Genetics: Rep/Transcript/Translate/Modification Flashcards Preview

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Flashcards in Genetics: Rep/Transcript/Translate/Modification Deck (77)
1

Direction of DNA Polymerases (2)

Read in 3'-5' and synthesize in 5'-3'

2

DNA Gyrase

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

3

Mitotic Clock

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

4

Telomerase (2)

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

5

2.5 Processes of DNA Replication Initiation

Origin of Replication - DNA sequence/recognizing protein
DNA strand separation - Helicase loader, helicase, single-strand binding proteins

6

4 Steps of DNA Replication Strand Elongation

Primer
Elongation
Primer excision
Gap filling

7

DNA Ligase

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

8

Prok/Euk Difference in Origin DNA Sequence

Proks have discreet, clear AT-rich regions
Euks have broad, less clear AT-rich regions

9

Prok/Euk Difference in DNA Polymerization

Proks have 3 different DNA pols w/ different functions
Euks have 1 DNA pol with many subunits

10

Prok/Euk difference in Primer Excision

Proks: Pol I does it
Euks: Have ribonuclease

11

Deamination

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

12

Thymine Dimers

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

13

Psoralen (2)

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

14

Base Excision Repair 2 Repairs

1. Deamination of adenine, guanine, and cytosine
2. Losses of single bases

15

Nucleotide Excision Repair 2 Repairs

1. Intrastrand thymine dimers
2. Mismatches from errors in proofreading

16

DNA Repair of Double Strand Breaks (2)

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

17

4 Necessary Components for PCR

Template DNA
Primer DNA
dNTPs
Taq (temperature resistant) polymerase

18

Prokaryotic RNA Processing

tRNA and rRNA have modifications, mRNA has few little modification

19

Jobs of 3 Euk RNAPs

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

20

3 Euk Response Elements for RNA Transcription

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

21

3 Characteristics of Euk RNA Transcription

Nuclear membrane
Complex response elements
Complex mRNA processing

22

Euk RNA Transcription Initiation

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

23

Serine Phosphorylation and Regulation of RNAPII (4)

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

24

Euk RNA Transcription Termination

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

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