Functions/ Dysfunctions-protiein Processing Flashcards
Central dogma of molecular biology
DNA—>RNA—>Protein
What is the purpose of the genetic code
To convert a nucleotide sequence of a gene into an amino acid sequence of a protein using mRNA as an intermediate
(Gene —> protein)
Code can be degenerate (some codons can code for more than one amino acid and some codons do not code for any aa)
Start codon
AUG
Coding for methionine
Stop codons
UAA,
UAG,
UGA
Which point mutation does not cause change in the amino acid being coded
Silent mutation
Which point mutation changes the amino acid in the protein but does not effect the protein function dramatically
Missense mutation
Which point mutation deletes or inserts one or more nucleotides into or out of frame.
Frameshift mutation
Which point mutation changes the codon into a stop codon causing premature termination. Causes the formation of the truncated version of a protein
Nonsense mutation (null mutation)
What disease arises from a missense mutation of the 6th codon in the allele for human B-glowing (subunit of hemoglobin) ?
Changes GAG -> GTG
- valine -> glutamate
- hydrophobic -> negative and hydrophilic
*OPPOSITE
SICKLE CELL ANEMIA
- Hgb starts to aggregate and form rigid rod like structures which causes sickle cell RBC’s
- poor O2 binding capacity of Hgb and Hgb tends to clog capillaries
Large frameshift deletions of the dystrophin gene which leads to defective dystrophin proteins
- causes muscle wasting and eventual wheelchair need
- 1:3,500 males
Duchenne Muscular Dystrophy
Severe form of Duchenne muscular dystrophy is caused by
Out of frame deletions that result in little/no expression of dystrophin proteins
What causes Becker muscular dystrophy
In frame deletions result in the expression of truncated forms of dystrophin. This version is more midl than DMD
*muscle becomes replaced with fat and fibroid
What is the cap on mRNA comprised of
5’ cap is made of guanosine and 3 phosphates
7-methylguanosine cap
What is the tail on mRNA called
Poly(A) tail at the 3’ end made up of adenine
. tRNA serves as an adaptor by having a binding site for both codons in mRNA and amino acids. TRNA matches amino acids to ____ in mRNA
Codons
Describe the structure of tRNA
- cloverleaf structure
- has 2 regions of unpaired nucleotides that are crucial to function
- Anticodon loop where mRNA complementary sequence binds
- 3’ CCA terminal region which binds the matching amino acid [attached is Phe]
It also has a T and D loop
What activates the amino acid that is esterfied to the CCA sequence of tRNA
aminoacyl tRNA synthetase enzyme
- serves as a second genetic code
- each amino acid has its own
- important to maintain fidelity of protein synthesis
Explain how aminoacyl tRNA synthetase functions
- Links amino acid to tRNA by high energy bond
- TRNA the binds to its mRNA codon
This enzyme also catalyze the addition of AMP to COOH end of the amino acid
Where does protein synthesis (translation) occur?
In the ribosome
T/F
Large and small ribosomal subunits assemble together into an active complex in the presence of mRNA
True
Difference between eukaryotic and prokaryotic ribosomal subunits
Eukaryotic - 60S and 40S
Prokaryotic - 50S and 30 S
Important for antibiotic function
What are the 3 sites of a ribosomal complex that are important for translation
- A site. Acceptor site is where the mRNA codon …
- P site- peptidyl site is where aminoacyl tRNA is attached
- E site- exit site is when the tRNA exits the ribosome
What direction does translation occur
5’ —> 3’
What are the 3 steps of translation
- Initiation
- Elongation
- Termination
What happens in the initiation step of translation
Formation of mRNA, small ribosomal subunit, and initiator tRNA pre-initiation complex
What happens in the elongation step of translation
Activated amino acids attached to initiating MET residue by forming a peptide bond
What happens in the termination step of translation
The peptide chain is released from the ribosomal complex as coded by the stop codons
What is e1F2 in the initiation step of translation
E1F2 is the eukaryotic intiation factor
-MET first binds to the P site and E1F2
What is EIFG?
Eukaryotic initiation factor
What is the reading frame for prokaryotic mRNA in translation?
Shine-Dalgarno (SDG) sequence (AGGAGG)
What is the eukaryotic mRNA reading frame for translation
5’ cap and 3’ poly A tail; the Kodak sequence
Label the steps of translation initiation
- Pre-initiator complex is first assembled
- Large subunit ribosome is then added to form initiaion complex
- Initiator tRNA attaches to P site of the small subunit
- Other initiation factors are added
- Large subunit is then added
- Translation begins with the start AUG codon
What is the initiatior tRNA for eukaryotes ?
