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MCM Final > Functions/Dysfunctions Of Protein Processing > Flashcards

Functions/Dysfunctions Of Protein Processing Flashcards

1
Q

A protein is synthesized from the __________ to _______________

A

N-terminus

C-terminus

[sequentially adding aa’s to the C-terminus of the growing peptide chain

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2
Q

True or false: the mRNA sequence will be complementary to the coding strand

A

False, the mRNA will be identical, but replace the Ts with Us

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3
Q

How many codons code for amino acids?

A

61, 3 are stop codons that terminate translation

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4
Q

What is the start codon?

A

AUG - codes for methionine

[fMet in prokaryotes]

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5
Q

Why is the genetic code considered unambiguous and degenerate?

A

Unambiguous - each codon codes for only 1 aa

Degenerate - each amino acid can be coded for by more than one codon (exceptions = Met, Trp)

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6
Q

What type of mutation is this and what is the effect on the resulting protein?

New codon –> same amino acid

A

Silent; no effect on protein

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7
Q

What type of mutation is this and what is the effect on the resulting protein?

New codon –> new aa

A

Missense; variable effect on protein

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8
Q

What type of mutation is this and what is the effect on the resulting protein?

New codon –> stop codon

A

Nonsense; nonfunctional protein

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9
Q

What type of mutation is this and what is the effect on the resulting protein?

1+ nucleotides deleted or inserted

A

Frameshift; nonfunctional protein

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10
Q

Sickle cell anemia results from what type of mutation?

A

Missense mutation of 6th codon in allele of gene for human beta-globin, from GAG to GTG (substitutes Val for Glu)

The mutation alters the conformation of HbA, causing it to aggregate and form rigid rod-like structures which deform RBCs into sickle like shape

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11
Q

Duchenne Muscular Dystrophy results from what type of mutation?

A

Large in-frame and out of frame deletions to the dystrophin gene, leading to partially or non-functioning dystrophin protein

Leads to muscle wasting and wheelchair confinement by age 12, death by respiratory failure within 10 years

Muscle is replaced with fat and fibroid, elevated CK

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12
Q

What post translational modifications occur to pre-mRNA and what is the purpose of these?

A

5’ cap and polyA tail

Makes mRNA more soluble for transport to cytoplasm for translation

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13
Q

Each type of tRNA carries only one __________ amino acid, which is determined by its ___________ sequence

A

Activated; anticodon

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14
Q

Amino acid activation is catalyzed by _____________ ___________, which requires ______ high energy bonds from ATP

A

Aminoacyl-tRNA synthetase; 2

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15
Q

tRNA has an anticodon sequence that allows pairing with the mRNA codon, and transfers the activated amino acid on the ______ end of the correct tRNA

A

3’

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16
Q

How many aminoacyl tRNA synthetases are there?

A

20, one for each amino acid

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17
Q

What are the 2 uses of aminoacyl-tRNA synthetase?

A

Transfers AMP to the amino acid to form enzyme-bound aminoacyl-AMP

Transfers the aminoacyl group to the tRNA to activate the aa

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18
Q

There are 2 subunits to a ribosome that assemble around the mRNA: the _______ subunit positions the mRNA and the _______ removes each amino aicd and adds it to the growing peptide chain

A

Small; large

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19
Q

Compare/contrast the different ribosome structures in prokaryotes vs. eukaryotes

A

Prokaryotes = 70S (50S and 30S)

Eukaryotes = 80S (60S and 40S)

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20
Q

The ribosomal complex consists of 3 sites. At which site is the aminoacyl-tRNA attached to the growing peptide chain?

A

Peptidyl (P) site

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21
Q

The ribosomal complex consists of 3 sites. At which site does the mRNA codon accept the aminoacyl-tRNA?

A

Acceptor (A) site

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22
Q

The ribosomal complex consists of 3 sites. At which site does the tRNA sit prior to exiting the ribosome?

A

Empty (E) site

[aka Exit site]

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23
Q

Translation occurs in the 5’ to 3’ direction and consists of what 3 general steps?

A

Initiation
Elongation
Termination

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24
Q

What are the initiation sequences in prokaryotes vs. eukaryotes?

A

P = Shine-Dalgarno sequence (AGGAGG)

E = 5’cap, 3’polyA tail, Kozak sequence, and ATP dependent mRNA scan

[the initiation site determines the reading frame for the whole length of the mRNA]

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25
Q

The pre-initiator complex consists of:

an initiator tRNA to which _____ is bound, which attaches to the P site of a small subunit (_______________ tRNA in prokaryotes and ____________ tRNA in eukaryotes)

mRNA strand with ______ start codon

Other initiation factors (____ in prokaryotes, _____ in eukaryotes)

The large subunit is then added to complete the complex, which is driven by hydrolysis of ______.

A

GTP; N-formyl-methionyl tRNA; methionyl

AUG

IF; eIF

GTP

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26
Q

How can prokaryotic vs. eukaryotic translation be determined in a figure?

