Protein Processing Flashcards
This is where protein synthesis occurs.
Ribosomes
This contains codons to code for the amino acids in proteins.
mRNA
This type of RNA matches an mRNA codon with the amino acid it codes for (moves alone APE).
tRNA
These are tRNA and the amino acid bound together.
Aminoacyl tRNAs
These make sure the appropriate amino acids pair with their respective tRNAs.
Aminoacyl tRNA synthetases
What are the steps in amino acid activation?
1) Aminoacyl transferase binds ATP to amino acid, PP is released
2) Aminoacyl tRNA synthetase binds AMP-amino acid to tRNA, AMP is used
In this stage of translation, the ribosome assembles around mRNA and the first tRNA (carrying Met – AUG start codon).
Initiation
This is the stage of translation where the amino acid chain gets longer and moves along APE sites. Peptide bonds are formed between new amino acids.
Elongation
This stage of translation is when the finished polypeptide chain is released. It begins when the stop codon enters the ribosome, which triggers a series of events that separate the chain from its tRNA.
Termination
Why is it important to study the difference in protein synthesis between prokaryotes and eukaryotes?
- To be able to selectively inhibit prokaryotic protein synthesis (clinical use – molecular basis for the development of antibiotics)
- To be able to understand the mechanism of human diseases (research use – allow for the development of treatment and/or prevention)
What are the ribosome subunits for prokaryotes?
30S
50S
What are the ribosome subunits for eukaryotes?
40S
60S
Peptide transferase activity is housed in the (LARGE/SMALL) ribosomal subunits.
Large
This binds to 30S subunit and interferes with the binding of fmet-tRNA (starting residue in synthesis of proteins in bacteria) and impairs initiation. Interferes with 30S subunit association with 50S subunit.
Streptomycin
***Prokaryotic translation inhibitor (antibiotic)
These bind to large 50S subunit, blocking translocation of the ribosome (can’t move along APE).
Clindamycin
Erythromycin
***Prokaryotic translation inhibitors (antibiotics)
This binds to small 30S subunit, blocks entry of aminoacyl-tRNA to ribosomal complex and impairs elongation.
Tetracycline
***Prokaryotic translation inhibitors (antibiotics)
This inhibits peptidyl transferase activity and impairs peptide bond formation in prokaryotes.
Chloramphenicol
***Prokaryotic translation inhibitor (antibiotic)
These bind to large 60S subunit, blocking entry of aminoacyl-tRNA to ribosomal complex.
Shiga toxin
Ricin
***Eukaryotic translation inhibitors
This inactivates GTP-bound EF-2 (elongation factor), interfering with ribosomal translocation.
Diphtheria toxin
***Eukaryotic translation inhibitors
This inhibits peptide transferase activity and impairs peptide bond formation in eukaryotes.
Cycloheximide
***Eukaryotic translation inhibitor
This elongation inhibitor causes premature chain termination in prokaryotes and eukaryotes.
Puromycin
Puromycin resembles the 3’ end of the __________ and enters the ______ site and adds to the growing chain.
Aminoacylated-tRNA
A
T/F. Puromycin forms a puromycylated chain, leading to rapid chain elongation.
False. Puromycin forms a puromycylated chain, leading to premature chain release.
Puromycin is more resistant to _________ and stops the ribosome from functioning.
Hydrolysis
_______ mutations that affect a single base pair in the protein coding region or the open reading frame of a gene may result in a different amino acid being incorporated into protein.
Point
This type of mutation does NOT change the amino acid.
Silent mutation
This type of mutation changes the amino acid in the protein with either no effect on protein function or a protein with vastly different function.
Missense mutation
This type of mutation makes a codon change into a stop codon, causing premature chain termination. Protein is either degraded or formed as a truncated version.
