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MCM Exam 2 > Lect 2 Functions & Dysfunctions of Protein Processing > Flashcards

Lect 2 Functions & Dysfunctions of Protein Processing Flashcards

1
Q

Start Codon

A

Methionine (Met, M)

AUG

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2
Q

Stop Codon

A

UAA

UAG

UGA

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3
Q

What is the genetic code?

How many combinations of codons are there?

What does degenerate mean?

A
  • Set of rules that convert nucleotide sequences of a gene into the AA sequence of a protein using mRNA as an intermediary
  • 61 Triplet codons for 20 AAs, 3 Stop Codons
  • Some AAs can be coded by more than 1 codon
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4
Q

Point Mutations

Silent Mutation

Missense Mutation

Nonsense Mutation

Frameshift Mutation

A
  • Silent: Does not change the AA
  • Missense: Changes AA in protein (no effect or vastly different function)
  • Nonsense: Codon –> Stop Codon (premature chain termination forms truncated version)
  • Frameshift: 1+ Nucleotides deleted or inserted into ORF
    • Out of Frame: Change in codon sequence –> alteration in AA sequence
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5
Q

How does Sickle Cell Anemia arise?

What AAs are changed?

What does this cause to happen?

What is the impact of having deformed RBCs?

A
  • Missense mutation
    • GAG to GTG: substituting Val (hydrophobic) for Glu (negatively charged/hypophillic)
  • Causes HbA to aggregate and form rigid, rod-like structures and deforms the RBCs into sickle-like shape
  • Poor oxygen capacity and tend to clog capillaries
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6
Q

What causes Duchenne Muscular Dystrophy?

Results of OOF Deletions

What is the physical result?

Results of IF Deletions

A

Large IF and OOF deletions to dystrophin gene

Little/no expression of dystrophin protein –> Severe form DMD

Muscle wasting

Truncated forms of dystrophin –> Milder form Becker muscular dystrophy

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7
Q

After transcription, pre-mRNA edited to form mRNA and exported to cytoplasm for translation

What are the components of Eukaryotic mRNA?

A

Coding region

5’ and 3’ untranslated regions

7-methylguanosine 5’ Cap

Poly(A) tail at 3’ end

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8
Q

What is the general structure of tRNA?

What are the two regions of unpaired nucleotides and their functions?

A

Cloverleaf secondary structure

Anticodon Loop: pairs with complementary codon in mRNA

3’ CCA Terminal Region: Binds the AA matching the corresponding codon

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9
Q

Aminoacyl tRNAs are complexes of tRNA with AA

Where is the AA attached?

What catalyzes this process?

What are the steps?

A
  • AA esterified to CCA sequence at 3’ end of tRNA catalyzed by aminoacyl tRNA synthetases (unique to each AA)
    • Aminoacyl tRNA synthetase catalyzes addition of AMP to COOH end of AA
    • AA transferred to cognate tRNA
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10
Q

What composes Ribosomes?

How is the structure of prokaryotic and eukaryotic ribosomes medically relevant?

What size subunits in each?

A

Proteins and rRNA

Antibiotics target prokaryotic translational machinery (ribosomes)

Eukaryotic (80S) = 60S + 40S

Prokaryotic (70S) = 50S + 30S

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11
Q

What are the three important sites on the Ribosomal complex?

A
  • Acceptor (A) Site
    • ​mRNA codon exposed to receive aminoacyl tRNA, except Met tRNA
  • Peptidyl (P) Site
    • ​aminoacyl tRNA is attached
  • Empty (E) Site
    • ​occupied by empty tRNA before exiting ribosome
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12
Q

Translation occurs in this direction

It occurs in 3 steps

A

5’ –> 3’ direction

Initiation –> Elongation –> Termination

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13
Q

Initiation

What first binds to the P site?

What is the initiator tRNA-methionine complex?

What else is added?

Translation begins with what?

A

Initiator tRNA (bound GTP) attaches to P site of small su

Methioninyl tRNA in eukaryotes is loaded on the small subunit of ribosomes on the P-site

Initiation factors (IF in prokaryotes) and eukaryotic initiation factors (eIFs) are added

Initiation codon AUG (Met)

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14
Q

Elongation:

What is this process?

