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MCM Exam 2-RH > Functions & Dysfuncions Of Protein Processing > Flashcards

Functions & Dysfuncions Of Protein Processing Flashcards

1
Q

How does a codon recognize an amino acid?

A

Through genetic code

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2
Q

Genetic code

A

DNA (nucleotide sequence)—> protein (AA) using mRNA

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3
Q

Codon

A

Group of 3 nucleotides

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4
Q

What do codons code for?

A

61 triplet codons code for 20 Amino Acids or 3 stop translation codons

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5
Q

Characteristics of code

A

Degenerate (some AA are coded by multiple codons)
Standard, universal
Not punctuated
Non-overlapping

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6
Q

Silent mutation

A

Codon changes, AA is the same

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7
Q

Missense Mutation

A

New codon —> new amino acid

Can change protein or not

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8
Q

Nonsense mutation

A

Change in codon —> stop codon

Protein degrades or stops truncated

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9
Q

Frameshift mutation

A

One nucleotide is added/deleted it moves the entire sequence one over so AA sequence is disrupted; leads to nonfunctional protein

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10
Q

Sickle cell anemia

A

Due to missense mutation that changes GAG to GTG which changes Glutamic Acid (negatively, charged) to Valine (non polar, non charged)

Mutation causes the RBC to form a rigid, rod-like structure and deforms RBS-> clog capillaries b/c they cant carry O2

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11
Q

Duchenne Muscular Dystrophy

A

Frameshift mutations in dystrophin gene
(In-frame: mild form only truncated forms, out of frame: actual MD)—> little or no expression of the dystrophin gene —> muscle wasting

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12
Q

mRNA structure

A

5’ cap: 7-methylguanosine cap
3’ end: poly-A tail (lots of A amino acids)
coding region: codons for amino acids

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13
Q

tRNA structure

A

cloverleaf (secondary structure)

unpaired nucelotide regions: Anticodon loop (binds to codon on mRNA) & 3’ CCA terminal region

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14
Q

3’ region of tRNA

A

CCA region that binds the amino acid w the corresponding codon

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15
Q

Anticodon loop

A

3 nucleotides that pair w a complementary codon

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16
Q

Aminoacyl tRNA

A

tRNA that arrys the Amino Acid –> needs to be activated

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17
Q

Enzyme that activates Amino Acid

A

Aminoacyl tRNA synthetase

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18
Q

Aminoactyl tRNA synthetase

A

activate amino acids by serving as a second genetic code to maintain the fidelity of protein synthesis

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19
Q

Steps of Amino Acid Activation

A

using AMP to COOH end of amino acid (breaks the AMP) which gives energy to bind codon to the mRNA

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20
Q

Prokaryotic Ribosomes

A

Total: 70S
Small: 30s, Large: 50s
different structure so that antibiotics can target ONLY prokaryotic mechanism

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21
Q

eukaryotic ribosomes

A

Total: 80s
Small: 40s, Large: 60s

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22
Q

A site of ribosome

A

where the mRNA codon is exposed to receive the aminoacyl tRNA

***except Met tRNA (start codon)

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23
Q

P site of ribosome

A

where the aminoacyl tRNA is attached; holds the tRNA w the growing polypeptide chain

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24
Q

E site of ribosome

A

where the protein will exit the ribosome

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25
Q

Initiation of translation

A

small ribosomal sub unit binds to P site of SOMETHING where there is an EIF (EIF2) that is bound to GTP (source of energy). Large subunit attaches to form complex. Next tRNA comes in (based on sequence) and forms first peptide bond to methionine

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26
Q

Where are EIF4s attached?

A

Poly-A tail

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27
Q

What is the bond from one amino acid (in A site) to the growing chain (P site?) By which enzyme?

A

Peptide bond (CO-NH) by Peptidyl transferase

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28
Q

Elongation of Translation

A

purpose: links AA to growing polypeptide w elongation factors that play a a role in proofreading

aminoacyl tRNA is attached to GTP-bound elongation factor.
loading of AA: anticodon base pairs w codon on the A site

29
Q

Termination of Translation

A

Triggered by stop codons: UAA, UAG, UGA which are recognized by RELASE factors (RFs)
RFs bind to the A site and cleaves the ester bond between the Carbon & the tRNA (reacts w water to make the COOH group and makes the protein)
peptide chain is released from ribosomal complex and then ribosome dissociates by GTP hydrolysis

30
Q

Stop Codons

A

UAA, UAG, UGA

U Are Away, U are Gone, U Go Away

31
Q

Polysomes

A

cluster of ribosomes that collectively make polypeptide efficiently

32
Q

streptomycin

A

prokaryotic; binds to 30s to disrupt initiation

33
Q

chloramphenicol

A

inhibits peptidyl transferase in the mitochondria of prokaryotes

34
Q

clindamycin & erythromycin

A

prokaryotic; bind to 50s and blocks translocation of ribosome

35
Q

erythromycin

A

treats purtussis

36
Q

streptomycin

A

prokaryotic; binds to 30s and interfers with binding fmet-tRNA (first tRNA)–> interferes w joining 30s and 50s

