Functions and Dysfunctions of proteins Flashcards
Each group of 3 consecutive nucleotides in RNA is called a _______
Codon
Mutation that does not change the amino acid.
Silent
Mutation that changes amino acid in the protein with vastly different function.
Missense
Example of disease caused by missense mutation
Sickle Cell Anemia On 6th codon in the allele of the gene for human β-globin (HBB), a subunit of adult hemoglobin.
GAG (Glu) to GTG (Val)
Negatively charged hydrophilic to hydrophobic
Codon changes into a stop codon causing premature chain termination.
Nonsense Mutation (null mutation)
Protein either degraded or formed as a truncated version.
What mutation causes Duchenne Muscular Dystrophy (DMD) and Becker Muscular Dystrophy?
Nonsense mutations in the dystrophin gene lead to partially or non-functional dystrophin protein.
Out of frame deletions cause DMD.
In frame cause BMD (truncated forms)
Deletion or insertion where one or more nucleotides are deleted or inserted into the open reading frame.
Out of frame causes change in the codon sequence and consequently alteration in the amino acid sequence
Frameshift.
E.g. Duchenne Muscular Dystrophy, beta thalassemia
Components of mRNA
- Codons (present in coding region)
- 7-methylguanosine cap at the 5′ end
- Poly(A) tail at the 3′ end.
What makes up the structure of tRNA?
Set of 3 consecutive nucleotides that pair with mRNA.
3’ CCA terminal region which binds the amino acid that matches the corresponding codon.
“Cloverleaf”
How are amino acids bound to tRNA “ativated”?
Catalyzed by enzymes called aminoacyl tRNA
synthetases which help to add AMP to COOH end of amino acids.
Units of Eukaryotic Ribosomes in size.
Large 60s
Small 40s
Total 80s
Units of prokaryotes in size
50S Large
30S Small
70S Total
What does the A site of a ribosome do?
mRNA codon exposed to receive aminoacyl tRNA, except the met tRNA
What does the P site of a ribosome do?
Where aminoacyl tRNA is attached.
What does the E site do?
Location occupied by empty tRNA before exiting ribosome
How do Eukaryotes identify the start of translation?
mRNA 5’ cap, 3’ poly-A tail, the Kozak sequence and an ATP-dependent mRNA scan
mRNA molecules also contain signals that define the beginning of there polypeptide chain
How do Prokaryotes identify the start of translation?
Shine Dalgaro sequence or AGGAGG
What are the initiation factors mentioned in eukaryotic translation?
elF4E
elF4G
elF2
What is an intiator tRNA?
Bound to GTP and attaches to P site of small subunit
Codon is AUG (codes for methione)
N-formylmethioninyl tRNA in
prokaryotes and methioninyl tRNA in eukaryotes
What happens when the initiator tRNA’s GTP is hydrolyzed in initiation?
The large subunit binds to DNA and translation begins
What are the steps of elongation in translation?
The incoming aminoacyl tRNA is attached to a GTP-bound elongation factor.
Loading of an aminoacyl tRNA anticodon so it base pairs at the A site with codon
Loading accompanied by GTP hydrolysis and release of factor from aminoacyl tRNA
How is the peptide bond formed between the A and P site in elongation?
Catalyzed by peptidyl transferase.
What are the stop codons?
UAA, UAG and
UGA
What is a Release Factor?
Promote the release of a complete protein from tRNA
Bind to A site of ribosome containing the stop codon
and cleaves the ester bond between the C terminus of
the polypeptide and the tRNA.
Catalyze the addition of water instead of AA
Large ribosomal subunit leaves with hydralyzation of GTP
At the very end of translation, what fuels the dissociation of the ribosomal complex?
GTP hydrolysis
Prokaryote Elongation inhibitors
Streptomycin - 30s (30s and 50s association)
Tetracycline - 30s (aminoacyl-tRNA to complex)
Chloramphenicol -peptidyl transferase
Clindamycin and erythromycin - 50s (translocation of ribosome)
(STCCE)
“sticky”
What is erthromycin used to treat?
Purtussis
Inhibits peptidyl transferase
Cycloheximide
Toxin from Streptomyces griseus: inhibits peptidyl transferase (euk.)
Cycloheximide
From Corynebacterium diphtheriae: inactivates GTP-bound eEF-2, interfering with ribosomal translocation (euk.)
Diptheria toxin
Toxin that binds to large 60S SU (euk.), blocking entry of aminoacyl-tRNA to ribosomal complex
Shiga toxin and ricin
Binds to large 60S SU (euk.), blocking entry of
aminoacyl-tRNA to ribosomal complex
Puromicin
Enters A site of ribosome and creates puromycylated chains.
Pathway where synthesis begins and ends on free ribosomes in the cytoplasm.
Can be triggered by the absence or presence of certain translocation signals.