What catalyzes peptide bond formation?

A
  • Activated AA attaches to initiating methionine via peptide bond
    • aminoacyl tRNA anticodon base pairs with codon on A site
    • Prior to loading, aminoacyl tRNA attached to GTP bound elongation factor
    • Loading accompanied by GTP hydrolysis and release of factor from aminoacyl tRNA
  • Peptide bond formation between AA in A and P site catalyzed by Peptidyl Transferase
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15
Q

Termination:

What triggers termination?

Stop codons are recognized by _ which bind to the _ site and causes what?

What dissociates the ribosomal complex?

A

Triggered by Stop Codons (UAA, UAG, and UGA)

Release Factors (RFs) bind to A site and cleaves ester bond (via addition of water) between C-terminus of polypeptide and tRNA

GTP Hydrolysis

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16
Q

What are polysomes?

A

Clusters of ribosomes simultaneously translating a single mRNA molecule

17
Q

GTP Hydrolysis during Translation Steps

A

Initiation: Hydrolysis of 1 GTP

Elongation: Hydrolysis of 2 GTP per AA added

Termination: Hydrolysis of 1 GTP

18
Q

Prokaryotic Elongation Inhibitors

Streptomycin

Clindamycin/Erythromycin

Tetracyclines

Chloramphenicol

A

Streptomycin: 30S su to interfere with binding fmet-tRNA (interferes with 30S association with 50S)

Clindamycin and Erythromycin (Pertussis): 50S su to disrupt translocation of ribosome

Tetracyclines: 30S su to disrupt elongation (block entry of aminoacyl-tRNA to ribosomal complex)

Chloramphenicol: inhibits peptidyl trasferase

19
Q

Eukaryotic Elongation Inhibitors

Shiga Toxin/Ricin

Diptheria Toxin

Cycloheximide

A

Shiga Toxin & Ricin: 60S su to disrupt elongation (block entry of aminoacyl-tRNA to ribosomal complex)

Diptheria Toxin: inactivates GTP-bound eEF-2 interfering with ribosomal translocation

Cycloheximide: Inhibits peptidyl transferase (activity in large subunits)

20
Q

Eukaryotic/Prokaryotic Elongation Inhibitor

Puromycin

A

Puromycin: Causes premature chain termination (prok/euk)

21
Q

Cytoplasmic Sorting Pathway destinations and process

Secretory Sorting Pathway destinations and process

A
  • Cytoplasmic:
    • Destined for cytosol, mitochondria, nucleus, peroxisomes (No translocation signals - stay in cytoplasm)
  • Secretory:
    • Proteins destined for ER, lysosomes, plasma membranes, or secretion
22
Q

Proteins with specific signals trafficked to various organelles:

Mitochondrial signals include what?

The sequence helps them interact with what?

A

N terminal hydrophobic a-helix

Chaperone proteins

23
Q

Mitochondrial Protein Import includes the usage of these transporters

What type of proteins are the chaperones?

A

Transporter in Inner Membrane (TIM) and Transporter in Outer Membrane (TOM)

Heat Shock Proteins 70 (HSP70)

24
Q

Nuclear Import is performed with what?

Small proteins can pass through specific pores but large proteins require what?

Proteins destined for nucleus have this feature

A

Nuclear Pores

Nuclear Localization Signals

Four continuous basic residues (Lys,K and Arg,R)

25
Q

Signal Sequences:

Peroxisomes

ER Lumen

Lysosomes

Secretion

Membranes

A

Peroxisome: SKL signal sequence

ER Lumne: KDEL (Lys, Aspartate, Glutamate, Leucine)

Lysosome: Mannose-6-Phosphate

Secretion: Tryptophan domain

Membranes: N terminal apolar region (stop transfer sequence)

26
Q

Secretory Pathway:

Each protein in the pathway has what?

