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SFM Exam 2 > Protein Processing > Flashcards

Protein Processing Flashcards

1
Q

What does eukaryotic mRNA contain?

A

Codons (in the coding region), 7-methyl guanosine cap at the 5’ end and poly A tail at the 3’ end

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2
Q

What are the two regions of unpaired nts on tRNA that are crucial to its functions?

A

Anticodon loop, a set of 3 consecutive nts that pair with a complementary codon in mRNA
3’ CCA terminal region which binds the aa that matches the corresponding codon

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3
Q

Describe the activation of amino acids

A

Aminoacyl tRNA synthetases catalyzes addition of AMP to COOH end of AA
AA transferred to cognate tRNA

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4
Q

What are the three important binding sites of the ribosomal complex and what are their functions?

A

Acceptor (A) site: where mRNA codon exposed to receive aminoacyl tRNA (except the Met tRNA)
Peptidyl (P) site: where aminoacyl tRNA is attached
Empty or exit (E) site: location occupied by empty tRNA before exiting ribosome

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5
Q

What is the structure of prokaryotic ribosomes?

A

Large: 50s
Small: 30s
70s complete ribosome

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6
Q

Describe the structure of eukaryotic ribosomes

A

Large: 60s
Small: 40s
Complete ribosome 80s

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7
Q

Describe the events that occur during the initiation of translation

A

Pre-initiator complex assembled
Initiator tRNA bound to a GTP attaches to P site of small su
tRNA methionine complex is loaded onto the P site of small su (met-euk and fmet-pro)
Other IFs (pro) and eIFs (euk) are added
Large su added
Translation begins with the initiation codon AUG (codes for met)

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8
Q

Describe the events that occur in elongation of translation

A

Activated AA attached to initiating met via peptide bond
Amino acyl tRNA is loaded onto the ribosome w/ anticodon base pairing with codon on the A site
Loading accompanied by GTP hydrolysis and release of factor from aminoacyl tRNA
Peptide bond forms between aa in A site and P site catalyzed by peptidyl transferase

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9
Q

Describe the events of termination of translation

A

Peptide chain release from ribosome complex
Termination triggered by stop codons
Signal ribosome to stop translation
Stop codons are recognized by release factors
Water molecule is added instead of an AA (forms COOH end)
Completed protein released and GTP hydrolysis dissociates ribosome complex

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10
Q

What are polysomes?

A

Clusters of ribosomes simultaneously translating a single mRNA molecule
Each synthesizing a polypeptide
Makes protein synthesis more efficient

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11
Q

Which three codons are considered to be the stop codons?

A

UAA, UAG and UGA

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12
Q

List the characteristics of the genetic code

A

Degenerate (some AA can be coded by more than 1 codon and 3 codons do not code for any AA)
Standard but not universal
Not punctuated and is without commas
Non-overlapping (with some exceptions)

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13
Q

Which codons codes for Met (M)?

A

AUG

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14
Q

Why is it important to study the difference between prokaryotes and eukaryotes?

A

To be able to selectively inhibit prokaryotic protein synthesis (clinical use - molecular basis for Abx)
To be able to understand the mechanism of human disease (research use - allow for the development of Tx and/or prevention)

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15
Q

Name the prokaryotic translation inhibitors

A

Streptomycin, clindamycin and erythromycin, tetracycline, and cholamphenicol

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16
Q

Name the eukaryotic translation inhibitors

A

Shiga toxin and ricin, diptheria toxin and cycloheximide

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17
Q

How does the abx streptomycin work?

A

Binds to 30s subunit and interferes with the binding of fmet-tRNA and impairs initiation
Interferes with 30s subunit association with 50s subunit

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18
Q

How do the abx clindamycin and erythromycin work?

A

Bind to large 50s subunit blocking translocation of the ribosome

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19
Q

How does the abx tetracycline work?

A

Binds to small 30s su blocking entry of aminoacyl-tRNA to ribosomal complex and impairs elongation

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20
Q

How does the abx cholamphenicol work?

A

Inhibits peptidyl transferase activity and impairs peptide bond formation

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21
Q

How do shiga toxin and ricin work as eukaryotic translation inhibitors?

A

Binds to large 60s subunit blocking entry of aminoacyl-tRNA to ribosomal complex

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22
Q

How does diptheria toxin inhibit translation in eukaryotics?

A

Inactivates GTP bound EF-2 interfering with ribosomal translocation

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23
Q

How does cycloheximide work as a eukaryotic translation inhibitor?

A

Inhibits peptidyl transferase and impairs peptide bond formation

24
Q

What is the one and only elongation inhibitor and how does it work?