37
Q

cycloheximide

A

eukaryotic; inhibits peptidyl transferase

38
Q

diphtheria

A

eukaryotic; inactives GTP-bound eEF-2 and interferes w ribosomal translocation

39
Q

shiga toxin & ricin

A

eukaryotic; binds to 60s and blocks entry of aminoacyl-tRNA to ribosomal complex

40
Q

puromycin

A

prokaryotic/eukaryotic causes premature chain termination; exact mechanism is unknown but somehow it enters the A site and adds to the growing chain w a puromyclated chain which results in early release

41
Q

Cytoplasmic pathway

A

protein sorting pathway; for proteins that are destined to go to cytosol, mitochondria, nucleus and peroxisomes; translation begins & ends on free ribosomes; no signals –> stay in cytoplasm; those w signals will go to specific organelles w help of chaperone proteins (TrasnsporterInnerMembrane and TrasnporterOuterMembrane)

42
Q

secretory pathway

A

protein sorting pathway for proteins destined for ER, lysosomes, plasma membrane or for secretion;

43
Q

signal & pathway that sends to Mitochondria

A

cytoplasmic; N terminal hydrophobic alpha helix

44
Q

signal & pathway that sends to nucleus

A

cytoplasmic; lysine and arginine rich

45
Q

signal & pathway that sends to peroxisome

A

cytosplasmic; SKL sequence

46
Q

signal & pathway for secretory proteins

A

secretory pathway; Trp-rich domain

47
Q

signal & pathway that sends to lysosome

A

secretory pathway; Mannose 6 phopshate

48
Q

signal & pathway that sends out of cell

A

secretory pathway; Stop tsrf

49
Q

signal & pathway that sends to ER lumen

A

secretory pathway; lys-asp-glu-leu (KDEL)

50
Q

how do proteins pass through the mitochondrial membrane?

A

TOM (outer) & TIM (inner) and protected by binding to heat shock protein 70 (HSP70)

51
Q

Where does translation occur for secretory pathway?

A

translation begins on free ribosome but ends on ribosomes that are going to ER

52
Q

Signal peptide for secretory pathway

A

all have ER targeting (15-60 AA at N terminus w 1 or 2 basic AAs near N term and hydrophobic on C side)

53
Q

signal recognition particle (SRP)

A

binds to ER and ribosome, wraps itself around the ribosome mRNA peptide complex and stops translation for a brief sec (resumes when protein is directed into lumen)

54
Q

how does the protein get released?

A

enzymes on luminal side cleave the signal and release it additional signals will tell it where to go

55
Q

I-cell disease

A

due to: lack of mannose 6P enzyme

56
Q

protein folding

A

small proteins spontaneously fold into naive conformations; large proteins need chaperones & chaperonins to ensure protection and proper folding

57
Q

chaperonins

A

barrel shaped compartments that admit unfolded proteins and use ATP to help fold

58
Q

proteolytic cleavage

A

converts inactive zymogen –> active enzyme

59
Q

acetylation

A

adding a covalent bond to Amine (-NH3) on lysine; critical for gene regulation w histones (HAT/HDAC); patterns of histone modification are genetic

60
Q

O-glycoslyation

A

adds hydroxy group to serine or threonine

61
Q

n-glycosylation

A

acide-amide (-CONH2) to asparginine or glutamine; precursor sugar trasferred from phospho dolichol

62
Q

phosphorylation

A

phosphate linked via creating ester, uses OH group to serine, tyrosine kinase, threonine and also asparatate and histidine; phosphate group is ultimately removed by phosphatase; seen in cell growth, proliferation, differentiation, oncogenesis

63
Q

Disulfide bonds

A

inter/intra molecular disulfide (SH) bonds stablize proteins; bond between SH groups of two cysteines in ER lumen; enzyme: protein disulfide isomerase

64
Q

modifications of collagen

A

modifications are important for assembly of collagen; utilizies lysyl hydroxylases + ascorbic acid (defects–> skin/bone/join disorders

65
Q

ehlers-danlos snydrome

A

overly flexible joints due to lysyl hydroxlase defects

66
Q

Alzheimer’s Disease: mechanism

A

when normal Amyloid precurose protein breaks down to form Amyloid beta peptide more than normal
AD: misfolding/aggregation of AB –>clumps/plaques
Also: hyperphosphorylation of Tau–> neurofibrillary tangles
both mutations in APP and Tau–> familal forms , aging–> sporadic forms

67
Q

Parkinson’s

A

caused by: alhpha synuclein (AS) –> insoluble fibrils–> lewy bodies in dopamingergic neurons in substania nigra– > death of neurons–> reduced dopamine –> motor impariment

mutations of AS–> familial form, aging–> sporadic

68
Q

Huntington’s

A

mutation in huntingtin gene–> expansion of GAG triplet polyglutamine repeats –> intramolecular hbonds are formed–> misfold and aggregate–> selective death in basal ganglia

69
Q

Creutzfelt-Jacob Disease

A

cause: misfolding of prion proteins –> transmisslbe spongiform encephalopathies
danger: transmissible: can convert regular proteins to misfolded

MCM Exam 2-RH (9 decks)

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