Cytoplasmic pathway
Pathway of protein sorting destined for the ER, lysosomes, plasma membranes, or for secretion.
Synthesis begins at the ribosomes, ends at the ER
First 20 amino acid residues of the polypeptide have ER
targeting signal sequences
Secretory pathway
Signal for transportation into mitochondria and its purpose.
N terminal alpha-helix
Helps them to interact with chaperone proteins (heat shock family)
Translocation sequences recognize TIM and TOM on the mitochondrial membrane
How are large proteins >40 kDa moved into the nucleus?
Nuclear localization signals
What do nuclear localization signals have as AA residues?
Lys and Arg
What is the signal sequence for ER Lumen proteins?
KDEL
K=lysine
D=aspartic acid
E=Glutamate
L=Leucine
What is the signal sequence for lysosomal proteins?
Mannose 6-phosphate
Signal sequence for membrane proteins
N terminal a polar region
The signal sequence for secretory proteins.
Tryptophan
What does each protein in the secretory pathway have?
An ER targeting signal peptide
What are the features of an ER target signaling peptide?
15-60 amino acids at N terminus of protein
1 or 2 basic amino acids (Lys or Arg) near N terminus
Hydrophobic sequence (10-15 residues) on C terminus of the basic residues
______ wraps itself around the ribosome-mRNA-peptide complex, tethering it to the ER membrane, halting it and redirecting it to the ER lumen.
Signal recognition particle (SRP)
Enzymes on luminal side cleave the protein.
PTM mods then occur in ER or GA
What is a disease in which tagging of lysosomal proteins with mannose 6p is defective?
I-cell disease
A severe form of lysosomal storage disease
High plasma levels of lysosomal enzymes
By 6 months: failure to thrive and developmental delays and physical manifestations
Abnormal skeletal development, coarse facial features, restricted joint movement,
stiff claw-shaped hands, short-trunk dwarfism, clouding on the cornea
Hepatomegaly, splenomegaly, occasionally heart valves
Development delays of their motor skills, cognitive delays
Recurrent respiratory tract infections:
Death frequently occurs by age 7, usually due to congestive heart failure or recurrent respiratory tract infections
Proteins that help protect large proteins and assist in folding them into their proper shape.
Chaperons
Large barrel shape compartments for unfolded proteins that catalyze their folding in an ATP-dependent manner.
Chaperonins
Converts inactive forms to active enzymes by
unmasking active site.
&
Converts nascent precursor proteins to mature
ones
Proteolic cleavage
What is essential to the enzymes involved in the post-translation modification of collagen?
Ascorbic acid is essential for the activity of lysyl and prolyl hydroxylases.
What types of proteins are glycosylated?
Where are they glycosylated?
Extracellular proteins
the ER lumen, processed to mature protein as traveled through ER and Golgi.
What are the O glycosidic proteins links?
O-links are formed with the hydroxyl groups of Ser or
Thr residues.
What are the N-glycosidic protein links?
N-linked are always with Asparagine. Precursor sugar
transferred from phospho Dolichol
Formation of an ester bond between phosphate and OH of an amino acid
The activity of serine/threonine and tyrosine kinase
Where are disulfide bonds formed?
What facilitates their formation?
The ER Lumen
Protein disulfide isomerases
Where are proteins usually acetylated?
Lysine residues.
What are the three modifications in collagen?
Lysines in collagen modified to form 5-hydroxylysines
Some lysines deaminated to aldehydes
Some prolines hydroxylated to hydroxyprolines.
Defects in lysyl hydroxylases
Ehlers-Danlos Syndrome - overly flexible joints, walls of blood
vessels, intestines or uterus may rupture
Epidermolysis Bullosa Simplex – blisters on skin
Characteristics of Alzheimer’s
Amyloid precursor protein (APP) breaks down to form
amyloid beta peptide (Aβ)
Misfolding/Aggregation of Aβ forms plaques in the brain
(extracellular)
Hyperphosphorylation of Tau (neurofibrillary tangles)
(intracellular)
What is the cause of familial vs sporadic Alzheimer’s.
Mutations APP and Tau are familial form
Aging is common in sporadic form
A disease characterized by the aggregation of α-synuclein (AS) protein forms insoluble fibrils which deposit as Lewy bodies in dopaminergic neurons in the substantia nigra
Symptoms due to reduced availability of dopamine.
Parkinson’s disease
Familial = Mutations in AS
What disease is characterized by CAG triplet repeats?
What do these triplets result in?
Huntington’s disease (mutation in Huntingtin gene)
Results in Polyglutamine repeats, which form H-bonds and misfold and aggregate
Basial ganglia cell death
Disease caused by misfolding of prion proteins
What type of encephalopathy is this?
Creutzfeldt-Jakob disease (HD)
Spongiform - appearance of infected brains, filled with holes
and resemble sponges under a microscope.
