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MCM Exam 2 > (3) Functions and Dysfunctions of Protein Processing > Flashcards

(3) Functions and Dysfunctions of Protein Processing Flashcards

1
Q

What does AUG code for?

A

Met (M), START codon

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2
Q

What are the three STOP codons?

A

UAA, UAG, UGA

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3
Q

What is a codon?

A

A group of 3 consecutive nucleotides

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4
Q

What are the four different categories of mutations?

A
  1. Silent mutation
  2. Missense mutation
  3. Nonsense mutation
  4. Frameshift mutation
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5
Q

What happens with a silent mutation?

A

Does not change the amino acid

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6
Q

What happens with a missense mutation?

A

Changes amino acid in the protein

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7
Q

What happens with nonsense mutation?

A

Codon changes into a STOP codon;

protein either degraded or formed as a truncated version

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8
Q

What happens with a frameshift mutation?

A

Change in the codon sequence and consequently alteration in the amino acid sequence

*MAJOR EXAMPLE: Duchenne Muscular Dystrophy

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9
Q

CLINICAL CORRELATION:

Sickle Cell anemia:

A

MISSENSE mutation

  • Substitutes Val (hydrophobic) for Glu (neg., hydrophilic)
  • Deforms RBCs
  • Deformed erythrocytes have poor oxygen capacity and clog capillaries
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10
Q

CLINICAL CORRELATION:

Duchenne Muscular Dystrophy

A

FRAMESHIFT MUTATION

  • Deletions in dystrophin gene
  • Muscle wasting
  • In-frame deletions result in expression of truncated forms of dystrophin: milder form BECKER muscular dystrophy
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11
Q

What is the mRNA 5’ cap made of?

A

7 Methyl Guanosine at 5’ end

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12
Q

What is the mRNA poly(A)tail?

A

Repeating A’s at the 3’ end

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13
Q

What are tRNA?

A

“Transfer” RNAs

  • Have binding site for both codons (in mRNA) and amino acid)
  • Match amino acids to codons in mRNA
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14
Q

What is the structure of tRNA?

A

Cloverleaf Shape:

ONE END=Anticodon loop

OTHER END= 3’ CCA Terminal region, binds amino acid that matches corresponding codon

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15
Q

Aminoacyl tRNAs?

A
  • complex of tRNA w/ AA
  • catalyzed by AMINOACYL tRNA synthetases
  • each tRNA charged with the correct AA to maintain fidelity of protein synthesis
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16
Q

Ribosomes have ____ subunits

A

2; a large and small subunit

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17
Q

What is the difference b/w prokaryotic and eukaryotic ribosomes?

A

Prokaryotic: 70S, large=50S, small=30S

Eukaryotic: 80S, large 60S, small=40S

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18
Q

What are the three important sites of the ribosomal complex?

A
  1. Acceptor site (A) site
  2. Peptidyl (P) site
  3. Empty (E) exit site
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19
Q

What are the three steps of translation?

A
  1. Initiation
  2. Elongation
  3. Termination
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20
Q

Describe INITIATION of translation, elongation and termination via WHITEBOARD GO!

A

Did you do it? Hope so.

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21
Q

What are polysomes?

A
  • Clusters of ribosomes simultaneously translating a single mRNA molecule
  • Makes protein synthesis more efficient
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22
Q

What are the two major pathways for protein sorting?

A
  1. Cytoplasmic pathway

2. Secretory pathwy

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23
Q

What is the function of the cytoplasmic pathway?

A

*For proteins destined for CYTOSOL, MITOC., NUCLEUS, and PEROXISOMES

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24
Q

What is the function of the secretory pathway?

A

*For proteins destined for ER, LYSOSOMES, PMs, or for FAT SECRETION

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25
Q

Proteins that are targeted for the mitochondria have…

A

N-terminal hydrophobic alpha helix

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26
Q

Proteins that are signaled to the nucleus have…

A

Lots of Lys(K) and Arg(R)

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27
Q

Proteins that are signaled to the peroxisome have…

A

-SKL

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28
Q

Secretory pathway:

What is the ER targeting signal?

A

(+) charged aa sequence at N terminus

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29
Q

Secretory pathway:

What signals proteins to stay in RER?

A

K(Lysine)
D(Aspartic acid)
E(Glutamic Acid)
L(Leucine)

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30
Q

Secretory pathway

What signals protein to lysosome?

A

Mann 6-P

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31
Q

Secretory pathway:

What signals protein to secrete protein out into cytosol?

A

Trp-rich domain

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32
Q

Nuclear Import:

How do materials get into the nucleus?

A
  • Imported via nuclear pores
  • Small proteins able to pass through specific pores
  • Large proteins >40kDa require a NUCLEAR LOCALIZATION SIGNALS
  • FOUR continuous basic residues (Lys and Arg)
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33
Q

What is Alzheimer’s disease?