Nonsense mutation
***Also called null mutation
In this type of mutation, one or more nucleotides are deleted or inserted into ORF. Out of frame causes change in the codon sequence and consequently alteration in the amino acid sequence of the protein (i.e., DMD, beta thalassemia)
Frameshift mutation
This disease arises from a missense mutation of the 6th codon in the allele of the gene form human Beta-globin (HBB), a subunit of adult hemoglobin.
Sickle cell anemia
What type of mutation is sickle cell anemia?
Missense mutation
In sickle cell anemia, the mutation changes ______ to ______ which changes ________ (negatively charged, hydrophilic) to _______ (hydrophobic).
GAG
GTG
Glutamic acid
Valine
In sickle cell anemia, change in the amino acid alters conformation of ______ which causes it to aggregate and form rigid, rod-like structures. This deforms the RBCs into the sickle-like shape.
HbA
In sickle cell anemia, deformed erythrocytes have poor _______ capacity and tend to clog _________, further restricting blood supply to tissues.
Oxygen
Capillaries
What type of mutation is DMD?
Frameshift mutation
DMD consists of large in-frame and out-of-frame deletions to the ________ gene, which leads to partially or non-functioning ________ protein.
Dystrophin
Dystrophin
OOF (out-of-frame) deletions result in little/no expression of dystrophin protein, giving rise to a (MILD/SEVERE) form of DMD. Presented in 1:3500 males.
Severe
DMD leads to muscle wasting, confinement to wheelchair by the age of ______ and death by respiratory failure within 10 years, symptoms typically onset by years ______.
12
3-5
In-frame deletions result in expression of truncated forms of dystrophin, giving rise to a milder form of the disease called ________ muscular dystrophy.
Becker
What steps are taken after protein synthesis?
Protein sorting Post-translational modifications Protein folding Proteolysis Degradation
What two pathways can protein sorting take?
Cytoplasmic pathway
Secretory pathway
What are the types of post-translation modifications?
Glycosylation
Phosphorylation
Disulfide bonds
Acetylation
The cytoplasmic pathway for protein sorting is for proteins destined for…
Cytosol
Mitochondria
Nucleus
Peroxisomes
In the cytoplasmic pathway, protein synthesis begins and ends on ______ ______ in cytoplasm.
Free ribosomes
In the cytoplasmic pathway, the absence or presence of certain translocation _______ play a role in final targeting.
Signals
The secretory pathway for protein sorting is for proteins destined for…
ER
Lysosomes
Plasma membranes
For secretion
In the secretory pathway, translation begins on free ribosomes but terminates on ribosomes sent to the _____. These proteins have ______ targeting signal sequences present on the first ______ amino acid residues of the polypeptide.
ER
ER
20
What is the translocation signal for mitochondria (cytoplasmic pathway)?
N-terminal hydrophobic alpha-helix
What does the mitochondrial translocation signal allow the protein to interact with to keep the unfolded protein protected and reach the appropriate transporters?
Chaperones (HSP70)
The mitochondrial translocation signals are recognized by transporters present in the mitochondrial membrane. What are these transporters?
TIM (transporter in inner membrane)
TOM (transporter in outer membrane)
T/F. Proteins are passed across TOM and TIM once they reach the mitochondria.
True
In nuclear import of proteins, they are imported via nuclear ______. Small proteins are able to pass through specific ______, while large proteins require _______ _______ _______.
Pores
Pores
Nuclear localization signals
What does the nuclear localization signal consist of?
Four continuous basic residues (Lys and Arg)
***KKKRK
ALL secretory pathway proteins have an ER-targeting signal peptide that is 15-60 amino acids at N-terminus of protein. What does the signal consist of?
– 1 or 2 basic amino acids (Lys or Arg) near N-terminus
– Extremely hydrophobic sequence (10-15 residues) on C-terminus side of the previous basic residues
A _______ ______ _______ binds to the ER-targeting signal and the ribosome during translation. It wrap itself around the ribosome-mRNA-peptide complex, tethering it to the ER membrane and halting translation temporarily.