A

If the mRNA does not have a 5’ cap or polyA tail, it is prokaryotic

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27
Q

During elongation, the polypeptide chain is extended by the catalytic action of the ribosome:

Loading of an aminoacyl tRNA onto the ribosome, its anticodon base pairs with codon positioned on A site

Prior to loading, the aminoacyl tRNA is attached to GTP-bound ___________ _____________

Loading of tRNA is accompanied by _______ ___________ and release of GDP-bound EF from aminoacyl tRNA

Peptide bond formation is catalyzed by __________ __________

A

Elongation factor (EF)

GTP hydrolysis

Peptidyl transferase

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28
Q

What are 4 the prokaryotic elongation inhibitors?

A

Tetracycline
Chloramphenicol
Clindamycin
Erythromycin

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29
Q

______________ is a prokaryotic elongation inhibitor the inhibits peptidyl transferase in prokaryotes and mitochondria

A

Chloramphenicol

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30
Q

_____________ is a prokaryotic elongation inhibitor that binds to the small 30S subunit, blocking entry of aminoacyl tRNA to the ribosomal complex

A

Tetracycline

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31
Q

______________ and ___________ are prokaryotic elongation inhibitors that bind to large 50S subunit and block translocation of the ribosome

A

Clindamycin; erythromycin

[note that erythromycin is commonly used to treat pertussis]

32
Q

What are the 4 eukaryotic elongation inhibitors?

A

Cyclohexamide
Diphtheria toxin
Shiga toxin
Ricin

33
Q

Which eukaryotic elongation inhibitor inactivates GTP-bound eEF-2, interfering with ribosomal translocation?

A

Diphtheria toxin

34
Q

Which eukaryotic elongation inhibitor inhibits peptidyl transferase?

A

Cyclohexamide

35
Q

Which eukaryotic elongation inhibitors bind to large 60S subunit and block entry of aminoacyl tRNA to ribosomal complex?

A

Shiga toxin and Ricin

36
Q

Which elongation inhibitor causes premature chain termination in both prokaryotes and eukaryotes?

A

Puromycin

[resembles the 3’ end of the aminoacyl tRNA, enters A site and adds to growing chain, leads to premature release, mroe resistant to hydrolysis, stops the ribosome]

37
Q

What are the 3 stop codons?

A

UAA
UAG
UGA

38
Q

Termination is triggered when a stop codon resides in the ____ site, and ______ ________ are loaded

A 
A
Release factors (RFs)

This triggers peptidyl transferase to cleave the ester bond between the C terminus of the chain and the tRNA

39
Q

What is the last event prior to dissociation of the ribosomal complex?

A

GTP hydrolysis

40
Q

The __________ pathway of protein sorting typically consists of proteins destined for the cytoplasm, mitochondria, nucleus, and peroxisomes. Synthesis usually begins and ends on ribosomes in the cytoplasm.

A

Cytoplasmic

41
Q

The __________ pathway consists of proteins destined for the ER, lysosomes, secretion, or membranes. The first 20 AA of the polypeptide contains an ER-targeting signal

A

Secretory

42
Q

If any protein lacks a translocation signal, it will remain in the _____________

A

Cytoplasm

43
Q

If there is an N-terminal hydrophobic alpha helix signal peptide, where is that protein destined to go?

A

Cytoplasmic pathway - mitochondria

44
Q

If there is a KKKRK translocation signal sequence, where is the protein destined to go?

A

Cytoplasmic pathway - nucleus

45
Q

If there is a C-terminal SKL translocation signal sequence, where is the protein destined to go?

A

Cytoplasmic pathway - Peroxisomes

46
Q

If there is a C-terminal KDEL retention signal, where is the protein destined to go?

A

Secretory pathway - ER lumen

[each protein in secretory pathway contains the N-terminal hydrophobic alpha-helix ER signal peptide]

47
Q

If there is a mannose 6-phosphate translocation signal, where is this protein destined to go? What pathological condition is associated with this?

A

Secretory pathway - Lysosomes

I-cell disease

[each protein in secretory pathway contains the N-terminal hydrophobic alpha-helix ER signal peptide]

48
Q

If there is a tryptophan-rich domain signal region and absence of retention motifs, where is the protein destined to go?

A

Secretory pathway - secretion

[each protein in secretory pathway contains the N-terminal hydrophobic alpha-helix ER signal peptide]

49
Q

If there is an N-terminal apolar region (stop-transfer sequence), where is the protein destined to go?

A

Secretory pathway - membranes

[each protein in secretory pathway contains the N-terminal hydrophobic alpha-helix ER signal peptide]

50
Q

What is the purpose of the N terminal hydrophobic alpha-helix on mitochondrial proteins?

A

Allows interaction with chaperone proteins (HSP70 family)

Translocation sequences for mitochondria are recognized by TIM and TOM

51
Q

Proteins in the secretory pathway contain an ER-targeting signal peptide with 1 or 2 basic amino acids like _______ or _______, and a 10-15 residue ____________ sequence

A

Lys; Arg

Hydrophobic

52
Q

With the secretory pathway, post-translational modifications occur in the ER and/or golgi. This occurs when the _________ wraps itself around the ribosome-mRNA-peptide complex, tethering to the membrane and temporarily halting translation.

