Functions and Dysfunctions of Protein Processing Flashcards
nonsense mutation
codon changes into a stop codon
cause of sickle cell anemia
missense mutation of 6th codon in the allele of the gene for human beta-globin (HBB)
GAG –> GTG
Glutamate (hydrophilic) –> Val (hydrophobic)
cause of Duchenne muscular dystrophy
large in frame and out of frame deletions to the dystrophin gene
results in little to no expression of the dystrophin protein
in frame deletions result in milder form (Becker muscular dystrophy)
3’ CCA terminal region
region of tRNA that binds the AA that matches the corresponding codon
makes sure that the correct AA is being matched
two step process of amino acid activation
- aminoacyl tRNA synthetase catalyzes addition of AMP to COOH end of AA (AA + AMP)
- AA transferred to cognate tRNA (AA + tRNA)
aminoacyl tRNA synthetase
serves as the second genetic code
is specific for each AA
maintains the fidelity of protein synthesis but ensuring the correct AA is bound
EIF2, 4E, 4G
- what are these
Eukaryotic initiation factors
Shine delgarno sequence
Site of initiation for prokaryotes
Initiator tRNA
Binds to GTP during initiation, which is bound to the P site of the small subunit; forms the methioninyl tRNA
What do elongation factors do
Proofreading
Release factors
Recognize stop codons and promote the release of completed proteins from the tRNA; they bind to the A site and cleave the ester bond between the C terminus of the polypeptide and the tRNA
What dissociates the ribosomal complex
GTP hydrolysis
How does streptomycin work
Binds to 30S subunit of prokaryotic ribosomes to disrupt initiation of translation; interferes with the binding fmet-tRNA; interferes with 30s subunit association with the 50s subunit
How does shiga toxin work
Binds to the 60s subunit of eukaryotic ribosomes to disrupt elongation
How do clindamycin and erythromycin work
They bind to the 50s subunit of prokaryotic ribosomes to disrupt translocation of the ribosome; commonly used to treat pertussis
How do tetracyclines work
They bind to the 30s subunit of prokaryotic ribosomes to disrupt elongation; blocks the entry of aminoactyl tRNA to the ribosomal complex
What does initiation require to start
Hydrolysis of one GTP (equivalent to one ATP)
What does elongation require
Hydrolysis of two GTP per amino acid added (equivalent to two ATP)
What does termination require
Hydrolysis of one GTP (equivalent of one ATP)
How does the diptheria toxin work
Inactivates GTP bound to eEF-2 and inhibits elongation in eukaryotes
How does chloramphenicol work
Inhibits peptidyl transferase in prokaryotes and mitochondria, which forms the peptide bond between the amino acid in the A site with the AA in the P site
How does cycloheximide work
Toxin from streptomyces griseus
Inhibits peptidyl transferase in eukaryotes; blocks elongation
Puromycin
From streptomyces alboniger
Causes premature chain termination in prokaryotes and eukaryotes; resembles the 3’ end of aminoacylated tRNA and enters the A site which stops the ribosome
Inhibits elongation
Proteins that use the cytoplasmic pathway for protein sorting are destined for where
Cytosol, mitochondria, nucleus, peroxisomes
Proteins that use the secretory pathway for protein sorting are destined for where
ER, lysosomes, plasma membranes, or for secretion
What type of amino acid chains are characteristic of the cytoplasmic pathway
Hydrophobic
What kind of amino acids are characteristic of the secretory pathway
Positive charged
NH3+
The proteins going to the nucleus in the cytoplasmic pathway are special in what way
Rich in lysine and arginine
The proteins going to the peroxisome are special in what way
They have an SKL sequence
Proteins destined for the mitochondria in the cytoplasmic pathway of protein sorting are special in what way
N terminal hydrophobic alpha helix
Require TIM and TOM
N terminal hydrophobic alpha helix
Sequence for proteins destined for the mitochondria in protein sorting
Helps the proteins interact with chapter one proteins
TIM and TOM
Transporter in inner membrane (TIM)
Transporter in outer membrane (TOM)
Transporters that pass protein across the mitochondrial membranes
Heat shock proteins 70 (HSP70)
Important chaperone that protects unfolded proteins in the mitochondria
How are proteins destined for the nucleus imported
through nuclear pores; small proteins don’t have to unwind; large proteins require nuclear localization signals
Translocation signal for proteins destined fro the mitochondria
N terminal hydrophobic alpha-helix signal peptide
Translocation signal for proteins destined for the nucleus
KKKRK signal sequence
Translocation signal for proteins destined for the peroxisomes
C-terminal SKL signal sequence
Translocation signal for proteins destined for the ER lumen
C-terminal KDEL retention signal
K - lysine
D - aspartic acid
E - glutamic acid
L - leucine
Translocation signal for proteins destined for lysosomes
