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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
Lariats (2)
What introns are cast off as, formed by 2 transesterification reactions
26
Rifampin Mech and Use
Binds bacterial RNAP adjacent to P active site and prevents elongation of RNA Used for TB treatment
27
Actinomycin D Mech and Use
Inhibits euk RNA transcription by binding DNA template at PIC First antibiotic for cancer
28
Difference in P/E Promoters
Proks are -10/-35 | Euks have CREs (-25), PREs (-75), and DREs
29
Difference in P/E RNA Polymerases
Prok: core-RNAP does everything Euk: 3 RNAPs
30
Difference in P/E Promoter Recognition
Prok: sigma factor Euk: GTFs and Mediator
31
Rho-Independent Transcription Termination (3)
In proks GC-rich hairpin folds in on itself Poly-U sequence is weak and dissociates from complex
32
Rho-Dependent Transcription Termination (2)
In proks | Rho helicase recognizes poly-C sequence upstream of termination site and dislodges everything
33
Transcription Bubble (2)
Core-RNAP moving through/separating dsDNA. Maintains RNA-DNA hybrid
34
Difference bw core-RNAP and holo-RNAP (2)
In proks | Sigma factor required to join core-RNAP to form holo-RNAP and initiate promoter contact
35
Closed vs. Open Complex (2)
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
Difference in Prok/Euk Transcription Promoter Clearance
Prok: Polymerization clears >10 nt, sigma released Euk: Clears >23 nt, TFs/Mediator released
37
Difference in Prok/Euk Transcription Termination
Prok: GC rich inverted repeat + poly-U sequence or C-rich rho helicase recognition sequence Euk: Poly-A termination sequence
38
Difference in P/E mRNA Processing
P: Not much E: 5'capping, poly-A tail, splicing, export from nuc to cyt
39
2 Steps of aa-tRNA formation
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
Shine-Dalgarno Sequence (2)
Slightly upstream of start codon in Proks | Base pairs w/ 30S 16S rRNA and guides "AUG" start codon into P site on ribosome
41
Transformylase (3)
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
IF1 Role
Binds 30S A-site in proks which blocks binding of f-Met-tRNA there and guides it to P
43
IF2 role (3)
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
Delivery of aa-tRNA to A site in Proks (3)
EF-Tu-GTP binds aa-tRNA and loads, GAR stimulates GTPase to release, then EF-Ts act as GEF to reset
45
Prok Peptide Bond Formation
Peptidyl transferase center (PTC, a ribozye) moves peptide from P site to new AA at A site
46
Prok Translocation During Peptide Elongation
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
Fate of N-terminal f-Met
Removed before translation completed
48
5 Prokaryotic Translation Inhibitor Antibiotics
``` Streptomycin Tetracycline Chloramphenicol Erythromycin Puromycin ```
49
2 Eukaryotic Translation Inhibitor Antibiotics
Cyclohexamide | Puromycin
50
2 Eukaryotic Protein Toxins
Diphtheria toxin | Ricin
51
43S Pre-Initiation Complex (6)
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
48S Initiation Complex (4)
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
Formation of 80S Initiation Complex (4)
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
Difference in Prok/Euk Stop Codon Recognition
Ps have RF1 and 2, Es just have eRF1
55
Difference b/w P/E Ribosomal Subunit Dissociations
Ps require RRF to recruit EF-G-GTP for hydrolysis | Es just have eIF1/1A and eIF3 do it
56
P vs. E GTP hydrolysis
P: 1 initiation, 2/residue elongation, 2 termination E: 2 initiation, 2/residue elongation, 1 termination So roughly the same
57
Fate of N-terminus of mt-targeted protein
Sent through TOM and TIM and then cleaved off inside matrix by mitochondrial processing peptidase (MPP)
58
4 Internal Sequence-directed Locations for mt Proteins from TOM
Translocase of inner membrane (TIM) Mitochondrial intermembrane space assembly machinery (MIA) Mitochondrial Import Complex (MIM) Sorting and Assembly Machinery (SAM)
59
ER Targeting Pathway (6)
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
N-Linked Glycosylation of RER Prots (5 general)
Mannose oligosaccharide assembled on outside, flipped inside, addition, transfer, and trimming
61
2 Categories of Glycoproteins from Oligosaccharide Completion in Golgi
Complex | High mannose
62
Mannose-6-Phosphate
Added in Golgi to target protein to lysosome
63
Nuclear Import/Export Main Point
Ran-GTP required to bind to importin or exportin and take out of nucleus and its GAP is outside and GEF is inside
64
Difference b/w 3 Methods of Ingestion for Lysosomal Degradation
Autophagy - for cytosolic components Endocytosis - for membrane components Phagocytosis - for EC components
65
Lysosomal vs. Ubiquitin-Proteasome Degradation
Lysosome only Cytoplasm NOT nucleus | Ub-Proteasome both
66
Proteasome Structure/Action (2)
Ub binds to regulatory cap and opens it and spools protein into central channel where it gets hydrolyzed
67
Disulfide Bonds (residues/enzyme/e- acceptor/reversible)
Residues: side chain -SH of 2 Cys Enzyme: Disulfide isomerase (in ER) e- Acceptor: Glutathione Reversible: Disulfide isomerase, thioredoxin
68
2 Notable Aspects of Proteolytic Cleavage Modification
Peptide bond hydrolyzed by H2O | Irreversible
69
2 Neutral->Negative Protein Modifications
Phosphorylation and sulfation
70
2 Positive->Neutral Protein Modifications
Acetylation and methylation
71
3 Differences b/w Phosphorylation and Sulfation
- 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
Methylation Donor
S-adenosylmethionine (SAM)
73
Lipid Attachment Protein Modification Donor (2.4)
Myristoylation and palmitoylation are CoA | Farnesylation and geranylgeranylation are pyrophosphate
74
Lipid Attachment Protein Modification Residue (2)
All are on side chain -SH of Cys except Myristoylation which is on -NH3+ of N-term
75
Main function of lipid attachment protein modification
Insert protein onto surface of membrane
76
Enzyme for Proline or Lysine Hydroxylation
Prolyl or Lysyl Hydroxylase
77
4 Donors for Proline and Lysine Hydroxylation
O2, alpha-ketoglutarate, Fe, ascorbic acid

Biochemistry (23 decks)

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