Once the protein is directed into the ER lumen, translation resumes and is directed to the ____________ space.

Enzymes then cleave the _________ to release the protein

A

SRP (signal recognition particle)

Luminal

Signal

53
Q

I-cell disease, or Mucolipidosis II, is a severe form of _____________ storage disease where the tagging of lysosomal proteins with _________ is defective, resulting in high plasma levels of those enzymes.

A

Lysosomal

Mannose 6P

54
Q

What are the clinical manifestations of I cell disease?

A

By 6 months: failure to thrive, developmental delays, physical manifestations

Abnormal skeletal development, coarse facial features, restricted joint movement, stiff claw-shaped hands, dwarfism, clouding on corneas, hepatomegaly, splenomegaly, recurrent respiratory tract infections

Death usually by age 7 due to CHF or respiratory tract infection.

55
Q

________ proteins can spontaneously fold into native conformations, ________ proteins cannot due to risk of aggregation and proteolysis.

A

Small; large

56
Q

______________ are auxiliary proteins that protect the protein, and help it to fold into its proper tertiary structure

A subset of these proteins are called ____________, which are barrel-shaped compartments that admit unfolded proteins, and catalyze their folding in an ATP-dependent manner

A

Chaperones

Chaperonins

57
Q

What disease results from a mutation in the gene for the human B-globin, which alters the conformation of HbA, causing it to aggregate and form rigid, rod-like structures?

A

Sickle cell anemia

58
Q

Alzheimer’s disease results from a mutation in the gene for __________ __________ __________, which predisposes it to misfold and aggregate to form neuritic plaques in the brain.

Supplementation with ____________ has recent clinical significance.

A

Amyloid precursor protein (APP)

Lysine

59
Q

What are prions?

A

Transmissible misfolded proteins that convert their properly folded host counterparts to the same misfolded structure that they posses

Cause diseases like CJD, Kuru, and Mad Cow

60
Q

What causes Huntington disease?

A

Mutation in the Huntington gene results in the expansion of CAG triplet repeats which results in a polyglutamine tract, resulting in an abnormal HTT protein. mHTT forms intramolecular H-bonds, which eventually misfold and aggregate

61
Q

_______________ disease results from mutated a-synuclein that aggregates to form insoluble fibrils called Lewy bodies

This is caused by an N-terminal apolar sequence (the functional form has ___________, and the __________ form has insoluble beta sheets.

Results in neuronal death in the midbrain, reducing the availability of _____________

A

Parkinson

Alpha-helix; fibril

Dopamine

62
Q

Proteolytic cleavage converts inactive forms (zymogens) to active enzymes by “unmasking” the active site. How does this apply to digestive enzymes?

A

Trypsinogen –> trypsin

Chymotrypsinogen –> chymotrypsin

63
Q

______________ is a post-translational modification where the N-terminus is bonded to an acetyl or long-chain acyl residue, or thioesterification with a long-chain acyl group

Affects N-terminus and Cys residues

A

Acylation

64
Q

______________ is a post-translational modification involving covalent linkage to an amine.

What residue does this affect?

A

Acetylation

Lysine

65
Q

______________ is a post-translational modification with a covalent bond to sugar residues and occurs in the ER as they are translated

What residues does this effect?

A

Glycosylation

O-glycosylation affects Ser, Thr

N-glycosylation affects Asn, Gln

66
Q

______________ is a post-translational modification where a phosphate is linked via formation of an ester bond between phosphate and an -OH of an amino acid

What residues are affected?

A

Phosphorylation

Ser, Tyr, Thr, Asp, His

67
Q

______________ is a post-translational modification with the addition of a -COOH group?

What residue is affected?

A

g-carboxylation

Glu

68
Q

______________ is a post-translational modification with the covalent modification with ubiquitin?

What residue is affected?

A

Ubiquitination

Lysine

69
Q

______________ is a post-translational modification with the addition of an -OH group?

What residues are affected?

A

Hydroxylation

Pro and Lys

70
Q

______________ is a post-translational modification where oxidation achieves covalent linkages of Cys residues?

A

Disulfide bonds

71
Q

______________ is a post-translational modification where an isoprenoid group such as farnesyl or geranyl-geranyl groups are added to cysteins in C-terminal CAAX or CC motifs?

A

Prenylation

72
Q

What post-translational modification is thought to play a role in diabetic cataract formation?

A

Glycosylation of lens crystallins

73
Q

What is the most common glycosylation?

A

N-linked: -NH of Asn

74
Q

Glycosylation occurs when a precursor oligosaccharide (14-residue) is synthesized on membrane-embedded dolichol, catalyzed by glycotransferases. These glycotransferases can be inhibited by antibiotic _____________

A

Tunicamycin

75
Q

What is the general result of disulfide bond formation on protein stability?

A

Makes them more stable, but can be reduced in certain conditions

76
Q

Where does the formation and reorganization of disulfide bonds occur?

A

In the ER lumen

MCM Final (14 decks)

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