2. Functions and Dysfunction of Protein Processing Flashcards
What is a Missense mutation?
A mutation that changes a single amino acid. May do nothing, or change the protien entirely.
What is a Nonsense mutation?
A mutation that changes a codon into a stop codon.
(This is also caused a null mutation)
You think you can stop? Nonsense!
What is a Frameshift mutation?
When a nucleotide is deleted or added, causing all the others to be wrong.
Like when you accidentally skip a bubble on a scantron and get a 3% on a test
What is a silent mutation?
A mutation that does not change the resulting amino acid sequence.
What occupies the 3’ end of mRNA?
A poly(A) tail.
What occupies the 5’ end of mRNA?
7-Methyl Guanosine
Sickle Cell Anemia comes from what kind of mutation?
Missense.
In Sickle Cell Anemia, what amino acid is substituted for which other amino acid?
Glutamate (Negative charge and Hydrophillic) becomes Valine (hydrophobic)
In Duchenne’s Muscular Dystrophy - what sort of mutation is found?
Frame shift due to deletion, either out of frame (Severe) or in-frame (less severe)
What gene has deletions in Duchenne Muscular Dystrophy?
The dystropin gene.
What terminal region of tRNA binds the amino acid?
The 3’ CCA Terminal Region
What enzyme serves to “activate” an Amino Acid to tRNA, and helps to ensure the fidelity of the genetic code?
Aminoacyl tRNA Synthetase
For Prokaryotic Ribosomes
What is the total Svedberg unit for the entire size?
For the large portion?
For the small portion?
Prokaryotes are 70S total
The large subunit is 50S
The small unit is 30S
For Eukaryotic Ribosomes
What is the total Svedberg unit for the entire size?
For the large portion?
For the small portion?
Eukaryotes are 80S total
The large subunit is 60S
The small subunit is 40S
In which direction does Translation occur?
5’ to 3’
Same as DNA replication
What is the initiation codon, and what does it code for?
AUG, Methionine
What high energy compound is hydrolysed to help with loading of aminoacyl tRNA?
GTP
What enzyme attaches the second peptide to the first, releasing it from the tRNA?
Peptidyl Transferase
Where does the energy for peptide transfer come from?
From the high energy bond between the amino acid and tRNA.
What binds to stop codons?
Release Factors
(Not any tRNA / amino acid)
What sort of bond is cleaved by release factor, and where is it located?
Ester Bond
Between the C terminus of the polypeptide and the tRNA’s CCA terminal region.
When all is said and done, what dissociates the entire ribosomal complex?
GTP
In which subunit does peptidyl transferase activity occur?
The large subunit, for both prokaryotes and eukaryotes.
For Streptomycin:
Does it affect Prokaryotes or Eukaryotes?
Where does it bind?
What does it disrupt?
It affects prokaryotes
It binds to the 30S subunit
It disrupts initiation of translation via binding formylmethionine-tRNA
For Shiga Toxin and Ricin:
Does it affect Prokaryotes or Eukaryotes?
Where does it bind?
What does it disrupt?
It affects Eukaryotes
It binds to the 60S subunit
Disrupts elongation
For Clindamycin and Erythromycin:
Does it affect Prokaryotes or Eukaryotes?
Where does it bind?
What does it disrupt?
It affects prokaryotes
It binds to the 50S subunit
It disrupts translocation of the ribosome
Clinda with the fat red (erythromycin) face yells at the 50 ribosomes to stop running.
For Tetracyclines:
Does it affect Prokaryotes or Eukaryotes?
Where does it bind?
What does it disrupt?
It affects prokaryotes
It binds to the 30S subunit
It disrupts elongation
For Chloramphenicol:
Does it affect Prokaryotes or Eukaryotes?
What does it disrupt?
It affects both Prokaryotes and Eukaryotes
It inhibits prokaryotic / mitochondrial peptidyl transferase
For Cycloheximide:
Does it affect Prokaryotes or Eukaryotes?
What does it disrupt?
It affects eukaryotes
It disrupts peptidyl transferase
What does Puromycin cause?
Premature chain release, which stops the ribosome.
Where does the cytoplasmic pathway send protiens? (4 places)
- Cytosol
- Mitochondria
- Nucleus
- Peroxisomes
Where does the secretory pathway send protiens?
- Endoplasmic Reticulum
- Lysosomes
- Plasma Membranes
- Secretion
(All of these are secretion / vesicle related places)
What feature of amino acids determine sorting into the cytoplasm?
A lack of sorting signal altogether.
What signal sorts amino acids into the mitochondria?