Signal recognition particle (SRP)
When the SRP tethers the complex to the ER membrane, translation resumes when the protein is directed where?
Into ER lumen
***Enzymes on luminal side cleave the signal to release the protein
After the protein is in the ER lumen, it undergoes post-translational modifications in the ER and/or _______. Additional signal sequences serve to guide each protein to their final destination.
Golgi
What is the signal sequence for proteins destined for ER lumen (secretory pathway)?
KDEL
Lysine – Aspartic acid – Glutamic acid – Leucine
What is the signal sequence for proteins destined for lysosomes (secretory pathway)?
Mannose-6-phosphate
What is the signal sequence for proteins destined for the membrane (secretory pathway)?
N-terminal apolar sequences
What is the signal sequence for proteins destined for secretion (secretory pathway)?
Tryptophan-rich domain
In this disease, the tagging of lysosomal proteins with mannose-6P is defective. Due to this, the proteins are secreted from the cell rather than being sent to lysosomes.
I-cell disease
I-cell disease causes high plasma levels of lysosomal enzymes, and by 6 months there is FTT and developmental delays and physical manifestations. There are recurrent _______ _______ _______ and death frequently occurs by age 7, usually due to _______ or the recurrent _______ ________ _______.
Respiratory tract infections
CHF
Respiratory tract infections
In post-translational processing, protein folding occurs. (SMALL/LARGE) proteins can fold into native conformations spontaneously. (SMALL/LARGE) proteins cannot and are at risk for aggregation and proteolysis.
Small
Large
Large proteins need auxiliary proteins called _________, which protect the protein and help fold it into the proper tertiary structure.
Chaperones (HSP70)
Other proteins called ________ have barrel-shaped compartments that admit unfolded proteins and catalyze their folding in an ATP-dependent manner.
Chaperonins (HSP60)
In this post-translational process, it converts inactive forms to active enzymes by unmasking active site (i.e., trypsinogen to trypsin and chymotrypsinogen to chymotrypsin).
Proteolytic cleavage
In this post-translational process, it converts nascent precursor proteins to mature ones (i.e., proinsulin to insulin).
Proteolytic cleavage
What are the possible post-translational covalent modifications?
Glycosylation
Phosphorylation
Disulfide bond formation
Acetylation
This PTM is a covalent linkage to amine.
Acetylation (-NH3+)
In O-glycosylation, the functional group is ______. In N-glycosylation, the functional group is _______.
Hydroxyl (-OH)
Acid-amide (-CONH2)
In PTM acetylation, what amino acid undergoes the modification?
Lys
In glycosylation, what amino acids undergo the modification?
- O-glycosylation = Ser; Thr
- - N-glycosylation = Asn (could be Gln)
In PTM phosphorylation, there is a phosphate linked via esterification. What amino acids undergo the modification?
Ser, Tyr, Thr, Asp, His
This PTM is the oxidation to achieve covalent linkage of cysteine residues.
Disulfide bonds (-SH)
What amino acid is affected in disulfide bonds?
Cys
Extracellular proteins (cell surface proteins and plasma proteins) are __________. They are covalently linked to sugar residues in the ER lumen.
Glycosylated
N-linked glycosylated proteins have precursor sugar transferred from…
Phospho Dolichol
In PTM phosphorylation, there is a formation of an _______ bond between phosphate and -OH of an amino acid.
Ester
In PTM phosphorylation, the ester bond is formed by using the activity of _______/_______ and ________ ________.
Serine/Threonine (-OH group)
Tyrosine kinase
Inter- and intra-molecular disulfide bonds stabilize many proteins. These bonds form between _______ (SH) groups of 2 _______ residues.
Thiol
Cysteine
Formation and reorganization of disulfide bonds occur where?
ER lumen
What are disulfide bonds facilitated by?
Protein disulfide isomerases
Proteins are typically acetylated on ________ residues, and use ________ as the acetyl group donor.