Mannose-6-phosphate signal group
Disease: I-cell disease
Translocation signal for proteins destined for secretion
Tryptophan-rich domain signal region absence of retention motifs
Translocation signal for proteins destined for the membrane
N-terminal apolar region (stop transfer sequence)
Each protein in the secretory pathway has what
An ER—targeting signal peptide (15-60 amino acids at N terminus of the protein)
- 1-2 basic amino acids (Lys or Arg) near N terminus
- extremely hydrophobic sequence on C terminus
Signal recognition particle (SRP)
In the secretory pathway
Binds to the ER-targeting signal on the protein and the ribosome during translation; wraps itself around the ribosome-mRNA-peptide complex, tethering it to the ER membrane and halting translation temporarily
I-cell disease
Severe form of lysosomal storage disease; Defect in tagging of lysosomal proteins with mannose 6-P; lysosomes won’t be able to break down molecules which causes a large # of symptoms
Chaperones
Protects large proteins and helps them fold into proper tertiary structure
Ex: HSP70 (uses ATP)
Chaperonins
Have barrel shaped compartments that admit unfolded proteins and catalyze their folding in an ATP dependent manner
Ex: HSP60 (uses ATP)
How does proteolytic cleavage work
Unmasking the active site which converts inactive forms to active enzymes
Trypsinogen —> chymotrypsinogen
Trypsin —> Chymotrypsin
Also converts nascent precursor proteins to mature ones
Proinsulin —> insulin
Acetylation
- what type of linkage
- functional group
- where does it get the functional group
- happens to what amino acid post translationally
Covalent linkage to amine
Amine (-NH3+)
Acetyl CoA
Lysine
O-Glycosylation
- what proteins
- Functional group
- happens to which amino acids post translationally
extracellular proteins (cell surface and plasma proteins)
Hydrolysis (-OH)
Serine, threonine
N-glycosylation
- what proteins
- functional group
- happens to which amino acids post translationally
extracellular proteins
Acid-amine (-CONH2)
Asparagine
Phosphorylation
- linkage
- functional group
- happens to which amino acids post translationally
- what is the purpose
Ester bond between phosphate and -OH of AA
Hydroxyl (-OH)
Serine, tyrosine, threonine
- also aspartate, histidine
regulates enzyme activity, protein function, cell growth
Disulfide bonds
- linkage
- functional group
- happens to which amino acids post translationally
- where does this occur
- facilitated by
Oxidation —> covalent linkage of cysteine residues Sulfhydryl (-SH) Cysteine ER lumen protein disulfide isomerases
Disulfide bonds in post translational modification
Form between thiol (SH) group of 2 cysteine residues
Occurs in the ER lumen
Protein disulfide isomerases
Facilitates disulfide bond formation in post translational modification of proteins
Ehlers-Danlos Syndrome
Results from a defect in Lysyl hydroxylase in post translational modification; cannot assemble collagen correctly
Characterized by overly flexible joints, blood vessel walls, intestines, or ruptured uterus
Epidermolysis Bullosa Symplex
Defect in lysyl hydroylase; cannot form collagen correctly
Blisters on skin
How does Alzheimer’s disease form
Misfolding/aggregation of amyloid beta peptide (AB) that forms plaques in the brain WITH hyperphosphorylation of Tau (microtubullary stimulating agent)
Sporadic form cause versus familial form cause of AD
Familial: mutations in APP (Amyloid precursor protein) and Tau
Sporadic: brain aging
How is Parkinson’s caused
Aggregation of a-synuclein (AS) forms insoluble fibrils that deposit as Lewy bodies in dopaminergic neurons in substantial nigra
Selective death of these neurons and reduced availability of dopamine
Familial form of PD versus sporadic form
Familial: mutations in AS (a synuclein)
Sporadic: brain aging
How is Huntington’s disease caused
Mutation in the Huntington gene that causes expansion of CAG triplet repeats
Results in polyglutamine repeats, forming intramolecular H-bonds which will misfold and aggregate
Selective death of cells in basal ganglia
How is Creutzfeldt-Jacob disease caused
Misfolding of prion proteins
It’s a type of transmissible spongiform encephalopathies
missense mutation
changes amino acid
frameshift mutation
one or more nucleotides are deleted or inserted into out of frame; change in the codon sequence and consequently alteration in the amino acid sequence
aminoacyl tRNAs
tRNA + amino acid
catalyzed by aminoacyl tRNA synthetase
what forms during initiation of translation (3 things)
formation of 1) mRNA, 2) small ribosomal subunit, and 3) initiator tRNA pre-initiation complex
what are the three stop codons
UAA
UAG
UGA
what does the release factor do
cleaves ester bond between C terminus of polypeptide and the tRNA
catalyze the addition of water instead of an AA
HSP60
heat shock protein 60
chaperonin; folds large proteins
what is essential for activity of lysyl and prolyl hydroxylase
ascorbic acid