Two properties of each protein

Describe the pathway

A
  • ER-targeting signal peptide
  • 1 or 2 basic AA (Lys or Arg) near N terminus & an extremely hydrophobic sequence (10-15) on C terminus of basic residues
  1. SRP binds to ER-targeting signal and ribosome
  2. SRP wraps around ribosome-mRNA-peptide complex, tethering to ER membrane and halting translation temporarily
  3. Translation resumes when protein directed into ER lumen
  4. Enzymes on luminal side cleave the signal to release protein
  5. Protein undergoes PTMs in ER and/or Golgi
  6. Additional signal sequences serves to guide each protein to final destination
27
Q

Lysosomal Proteins: I-Cell Disease

Tagging of lysosomal proteins with _ is _, leading to _

A

Tagging mechanism with Mannose 6 Phosphate is defective leading to high plasma levels of lysosomal enzymes

28
Q

Protein Folding

Which proteins can fold into native conformations spontaneously, and which are at risk for aggregation and proteolysis?

What is the function of chaperones (HSP70)?

What is the function of chaperonins (HSP60)?

A

Small proteins can fold spontaneously

Large proteins are at risk

Protect the protein and help fold into proper tertiary structure

Barrel shaped compartments that catalyze folding of proteins in an ATP-dependent manner

29
Q

Proteolytic Cleavage function:

A

Conversion from inactive to active form by unmasking active site

30
Q

Glycosylation

Differences between O-glycosidic and N-glycosidic

A

O-Glycosidic: O-links with -OH groups of Ser/Thr residues

N-Glycosidic: N-links with Asparagine. Precursor sugar transferred from phospho Dolichol

31
Q

Phosphorylation is the formation of an _ bond between _ and _ of an AA via the activity of this enzyme

How are phosphates removed?

Phosphorylation function?

A

Ester bond between phosphate and OH of an AA via the activity of serine/threonine and tyrosine kinase

Phosphatases

Regulates enzyme activity and protein function particularly in signaling

32
Q

Disulfide Bond Formation function and locations

Facilitated by which enzymes?

A

Inter and intra-molecular disulfide bonds stabilize proteins and form between thiol (SH) group of 2 cysteine residues (formation occurs in ER lumen)

Protein Disulfide Isomerase

33
Q

Acetylation

Proteins are typically acetylated on what AA?

What is the acetyl group donor?

Reactions are catalyzed by what enzymes?

A

Lysine Residues

Acetyl CoA

Histone acetyltransferase (HAT) or Histone Deacetylase (HDAC)

34
Q

Post Translational Modifications are important for assembly of Collagen

What is required for activity of lysyl and prolyl hydroxylases?

What results in skin, bone, and joint disorders (Ehlers-Danlos Syndrome)?

A

Ascorbic Acid

Defects in lysyl hydroxylases

35
Q

Alzheimer’s Disease

Amyloid precursor protein (APP) breaks down to form _

Misfolding/Aggregation of AB results in _

Neurofibrillary tangles results from what?

Mutations in APP and Tau cause _ of AD

Brain aging is the common denominator for _

A

Amyloid Beta Peptide (AB)

Plaques in brain (extracellular)

Hyperphosphorylation of Tau (intracellular)

Familial Forms

Sporadic Form

36
Q

Parkinson’s Disease (PD)

Aggregation of _ protein forms insoluble fibrils which deposit as _ and results in selective death in neurons

Symptoms are due to _

Mutations in AS cause _ of PD

Brain aging is the common denominator for the _

A

a-synuclein (AS)

Lewy bodies in dopaminergic neurons in substantia nigra

Reduced availability of dopamine

Familial forms

Sporadic form

37
Q

Huntington’s Disease (HD)

Cause of disease and consequences

What causes the symptoms?

A
  • Mutation in Huntingtin gene –> expansion of CAG triplet repeats
    • Causes polyglutamine repeats in abnormal HTT protein
  • Selective death of cells in BG cause the symptoms
38
Q

Creutzfeldt-Jakob Disease

Caused by what?

What does Transmissible mean?

A
  • Caused by misfolding of prion proteins
  • Infection by misfolded proteins convert normal proteins to misfolded form
    • ​Transmissible spongiform encephalopathies (TSEs)

MCM Exam 2 (14 decks)

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