A

Loss of memory, cognitive function, language

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34
Q

What is Parkinson’s disease?

A

Impairment of fine motor control

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35
Q

What is Huntington’s disease?

A

Loss of movement and cognitive functions and psychiatric problems

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36
Q

What is Crutzfeldt-Jacob disease?

A

Failing memory, behavioral changes, lack of coordination and visual disturbances. Late stages involve mental deterioration blindness, weakness of extremities and coma

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37
Q

What is the manifestation of Alzheimer’s disease?

A
  • Amyloid beta peptide (ABeta)
  • Amyloid beta plaques in brain
  • Hyperphosphorylation of Tau (neurofibrillary tangles
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38
Q

What is the manifestation of Parkinson’s disease (PD)?

A
  • Aggregation of alpha-synuclein (AS) –> deposit as LEWY bodies in dopaminergic neurons in substantia nigra
  • Sx. due to reduced availability of dopamine
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39
Q

What is the manifestation of Huntington’s disease (HD)?

A
  • Mutation in Hungingtin gene; results in expansion of CAG triplet repeats
  • Results in Polyglutamine repeats
  • Selective death of cells in basal ganglia cause the sxs
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40
Q

What is the manifestation of Creutzfeldt-Jakob disease (HD)?

A
  • Caused by misfolding of PRION proteins
  • **Transmissible
  • Belongs to Transmissible spongiform encephalopathies (TSEs)
  • SPONGIFORM
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41
Q

What is the central dogma of molecular biology?

A

Replication - Transcription - Translation

42
Q

How are tRNAs activated?

A

AMINOACYL tRNA SYNTHETASE catalyzes the addition of AMP to COOH at the end of AA

43
Q

Ribosome structures differ between prokaryotes and eukaryotes. How is this medically relevant?

A

Use antibiotics to target prokaryotic translational machinery

44
Q

Translation occurs in the ___’ to ____’ direction

A

5’ –> 3’

45
Q

Translation initiation:

Where does it occur in prokaryotes?

A

Shine-Delgarno (SDG) sequence (AGGAGG)

46
Q

Translation initiation:

Where does it occur in eukaryotes?

A

5’ cap, 3’ poly-A tail

47
Q

Translation initiation:

All known mRNA molecules contain …

A

signals that define the beginning of each encoded polypeptide chain

48
Q

Translation initiation:

Where does the MET add?

A

Small SU of ribosomes on the P site

49
Q

Translation initiation:

What initiation factors are included in prokaryotes vs eukaryotes?

A

Proks: IF

Euks: eLFs

50
Q

Translation begins with the initiation codon _____

A

AUG (Methionine)

51
Q

WHITEBOARD: Explain ELONGATION

A

GOOOOoooOOOoo

52
Q

Elongation:

Activated aa attached to initiating methionine via a ______ bond

A

peptide

53
Q

Elongation:

How is the polypeptide chain extended?

A

Loading of aminoacyl tRNA onto the ribosome so that the anticodon base pairs with codon positioned on A site

54
Q

Elongation:

Prior to loading, the aminoacyl tRNA is attached to a ____ bound elongation factor

A

GTP

55
Q

Elongation:

Loading accompanied by ____ and _____ from aminoacyl tRNA

A

GTP hydrolysis; release of factor

56
Q

Elongation:

What is the peptide formation between aa in the A and P site catalyzed by?

A

Peptidyl transferase

57
Q

Termination:

What is termination triggered by?

A

STOP CODONS

UAA, UAG, UGA

*Release factor binds to the A site

58
Q

Termination:

Stop codons are recognized by:

A

Release factors (RFs)

59
Q

Termination:

RFs bind to the _____ of the ribosome containing the stop codon and cleaves the ______

A

A site; ester bond b/w the C terminus of the polypeptide and the tRNA

60
Q

Termination:

______ dissociates ribosomal complex

A

GTP Hydrolysis

61
Q

What are the ribosome subunits for prokaryotes?

A

30S, 50S [70S]

62
Q

What are the ribosome subunits for eukaryotes?

A

40S, 60S [80S]

63
Q

Ribosome key components to remember:

What binds to the 30S subunit to disrupt initiation of translation?

A

Streptomycin

64
Q

Ribosome key components to remember:

What binds to the 60S subunit to disrupt elongation?

A

Shiga Toxin

65
Q

Ribosome key components to remember:

What does Streptomycin do?

A

Binds to the 30S subunit to disrupt initiation of translation

66
Q

Ribosome key components to remember:

What does Shiga toxin do?

A

Binds to the 60S subunit to disrupt elongation

67
Q

Ribosome key components to remember:

What two medications bind to the 50S subunit to disrupt translocation of the ribosome?

A

Clindamycin and erythomycin

68
Q

Ribosome key components to remember:

What to Clindamycin and erythomycin do?