Lysine
Acetyl CoA
Histones are acetylated and deacetylated on their N terminal lysines – critical for gene regulation. Acetylation reaction is catalyzed by ________ _________ and deacetylation is catalyzed by _________ _________.
Histone acetyltransferase (HAT) Histone deacetylase (HDAC)
Pattern of histone modifications are _________.
Heritable
This is the most abundant structural protein in vertebrates, and is heterotrimeric.
Collagen
Lysines in collagen are modified to form __________, further glycosylated with addition of glucose and galactose. Some lysines are deaminated to _________.
5-hyrdoxylysines
Aldehydes
Some pralines in collagen are hydroxylated to __________.
Hydroxyprolines
This is essential for the activity of lysyl and prolyl hydroxylases.
Ascorbic acid (vitamin C)
What happens when there are defects in lysyl hydroxylases?
Skin, bone, and joint disorders
i.e., Ehlers-Danlos syndrome; Nevo syndrome; Bruck syndrome; Epidermolysis Bullosa Simplex)
This collagen related disease involves overly flexible joints, walls of blood vessels, intestines, or uterus may rupture.
Ehlers-Danlos Syndrome
This collagen related disease occurs when there are blisters on the skin.
Epidermolysis Bullosa Simplex
This neurodegenerative disorder is a loss of memory, cognitive function, and language.
Alzheimer’s disease (AD)
This neurodegenerative disorder is an impairment of fine motor control, but cognition is fine.
Parkinson’s disease (PD)
This neurodegenerative disorder is a loss of movement and cognitive functions and psychiatric problems.
Huntington’s disease (HD)
This neurodegenerative disorder involves failing memory, behavioral changes, lack of coordination and visual disturbances. Late stages involve mental deterioration, blindness, weakness of extremities, and coma. It is infectious/transmissible.
Creutzfeldt-Jacob disease (CJD)
“Mad Cow”
In AD, the _______ _______ protein breaks down to form _______ ______ ________.
Amyloid precursor (APP) Amyloid beta peptide (AB)
In AD, the misfiling/aggregation of AB (amyloid beta peptide) forms ________ in the brain (occurs extracellular).
Plaques
In AD, there is __________ ______ ________, which is a protein in the cell (occurs intracellular).
Hyperphosphorylation of Tau (neurofibrillary tangles)
In AD, mutations in APP and Tau cause (SPORADIC/FAMILIAL) forms in which people get the disease in their 40s. Brain aging is the common denominator for the (SPORADIC/FAMILIAL) form of AD.
Familial
Sporadic
In PD, there is an aggregation of __________ protein that forms insoluble fibrils which deposit as _______ _______ in dopaminergic neurons in substantia nigra. Results in selective death of neurons.
Alpha-synuclein (AS)
Lewy bodies
PD symptoms are due to reduced availability of what?
Dopamine
In PD, mutations in AS cause (SPORADIC/FAMILIAL) forms of the disease. Brain aging is the common denominator for the (SPORADIC/FAMILIAL) form.
Familial
Sporadic
In HD, there is a mutation in the Huntington gene that results in expansion of _______ triplet repeats. This results in abnormal _________ repeats in an abnormal Huntington protein. Forms intramolecular H-bonds, which eventually misfold and aggregate.
CAG
Polyglutamine
In HD, the selective death of cells in the ______ ______ cause the symptoms.
Basal ganglia
CJD is caused by misfolding of _______ proteins.
Prion
CJD is __________, meaning an infection by misfolded proteins convert other normal proteins to misfolded form.
Transmissible
CJD belongs to the group of _________ ________ _________.
Transmissible spongiform encephalopathies (TSEs)
**Spongiform = appearance of infected brains, filled with holes and looks like sponge under microscope
How many GTP are utilized in each step of translation?
Initiation = 1 GTP Elongation = 2 GTP for every amino acid Termination = 1 GTP (used to break last bond and release protein)
