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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
Initiation of translation
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
26
Where are EIF4s attached?
Poly-A tail
27
What is the bond from one amino acid (in A site) to the growing chain (P site?) By which enzyme?
Peptide bond (CO-NH) by Peptidyl transferase
28
Elongation of Translation
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
Termination of Translation
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
Stop Codons
UAA, UAG, UGA U Are Away, U are Gone, U Go Away
31
Polysomes
cluster of ribosomes that collectively make polypeptide efficiently
32
streptomycin
prokaryotic; binds to 30s to disrupt initiation
33
chloramphenicol
inhibits peptidyl transferase in the mitochondria of prokaryotes
34
clindamycin & erythromycin
prokaryotic; bind to 50s and blocks translocation of ribosome
35
erythromycin
treats purtussis
36
streptomycin
prokaryotic; binds to 30s and interfers with binding fmet-tRNA (first tRNA)--> interferes w joining 30s and 50s
37
cycloheximide
eukaryotic; inhibits peptidyl transferase
38
diphtheria
eukaryotic; inactives GTP-bound eEF-2 and interferes w ribosomal translocation
39
shiga toxin & ricin
eukaryotic; binds to 60s and blocks entry of aminoacyl-tRNA to ribosomal complex
40
puromycin
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
Cytoplasmic pathway
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
secretory pathway
protein sorting pathway for proteins destined for ER, lysosomes, plasma membrane or for secretion;
43
signal & pathway that sends to Mitochondria
cytoplasmic; N terminal hydrophobic alpha helix
44
signal & pathway that sends to nucleus
cytoplasmic; lysine and arginine rich
45
signal & pathway that sends to peroxisome
cytosplasmic; SKL sequence
46
signal & pathway for secretory proteins
secretory pathway; Trp-rich domain
47
signal & pathway that sends to lysosome
secretory pathway; Mannose 6 phopshate
48
signal & pathway that sends out of cell
secretory pathway; Stop tsrf
49
signal & pathway that sends to ER lumen
secretory pathway; lys-asp-glu-leu (KDEL)
50
how do proteins pass through the mitochondrial membrane?
TOM (outer) & TIM (inner) and protected by binding to heat shock protein 70 (HSP70)
51
Where does translation occur for secretory pathway?
translation begins on free ribosome but ends on ribosomes that are going to ER
52
Signal peptide for secretory pathway
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
signal recognition particle (SRP)
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
how does the protein get released?
enzymes on luminal side cleave the signal and release it additional signals will tell it where to go
55
I-cell disease
due to: lack of mannose 6P enzyme
56
protein folding
small proteins spontaneously fold into naive conformations; large proteins need chaperones & chaperonins to ensure protection and proper folding
57
chaperonins
barrel shaped compartments that admit unfolded proteins and use ATP to help fold
58
proteolytic cleavage
converts inactive zymogen --> active enzyme
59
acetylation
adding a covalent bond to Amine (-NH3) on lysine; critical for gene regulation w histones (HAT/HDAC); patterns of histone modification are genetic
60
O-glycoslyation
adds hydroxy group to serine or threonine
61
n-glycosylation
acide-amide (-CONH2) to asparginine or glutamine; precursor sugar trasferred from phospho dolichol
62
phosphorylation
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
Disulfide bonds
inter/intra molecular disulfide (SH) bonds stablize proteins; bond between SH groups of two cysteines in ER lumen; enzyme: protein disulfide isomerase
64
modifications of collagen
modifications are important for assembly of collagen; utilizies lysyl hydroxylases + ascorbic acid (defects--> skin/bone/join disorders
65
ehlers-danlos snydrome
overly flexible joints due to lysyl hydroxlase defects
66
Alzheimer's Disease: mechanism
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
Parkinson's
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
Huntington's
mutation in huntingtin gene--> expansion of GAG triplet polyglutamine repeats --> intramolecular hbonds are formed--> misfold and aggregate--> selective death in basal ganglia
69
Creutzfelt-Jacob Disease
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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