A

Bind to the 50S subunit to disrupt translocation of the ribosome

69
Q

Ribosome key components to remember:

________ bind to the 30S subunit to disrupt elongation

A

Tetracyclines

70
Q

Ribosome key components to remember:

What does Tetracycline do?

A

Binds to the 30S subunit to disrupt elongation

71
Q

Ribosome key components to remember:

_________ is housed in the large subunits

A

Peptidyl transferase activity

72
Q

Initiation requires hydrolysis of:

A

ONE GTP

73
Q

Elongation requires hydrolysis of:

A

TWO GTP per amino acid added

74
Q

Termination requires hydrolysis of:

A

ONE GTP

75
Q

What does Diphtheria do?

A

Inactivates EF2-GTP and inhibits elongation

76
Q

What are the (4) prokaryotic elongation inhibitors?

A
  • Tetracycline
  • Chloramphenicol
  • Clindamycin/Erythromycin
  • Streptomycin
77
Q

What does Chloraphenicol do?

A

Inhibits peptidyl transferase

*Prok

78
Q

What does Clindamycin/Erythromycin do?

A

Binds to large 50S SU blocking translocation of the ribosome

*Prok

79
Q

What does Streptomycin do?

A

Binds to 30S subunit, interferes with the binding fmet-tRNA. Interferes with 30S subunit association with 50S subunit

*Prok

80
Q

What are the four eukaryotic elongation inhibitors?

A
  • Cycloheximide
  • Diptheria toxin
  • Shiga Toxin
81
Q

What does Cycloheximide do?

A

Inhibits peptidyl transferase

*Euk

82
Q

What does Diphtheria toxin do?

A

Inactivates GTP bound- eEF-2 interfering with ribosomal translocation

*Euk

83
Q

What does Shiga toxin/Ricin do?

A

Binds to large 60S SU, blocking entry of aminoacyl tRNA to ribosomal complex

84
Q

What does Puromycin do?

A

Causes premature chain termination

*elongation inhibitor

85
Q

Cytoplasmic Pathway:

Proteins synthesized in this pathway have _________. Stay in cytoplasm

A

NO TRANSLOCATION SIGNALS

86
Q

What are TIM and TOM?

A

Transporters in the mitochondrial membrane

TOM: Transporter in Outer membrane

TIM: Transporter in Inner membrane

87
Q

Unfolded proteins are protected by binding to chaperones, in particular _______

A

Heat Shock Proteins 70 (HSP70)

88
Q

What is the fx of signal recognition particle (SRP)?

A

Binds to the ER-targeting signal and the ribosome during translation;

SRP wraps itself around the ribosome-mRNA-peptide complex, halts translation temporarily

89
Q

What are HSP60 and HSP70 examples of?

A

Chaperone proteins

90
Q

Post-translational processing:

What is proteolytic cleavage?

A

Converts inactive forms to active enzymes by unmasking active site

Converts nascent precursor proteins to mature ones

91
Q

What are the 4 post translational covalent modifications?

A
  1. Glycosylation
  2. Phosphorylation
  3. Disulfide bond formation
  4. Acetylation
92
Q

Post Translational Modifications:

Acetylation:

What? Functional Group? Residue Affected?

A

Covalent linkage to amine

Amine (-NH3)

Lys

93
Q

Post Translational Modifications:

Glycosylation

What? Functional Group? Residue Affected?

A

O-glycosylation(hydroxyl -OH) ; Ser, Thr

N-glycosylation (Acid Amide (-CONH2) ; Asn (Asparagine)

94
Q

Post Translational Modifications:

Phosphorylation

What? Functional Group? Residue Affected?

A

Phosphate linked via esterification

Hydroxyl (OH)

Ser, Thr & Tyrosine Kinase

*regulated enzyme activity and protein function

95
Q

Post Translational Modifications:

Disulfide bonds

What? Functional Group? Residue Affected?

A

Oxidation to achieve covalent linkage of cysteine residues

Sulfhydryl (-SH)

Cys

96
Q

Phosphate removed by:

A

Phosphatases

97
Q

Post Translational Modifications:

How are acetylation reactions catalyzed?

A

Histone acetyltransferases (HAT)

of

Histone deacetylase (HDAC)

98
Q

CORRELATION BOX:

Sickle cell anemia

A

MISSENSE MUTATION THAT….

changes HYDROPHOBIC (VAL) to HYDROPHILIC (GLU)

  • Aggregate and form rigid, rod-like structures
  • Deforms RBCs
  • Poor oxygen capacity, clog capillaries
99
Q

CORRELATION BOX:

Duchenne muscular dystrophy (DMD)

A
  • Large in-frame and out of frame deletions to the DYSTROPHIN GENE
  • Muscle wasting
100
Q

Initiation requires hydrolysis of _______

A

One GTP

101
Q

Elongation requires hydrolysis of _______

A

2 GTP per amino acid added

102
Q

Termination requires hydrolysis of _____

A

1 GTP

MCM Exam 2 (13 decks)

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