Functions and dysfunctions of protein processing Flashcards
Describe a silent mutation
A point mutation occurs, but it does not change the amino acid
Describe a missense mutation
A point mutation occurs, leading to a different amino acid
Describe a nonsense mutation
A point mutation occurs which leads to a stop codon. The protein synthesis stops there
Describe a frame shift mutation
Nucleotides are added or deleted, making all amino acids downstream incorrect
Describe sickle cell anemia
A missense mutation leads to a substitution of Val (hydrophobic) to Glu (negative). The protein (HbA) aggregates and RBCs are deformed
Describe Duchenne muscular distrophy
A large frame shift mutation occurs, leading to non-functional dystrophin. Leads to muscle wasting (wheelchair 12yrs and respiratory failure around 14yrs)
Describe the structure of mRNA
7-methylguanosine cap at the 5’ end and polyA at 3’ end. The coding region is located between two untranslated regions.
Describe tRNA
Cloverleaf shape;
anticodon loop is complementary to mRNA;
3’CCA terminal region where aa is attached
describe aminoacyl tRNA synthetase
attached appropriate tRNA to it’s aa
why is aminoacyl tRNA synthetase considered the “second genetic code”?
It binds the correct aa to it’s correlated tRNA. If this makes an error, then the wrong protein will be translated. It is the same as if it was transcribed incorrectly from the DNA
Describe ribosomes
translation center; 2 subunits; different in structure in eu vs prokaryotes
3 sites of action
why is the different structure in eukaryotic ribosomes and prokaryotic chromosomes significant?
certain antibiotics and toxins can target one organism’s while not effecting the other
What are the 3 sites on the ribosome? what do they do?
Acceptor site-where mRNA sites to interact with tRNA
Peptidyl site-where tRNA attaches
Empty/Exit site-where empty tRNA sits before exiting ribosome
what are the 3 stages of translation?
initiation, elongation, termination
describe initiation phase of translation
formation of mRNA, small subunit and initiator tRNA make a complex
Describe the elongation phase of translation
activated by AA attached to Met by forming peptide bond
Describe termination phase of translation
peptide chain is release from ribosome
What is the start codon in mRNA? Why is that significant?
AUG;
initiator rRNA is scanning for it to begin building polypeptide
What is eIF4E and eIF4G?
What are Eukaryotic initiation factors (eIFs)?
eIF4E (rate limiting step of translation because it’s got to meet ribosome)
What are Eukaryotic initiation factors (eIFs)?
proteins involved in the initiation phase of eukaryotic translation. These proteins help stabilize the formation of the functional ribosome around the start codon and also provide regulatory mechanisms in translation initiation.
What is eIF2?
eIF2 mediates the binding of tRNAiMet to the ribosome in a GTP-dependent manner.
It is hydrolized (released to form GDP) when tRNA finds the AUG codon
When does the large subunit bind in translation?
once AUG is found by tRNA and eIF2 is released from tRNA-Met molecule (making room for large SU).
When does the aminoacyl tRNA bind to ribosome?
After large SU attaches to small SU
When is the first peptide bond formed in the ribosome?
once the aminoacyl tRNA binds to the ribosome it then binds the aa with the initiator tRNA’s Met
What is the name for initiator tRNA when Met is attached? is it different in prokaryotes?
methioninyl tRNA;
N-formylmethiononinyl tRNA is prokaryotes
What are EF-1 and EF-2?
elongation factors. The first facilitates the loading of aatRNA to A-site, the second facilitates the shifting of tRNA down to the next site to vacate the A-site for the next aatRNA (prokaryotes EF-Tu adn EFG)
What is used to power enlongation?
GTP is bound to elongation factors and the hydrolyzation of it releases the factors
Describe peptidyl transferase and it’s function
it is located on the ribosome and it catalyzes the peptide bonding. It is regulated by rRNA.
Energy for this rxn comes from high energy bond between aa and tRNA
Describe the steps of termination
- Stop codons UAA,UAG or UGA terminate translation
- release factor (RF) binds to A-site;
- peptide released when RF moves to P-site
- COOH added to peptide
- GTP hydrolysis dissociates ribosome complex
how many GTP used in each step of translation?
one to initiate
two per amino acid to elongate
one to terminate
How does diptheria toxin work?
inactivates EF2-GTP to inhibit elongation
How does shiga toxin, streptomycin, clindamycin, tetracyclines work?
binds to ribosome subunit to disrupt translation
What signal needs to be added to a protein to send it to the cytoplasm?
no signal;
What signal needs to be added to a protein to send it to the mitochondria?