Methioninyl tRNA
What are the translation initiation factors in eukaryotes and prokarytoes
IF- in prokaryotes
eIFs- in eukaryotes
What steps begins with the activated amino acid attached to the INITIATING METHIONINE via a PEPTIDE BOND
Elongation
What are the steps of elongation by the ribosome
- Aminoacyl tRNA is attached to a GTP-bound elongation factor
- Loading of aminoacyl tRNA so the anticodon pair is positioned on the A site
- Loading is possible by hydrolysis of GTP and release of factor from aminoacyl tRNA
What is the type of bond formed between the amino acids in the A and P site in translation? And what is the enzyme that catalyzes it?
- Peptide bond
- Peptidyl transferase
*nrg comes from bond between aa and tRNA
What step in translation is related to the release of the peptide chain from the ribosomal complex and the dissociation of the ribosomal complex
Termination step of translation
What triggers termination
The stop codons of UAA, UAG, and UGA
What recognizes the stop codons in the termination step of translation
Release factors (RF’s)
*are proteins that catalyze the addition of water (instead of an amino acid) and form a COOH bond at the end of the polypeptide
Where do release factors in the termination step of translation bind on the ribosome
The RF’s bind to the A site and the cleave the ESTER BOND between the C terminus of the polypeptide and the tRNA
What functions to dissociate the ribosomal complex at the end of translation
GTP hydrolysis
What is a polysome
It is a cluster of ribosomes that are simultaneously translating a single mRNA molecule
- each synthesizing a polypeptide chain
- MAKES PROTEIN SYNTHESIS MORE EFFICIENT
What is the antibiotic that inhibits the assembly of the preinitiation complex during translation by binding to the 30S subunit (in prokaryotes)
Streptomycin
*binds to small subunit
Where does the Shiga toxin bind to disrupt elongation
The 60S subunit in eukaryotes
The large subunit
Where does Clindamycin and erythromycin bind to disrupt translation of the ribosome
The 50S subunit of prokaryotes
**the large subunit
Where does tetracycline bind to disrupt elongation
To the 30S subunit in prokaryotes
**the small subunit
Which subunit is peptidyl transferase activity mainly found?
It is housed in the large subunits
What is the hydrolysis of GTP requirements for each step of translation
- Initiation - 1 GTP
- Elongation- 2 GTP
- Termination- 1 GTP
What inactivates EF2-GTP and inhibits elongation
Diphtheria toxin
What are the prokaryotic inhibitors of elongation
Tetracycline (block aminoacyl-tRNA entry to ribosomal complex)
Chloramphenicol (inhibits peptidyl transferase in mitochondria)
Clindamycin and erythromycin block translocation of the ribosome
Streptomycin- interferes with 30s association with 50s
T C C E S (***)
Which prokaryotic elongation ihibibitor is commonly used to treat purtussis?
Erthromycin
What are the Eukaryotic elongation inhibitors
Cycloheximide- inhibits peptidyl transferase
Diphtheria toxin- inactivates GTP-bound eEF-2 which interferes with ribosomal translocation
Shiga toxin and Ricin - block entry of aminoacyl-tRNA to ribosomal complex
C D S R (**)
What does puromycin do ?
- causes premature chain termination in both prokaryotes and eukaryotes
- is more resistant to hydrolysis
What are the three steps after protein synthesis ?
- Protein sorting
- Post-translational modifications
- Folding and degradation
What are the 2 major pathways for protein sorting?
- Cytoplasmic pathway
2. Secretory pathway
Which protein sorting pathway is for proteins destined for the cytosol, mitochondria, nucleus, and peroxisomes ?
Cytoplasmic pathway
-protein synthesis begins and ends on free ribosomes in the cytoplasm
What protein sorting pathway is for proteins destined for the ER, lysosomes, plasma membranes, and for secretion ?
Secretory pathway
- translation begins on the free ribosome but it terminates on ribosomes sent to the ER
- *first 20 aa’s on polypeptide have ER targeting signal sequences
If the protein has an N- terminal hydrophobic a-helix signal, where does it go during sorting?
Mitochondria via the cytoplasmic pathway
**the sequence helps them to interact with chaperon proteins (heat shock family) which protect the linear structure of proteins
If a protein has lots of lysines and arginines, where will it end up after sorting?
The nucleus’s via the cytoplasmic pathway
If a protein has N-terminal a polar signal, where will it end up after protein sorting?
Peroxisomes via cytoplasmic pathway
If a protein has no signal, where will it end up after protein sorting?
In the cytoplasm via the cytoplasmic pathway
If a protein has lots of lysine, aspartate, glutamate, and leucine in its signal, where will it end up after protein sorting?
In the rough ER via the secretory pathway
If a protein has a Mannose 6-P signal, where will it end up after protein sorting?
Lysosomes via the secretory pathway
**defect is asssocated with I-cell disease
If a protein has lots of tryptophan on its signal, where will it end up after protein sorting?
In a secretory vesicle via the secretory pathway
If a protein has a Stop TRSF signal, where will it go after protein sorting?
