNA 5’ cap contains helicase that unwinds/drives movement
Poly(A)-binding protein (PABP) binds 3’poly(A) tail to form circular mRNA which associates w/ 43S to form 48S initiation complex
Then can begin unwinding/searching for AUG w/ Met-tRNAi

53
Q

Formation of 80S Initiation Complex (4)

A

In euks
After correct pairing of Met-tRNAi and AUG
eIF5B-GTP binds and promotes joining of 60S, releasing other prots
eIF5B-GTP hydrolyzes and dissociates, leaving active 80S initiation complex for peptide synthesis

54
Q

Difference in Prok/Euk Stop Codon Recognition

A

Ps have RF1 and 2, Es just have eRF1

55
Q

Difference b/w P/E Ribosomal Subunit Dissociations

A

Ps require RRF to recruit EF-G-GTP for hydrolysis

Es just have eIF1/1A and eIF3 do it

56
Q

P vs. E GTP hydrolysis

A

P: 1 initiation, 2/residue elongation, 2 termination
E: 2 initiation, 2/residue elongation, 1 termination
So roughly the same

57
Q

Fate of N-terminus of mt-targeted protein

A

Sent through TOM and TIM and then cleaved off inside matrix by mitochondrial processing peptidase (MPP)

58
Q

4 Internal Sequence-directed Locations for mt Proteins from TOM

A

Translocase of inner membrane (TIM)
Mitochondrial intermembrane space assembly machinery (MIA)
Mitochondrial Import Complex (MIM)
Sorting and Assembly Machinery (SAM)

59
Q

ER Targeting Pathway (6)

A

Hydrophobic signal sequence binds signal recognition particle (SRP) which targets to SRP R which cleaves GTP to open translocon and pass prot into ER

60
Q

N-Linked Glycosylation of RER Prots (5 general)

A

Mannose oligosaccharide assembled on outside, flipped inside, addition, transfer, and trimming

61
Q

2 Categories of Glycoproteins from Oligosaccharide Completion in Golgi

A

Complex

High mannose

62
Q

Mannose-6-Phosphate

A

Added in Golgi to target protein to lysosome

63
Q

Nuclear Import/Export Main Point

A

Ran-GTP required to bind to importin or exportin and take out of nucleus and its GAP is outside and GEF is inside

64
Q

Difference b/w 3 Methods of Ingestion for Lysosomal Degradation

A

Autophagy - for cytosolic components
Endocytosis - for membrane components
Phagocytosis - for EC components

65
Q

Lysosomal vs. Ubiquitin-Proteasome Degradation

A

Lysosome only Cytoplasm NOT nucleus

Ub-Proteasome both

66
Q

Proteasome Structure/Action (2)

A

Ub binds to regulatory cap and opens it and spools protein into central channel where it gets hydrolyzed

67
Q

Disulfide Bonds (residues/enzyme/e- acceptor/reversible)

A

Residues: side chain -SH of 2 Cys
Enzyme: Disulfide isomerase (in ER)
e- Acceptor: Glutathione
Reversible: Disulfide isomerase, thioredoxin

68
Q

2 Notable Aspects of Proteolytic Cleavage Modification

A

Peptide bond hydrolyzed by H2O

Irreversible

69
Q

2 Neutral->Negative Protein Modifications

A

Phosphorylation and sulfation

70
Q

2 Positive->Neutral Protein Modifications

A

Acetylation and methylation

71
Q

3 Differences b/w Phosphorylation and Sulfation

A
  • Phosphorylation on Side Chain -OH of Ser, Thr, or Tyr whereas sulfation only on -OH of Tyr
  • Phosphorylation primarily intracellular whereas sulfation extracellular
  • Phosphorylation reversible via phosphatases whereas sulfation irreversible
72
Q

Methylation Donor

A

S-adenosylmethionine (SAM)

73
Q

Lipid Attachment Protein Modification Donor (2.4)

A

Myristoylation and palmitoylation are CoA

Farnesylation and geranylgeranylation are pyrophosphate

74
Q

Lipid Attachment Protein Modification Residue (2)

A

All are on side chain -SH of Cys except Myristoylation which is on -NH3+ of N-term

75
Q

Main function of lipid attachment protein modification

A

Insert protein onto surface of membrane

76
Q

Enzyme for Proline or Lysine Hydroxylation

A

Prolyl or Lysyl Hydroxylase

77
Q

4 Donors for Proline and Lysine Hydroxylation

A

O2, alpha-ketoglutarate, Fe, ascorbic acid

Biochemistry (23 decks)

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