N terminal hydrophobic alpha helix
What does the N terminal hydrophobic alpha helix do?
it helps traffic proteins to the mitochondria;
it also helps proteins interact with chaperone proteins (heat shock: protect linear structure of proteins)
It also is recognized by transporters on mitochondrial membranes (TIM & TOM)
Describe mitochondrial protein import
Protein has signal sequence on it
- signal recognized by TOM complex
- protein sent linearly through TOM and TIM
- peptidase is in matrix to cleave signal i think
Describe nuclear import of proteins
nuclear pores allow small proteins through
Large proteins >40kDa require nuclear location signal (4 continuous basic residues i.e. Lys and Arg)
What are cytoplasmic protein pathway destinations?
cytoplasm, mitochondria, nucleus, peroxisomes
What is the nuclear signal sequence for proteins?
KKKRK
What is the peroxisome signal sequence for proteins?
SKL
Ser, lys, leu
What are the destinations of the secretory pathway of protein sorting?
ER lumen, lysosomes, secretion, and membranes
What is the signal sequence for sending proteins to the ER lumen?
C-terminal KDEL retention signal
What is the signal sequence for sending proteins to lysosomes?
Mannose 6-phosphate signal group
I-cell disease
What is the signal sequence for secretion of proteins?
Tryptophan-rich domain signal sequence, Absence of retention motifs
What is the signal sequence for sending proteins to the membrane?
N-terminal apolar region (stop transfer sequence
What is KDEL?
ER lumen protein sequence;
K-lysine, D-aspartic acid, E-glutamic acid, L-leucine
Describe the secretory pathway
protein has to go to ER to finish translation, then it is modified in the ER or Golgi
How does protein get tranlated into the ER?
- ER signal on N cap of protein on ribosome
- 15-60aa on N terminus
- 1 or two basic aa (Lys or Arg) near N terminus
- extreme hydrophobic sequence on C terminus of these basic residues
- SRP binds ER signal
- SRP receptor binds it to ER
- peptidase cleaves signal to restart translation into ER through protein translocator
describe chaperones and chaperonins
Chaperones aid in folding the protein correctly
Chaperonins are large, barrel structures that fold proteins inside with ATP energy
Describe HSP60
heat shock protein 60 is a chaperonin inside the mitochondria which aids in preventing misfolding of protein in stress and other times
describe HSP70
heat shock protein 70. The Hsp70s are an important part of the cell’s machinery for protein folding, and help to protect cells from stress
describe proteolytic cleavage
converts active enzymes by unmasking the active site.
it cleaves part of the zymogen and exposes the active site
name examples of proteolytic cleavage
trypsinogen (all in trypsin family
proinsulin to insulin
What are four post-translational modifications
glycosylation,
phosphorylation,
disulfide bond formation,
and acetylation
Describe glycosylation
extracellular proteins,
covalently linked to sugar in ER lumen,
o-glycosidic or n-glycosidic linkage
how are o-links formed in glycosylation?
hydroxyl groups of Ser or Thr residues
how are n-links formed in glycosylation?
Asp;
precursor sugar transferred from phospho Dolichol
Describe phosphorylation of proteins
Ester bond is formed between phosphate and OH of aa
Serine/threonine/tyrosine kinases
Describe disulfide bond formation
inter and intra-molecular disulfide bonds stabilize proteins
form between thiol (SH) group of cysteines
formed IN ER by protein disulfide isomerases
Describe acetylation
acetyl CoA is donor
lysine residues acetylated
Histones are Acetylated or deacetylated on N terminal
histone modifications are heritable
What role does vitamin C play in
Ascorbic acid is important to form lysyl hydroxylases
These enzymes are essential to collagen modification/assembly
Think lysine deamination and proline hydroxylation
What could defects in Lysyl hydroxylases result in?
skin, bone, and joint disorders:
Ehlers, Danlos, Nevo, Bruck, Epidermolysis
Describe Alzheimer’s disease
-Amyloid beta peptide is misfolded and forms plaques in brain (extracellular)
-hyperphosphorylation of Tau (neurofibrillary tangles; intracellular)
These are familial forms. Sporadic form is just from brain aging.
Describe Parkinson’s disease
aggregation of alpha-synuclein protein forms insoluble fibrils which deposit as Lewy bodies in dopaminergic neurons in substantia nigra
- results in death to neuron
- symptoms because of no dopamine
- mutations to AS cause familial form, brain aging is sporadic form
huntington disease
huntington gene mutation results in expansion fo CAG triptlet repeats
results in polyglutamine repeats in HTT protein
-misfolds and aggregates
-selective death of cells in basal ganglia causes symptoms
describe creutzfeldt-jakob disease
prions
infectious- causes other proteins to misfold
Transmissible spongiform encephalopathies (TSEs)
