Protein Processing Flashcards
What does eukaryotic mRNA contain?
Codons (in the coding region), 7-methyl guanosine cap at the 5’ end and poly A tail at the 3’ end
What are the two regions of unpaired nts on tRNA that are crucial to its functions?
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
Describe the activation of amino acids
Aminoacyl tRNA synthetases catalyzes addition of AMP to COOH end of AA
AA transferred to cognate tRNA
What are the three important binding sites of the ribosomal complex and what are their functions?
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
What is the structure of prokaryotic ribosomes?
Large: 50s
Small: 30s
70s complete ribosome
Describe the structure of eukaryotic ribosomes
Large: 60s
Small: 40s
Complete ribosome 80s
Describe the events that occur during the initiation of translation
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)
Describe the events that occur in elongation of translation
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
Describe the events of termination of translation
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
What are polysomes?
Clusters of ribosomes simultaneously translating a single mRNA molecule
Each synthesizing a polypeptide
Makes protein synthesis more efficient
Which three codons are considered to be the stop codons?
UAA, UAG and UGA
List the characteristics of the genetic code
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)
Which codons codes for Met (M)?
AUG
Why is it important to study the difference between prokaryotes and eukaryotes?
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)
Name the prokaryotic translation inhibitors
Streptomycin, clindamycin and erythromycin, tetracycline, and cholamphenicol
Name the eukaryotic translation inhibitors
Shiga toxin and ricin, diptheria toxin and cycloheximide
How does the abx streptomycin work?
Binds to 30s subunit and interferes with the binding of fmet-tRNA and impairs initiation
Interferes with 30s subunit association with 50s subunit
How do the abx clindamycin and erythromycin work?
Bind to large 50s subunit blocking translocation of the ribosome
How does the abx tetracycline work?
Binds to small 30s su blocking entry of aminoacyl-tRNA to ribosomal complex and impairs elongation
How does the abx cholamphenicol work?
Inhibits peptidyl transferase activity and impairs peptide bond formation
How do shiga toxin and ricin work as eukaryotic translation inhibitors?
Binds to large 60s subunit blocking entry of aminoacyl-tRNA to ribosomal complex
How does diptheria toxin inhibit translation in eukaryotics?
Inactivates GTP bound EF-2 interfering with ribosomal translocation
How does cycloheximide work as a eukaryotic translation inhibitor?
Inhibits peptidyl transferase and impairs peptide bond formation
What is the one and only elongation inhibitor and how does it work?
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
What is a silent mutation?
Doesn’t change the AA
What is a missense mutation?
Changes AA in the protein with either no effect on protein function or a protein with vastly different function
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
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
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
What disease is an example of a missense mutation?
Sickle cell anemia
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)
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)
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
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
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)
What is the mitochondrial translocation signal?
N terminal hydrophobic alpha helix signal peptide
What is the translocation signal for the nucleus?
KKKRK signal sequence
Lys Arg rich
What is the translocation signal for peroxisomes?
C terminal SKL signal sequence
Ser Lys Leu
What is the translocation signal for the cytoplasm?
None
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
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
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
What is the signal sequence for ER lumen proteins?
KDEL
Lys, Asp, Glu, Leu
What is the signal sequence for lysosomal proteins?
Mannose 6 phosphate (M6P)
What is the signal sequence for cell membrane proteins?
N terminal apolar sequences
What is the signal sequence for secretory proteins?
Tryptophan rich domain
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
What are the main methods of post translational processing?
Glycosylation, phosphorylation, disulfide bonds, acetylation
What occurs after protein synthesis?
Protein sorting, post translational modifications, protein folding, proteolysis and degradation
How are small proteins folded?
Can fold into native conformations spontaneously
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
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)
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
What is O linked glycosylation?
Formed with the hydroxyl groups of serine or threonine residues
What is N linked glycosylation?
Always formed with acid-amie of asparagine (and glutamate)
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
What are the 4 types of covalent modifications?
Glycosylation, acetylation, phosphorylation and disulfide bond formation