N-Terminal Hydrophobic alpha-helix (no + charges)
Imagine a cork shaped mitochondria, and the N terminal alpha helix is a corkscrew
What signal sorts into the Nucleus? (Nuclear Localization Signal)
Lysine and Arginine rich ends (four in a row)
- The Nucleus is invaded by lying pirate protiens (Lys and Arrrrg)*
- (But once the pirates get up to the membrane, they get scared and need chaperones)*
What signal determines transport into the peroxisomes?
-SKL
Surviving around all that peroxide takes SKL (skill)
What region determines protien ER entrance, and is common to every member of the secretory pathway? (ER Targeting Signal)
A positively charged alpha-helix
The protiens of the secretory pathway all start out feeling positive about their prospects. They’re going places! (Secretion)
What sequence causes an amino acid to be held in the ER? (ER retention sequence)
KDEL (Lysine Aspartate Glutamate Leucine)
_Leu_is _Ly_ed about an Asp biting his Glut, and got to stay in the ER and eat ice cream.
Out of the protiens sorted to the secretory pathway, which ones go through the golgi apparatus?
Lysosomal, cell membrane, and secretory vesicle protiens
What signal determines transport of a protien into the cell membrane?
A Stop Transfer sequence
Stop transfering me around the golgi apparatus and stick me in the membrane already!
What signal determines a protien be sent to a lysosome?
Mannose 6-Phosphate
A lysosome is a trash-_mann_
What signal determines a protien be sent from the golgi body to a secretory vesicle?
A tryptophan rich domain
The protien didn’t want to leave the cell, but it tripped (tryptophan) into the secretory vesicle.
What protien assists a nascent polypeptide get into the ER?
How does it do this?
SRP (Signal Recognition Particle)
SRP hugs the ribosome, checks for the positively charged helix, and then binds to SRP-receptor protien in the ER membrane. It does this to bring the ribosome-polypeptide close to an ER membrane protien translocator.
What is defective in I-Cell Disease? (aka Inclusion Cell Disease)
What happens as a result?
Mannose 6 phosphate
Protiens back up and lysosomes don’t work.
*The inclusions of stuff inside the lysosomes that aren't being broken down are the "inclusions" that give the disease its name. #DarrenFacts*
Oxidation of which amino acids can result in a di-sulfide bond?
Cystine
What residues can be affected by Acetylation?
Lysine
Lysine has the amine group at the end that makes a convenient target for acetylation.
What residues can be affected by Glycosylation?
Which ones are O-glycosylation targets?
Which ones are N-glycosylation targets?
Serine, Threonine, Asparagine, Glutamine
O-glycosylation: Serine, Threonine (They have the OH)
N-Glycosylation: Asparagine, Glutamine (They have the -CONH2)
- I’m Serious,There are Assassins, Glen!*
- (Sugar-high induced paranoid delusions)*
What residues are targets for Phosphorylation?
Serine Threonine Tyrosine
- Searing Three Tires*
- (Amino acids hate phosphates, so these Three kinases really Sear their Tires)*
Note: I find no evidence of relevant phosphorylation of Histidine or Aspartate residues anywhere, but it’s on the table so it goes in the last priority learning slot for me.
What two camps are there for the etiology of Alzheimers Disease
- APP to Amyloid Beta Peptide which forms plaques
- Hyperphosphorylation of Tau, which prevents it from doing its job of stabalizing microtubules, causing neurofibrillary tangles.
What causes familial Alzheimers?
What is the common factor for sporadic Alzheimers?
Mutations in APP and Tau
Brain aging. :(
What is the etiology of Parkinsons?
Hint: Protein, deposit, location
What causes the symptoms?
Aggregation of alpha-synuclein (AS) protien depositing as fibrils in the Lewy bodies of the Substantia Nigra
Reduced availability of dopamine
What causes familial Parkinsons?
What is the common denominator for the sporadic form?
Mutations in alpha-synuclein
Brain aging
What leads to Huntington’s disease?
What does this cause physiologically?
What causes the symptoms?
Mutation in Huntington Gene leads to a bunch CAG (glutamine) repeats
Polyglutamine repeats lead to misfolding and aggregations of the HTT (Huntington) protien
Selective cell death, speciffically in the basal ganglia.
What disease is characterized by infection with, or spontanious generation of, a scrapie version of the prion protein?
DarrenFacts
Creutzfeldt-Jacob Disease (CJD)
(Note: The word Scrapie is a classical name for a similar disease in sheep, thought to be caused by a misfolded prion protien)