A

Puromycin
Causes premature chain termination in pro and euk so only used for research purposes
Resembles the 3’ of the aminoacyl tRNA
Enters the A site and adds to the growing chain
Forms puromycylated chain leading to premature chain release

25
What is a silent mutation?
Doesn’t change the AA
26
What is a missense mutation?
Changes AA in the protein with either no effect on protein function or a protein with vastly different function
27
What is a nonsense mutation?
Codon changes into a stop codon causing premature chain termination Also called null mutation Protein either degraded or formed as truncated version
28
What is a frameshift mutation?
One or more nts are deleted or inserted into the ORF | OOF causes change in the codon sequence and alters the AA sequence of the protein
29
What is a point mutation?
Affects a single base pair in the protein coding region or the ORF of a gene may result in a different AA being incorporated into protein 4 types: silence, missense, nonsense and frameshift
30
What disease is an example of a missense mutation?
Sickle cell anemia
31
Describe the mutation that results in sickle cell anemia
Missense mutation of 6th codon in the allele of the gene for beta globin Hb Mutation changes GAG to GTG —> glutamic acid (- charge and hydrophilic) to valine (hydrophobic) Changes conformation of HbA which causes it to aggregate and form rigid rod like structures (RBCs are sickle shaped)
32
Describe Duchenne muscular dystrophy
Large in frame and OOF deletions to the dystrophin gene leading to non functioning dystrophin protein Leads to muscle wasting, wheelchair bound by 12 y/o, death by respiratory failure within 10 years, sx onset typically 3-5 yrs In frame deletion results expression of truncated forms of dystrophin giving rise to Becker muscle dystrophy (milder form)
33
Describe the cytoplasmic pathway of protein sorting
For proteins destined for cytosol, mitochondria, nucleus and peroxisomes Synthesis begins and ends on free ribosomes/polysomes in cytoplasm
34
Describe mitochondrial protein import
Translocation sequences recognized by transporters present in the mitochondrial membrane (transporter in inner membrane TIM and transporter in OMM TOM) Proteins are passed across TOM and TIM Hsp70 protects and binds to unfolded protein headed to mitochondria
35
Describe nuclear protein import
Imported via nuclear pores Small proteins able to pass thru specific pores Large proteins (>40kDa) require nuclear localization signals 4 continuous basic residues (Lys and Arg)
36
What is the mitochondrial translocation signal?
N terminal hydrophobic alpha helix signal peptide
37
What is the translocation signal for the nucleus?
KKKRK signal sequence | Lys Arg rich
38
What is the translocation signal for peroxisomes?
C terminal SKL signal sequence | Ser Lys Leu
39
What is the translocation signal for the cytoplasm?
None
40
Describe the secretory pathway for protein sorting
For proteins destined for ER, lysosomes, plasma membranes or for secretion Translation begins on free ribosomes but terminates on ribosomes sent to the ER Each protein has an ER targeting signal peptide
41
What are two properties of proteins in the secretory sorting pathway?
1 or 2 basic AA (Lys or Arg) near N terminus | An extremely hydrophobic sequence (10-15 AA) on C terminus of the basic residues
42
What role does the signal recognition particle (SRP) play in the secretory pathway of protein sorting?
SRP binds to the ER targeting signals and the ribosome during translation SRP wraps itself around ribosome mRNA peptide complex tethering it to the ER membrane and halting translation Translation resumes when protein goes into ER lumen Protein is released and undergoes post translational modifications in the ER/golgi Additional sequence serves to guide each protein to final destination
43
What is the signal sequence for ER lumen proteins?
KDEL | Lys, Asp, Glu, Leu
44
What is the signal sequence for lysosomal proteins?
Mannose 6 phosphate (M6P)
45
What is the signal sequence for cell membrane proteins?
N terminal apolar sequences
46
What is the signal sequence for secretory proteins?
Tryptophan rich domain
47
What is inclusion cell disease?
Lysosomal proteins not tagged with M6P Defective or missing GlcNAC phosphotransferase and enzyme that adds M6P to lysosomal hydrolase Enzymes are not phosphorylated so they’re not sorted into vesicles and not derived into lysosomes Instead they are carried to cell surface and severed (found in blood) High plasma levels of lysosomal enzymes
48
What are the main methods of post translational processing?
Glycosylation, phosphorylation, disulfide bonds, acetylation
49
What occurs after protein synthesis?
Protein sorting, post translational modifications, protein folding, proteolysis and degradation
50
How are small proteins folded?
Can fold into native conformations spontaneously
51
How are large proteins folded?
Cannot fold spontaneously and are at risk for aggregation and proteolysis Can either use a chaperone (Hsp70) which protects and helps the protein fold Or can use a chaperonin (Hsp60) which is a barrel shaped compartment that catalyzes the proteins folding in an ATP dependent manner
52
Describe proteolytic cleavage
Converts inactive forms to active enzymes by unmasking active site (e.g. trypsinogen and chymotrypsinogen to trypsin and chymotrypsin) Converts nascent precursor proteins to mature ones (e.g. pro-insulin to insulin)
53
What is glycosylation?
Extracellular proteins (cell surface and plasma proteins) are covalently linked to sugar residues in the ER lumen to form the mature protein
54
What is O linked glycosylation?
Formed with the hydroxyl groups of serine or threonine residues
55
What is N linked glycosylation?
Always formed with acid-amie of asparagine (and glutamate)
56
What is acetylation?
A way to regulate gene expression and protein function Histones are acetylated or deacetylated on lysine residues Acetylation catalyzed by HAT —> activates Deacetylation catalyzed by HDAC —> silences Heritable
57
What are the 4 types of covalent modifications?
Glycosylation, acetylation, phosphorylation and disulfide bond formation

SFM Exam 2 (25 decks)

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