To the cell membrane via the secretory pathway
T/F
Proteins synthesized in the cytoplasmic pathway have translocation signals
False
THEY HAVE NO TRANSLOCATION SIGNALS BC THEY STAY IN THE CYTOPLASM
What are the transporter present in the mitochondrial membrane that recognize sequences and allow proteins to pass across the membrane?
TIM (transporter in inner membrane)
TOM (transporter in outer membrane)
The unfolded proteins in mitochondrial protein import are protected by binding to chaperones in that are particularly called what ?
Heat shock proteins 70 (HSP70)
How do proteins import the nucleus
Through nuclear pores
*small proteins can pass through, but large proteins (>40) require NUCLEAR LOCALIZATION SIGNALS
What is the nuclear localization signals required for nuclear import made up of?
Four continuous basic residues of Lys and Arg
What is the KDEL signal sequence for?
For ER Lumen proteins
K-lysine
D-aspartic acid
E-glutamic acid
L-leucine
What does a signal recognition particle (SRP) do?
An SRP binds to the ER-targeting signal and the ribosome during translation. The SRP wraps around the ribosome-mRNA-peptide complex and STOPS translation temporarily. The translation resumes when the protein is directed into the ER lumen. Enzymes on the luminal side cleave the signal to release the protein so it can be recycled.
What is I-cell disease
- severe form of lysosomal storage disease
- caused by defective tagging of mannose 6P to lysosomal proteins
- results in high plasma levels of lysosomal enzymes
T/F
Small proteins can self fold into native conformations spontaneously
True
Large proteins can not self fold and are at risk for aggregation and proteolysis. Large proteins need what to help them fold.
Chaperones
-protect the protein and help them fold into tertiary structure
What proteins have a barrel shaped compartment that take unfolded proteins and catalyze their folding using ATP
Chaperonins
What part of post-translational processing converts inactive forms of an enzyme to active by unmasking active sites
Proteolytic cleavage
What are the 4 post-translational covalent modifications
Glycosylation
Phosphorylation
Disulfide bond formation
Acetylation
( GPDA **)
Postranslational modification of acetylation does what and affects what’s residue
Covalent linkage to amine
- affects Lysine
- NH3 functional group
Postranslational modification of glycosylation does what and affects what residue
O-type
- hydroxyl functional group
- affects Serine and threonine
N-type
- acid Amide functional group (CONH2)
- Asparagine and glutamine
**covalent linkage of sugar residues in the ER lumen
Postranslational modification of phosphorylation does what and affects what residue
Phosphate linked via esterificiation (form of ester bond between phosphate and OH of an aa)
- hydroxyl function group
- Ser, Tyr, Thr, Asp, His
- uses tyrosine kinase to add phosphate
Postranslational modification of disulfide bonds does what and affects what resuidue
Oxidation to achieve covalent linkage of cysteine residues
- SH functional group
- cysteine
Precursor sugar of N-linked glycoside links are transferred from what
Phospho dolichol
What postranslational modification is related to cell growth, proliferation, differentiation, and oncogenes
Phosphorylation
*activity of Ser/Thr and tyrosine kinase
What postranslational modification stabilizes many proteins
Disulfide bond formation
- can be inter or intramolecular bonds between thiol (SH) group and 2 cysteine residues
- formation of bond occurs in ER lumen
Disulfide bond formation of postranslational modification is faciliated by what enzyme
Protein disulfide isomerase
Proteins are typically acetyl ate do (in postranslational modification) on ____ residues
Lysine
Acetylation used what as the acetyl group donor
Acetyl CoA
-histones are acetylated or deacetylated on the N terminal lysines which is critical for gene regulation
Acetylation reactions are catalyzed by what enzymes
HAT- his tone acetyltransferase
Or
HDAC-his tone deactylase
T/F
Pattern of histone modification is heritable
True
Which postranslational mofication facilitates crosstalk between phosphorylation, methylation, etc.
Acetylation
*regulates protein function
What is the most abundant structural protein in vertebrates
Collagen
*heterotrimeric
What are the important factors of post-translational modification of collagen ?
- modification is important for proper assembly of collagen
- ASCORBIC ACID is essential for lysine and proline hydroxylases
- defects in lysyl hydroxylases result in skin, bone, and joint disorders
What causes Ehlers-Danlos Syndrome
*over-flexible joints, and rupturing of internal organs
Defect in lysyl hydroxylases; defect in collagen assembly
What causes Epidermolysis Bullosa Simplex?
Seen by blisters on the skin
Lysyl hydroxylase defect; defect in collagen assembly
What causes Alzheimer’s disease (AD)?
Amyloid precursor protein (APP) breaks down to form amyloid beta peptide (AB). Misfolding of the AB causes plaque formation in brain (extra cellular). Hyperphosphorylation of Tau causes intracellular neurofibrillary tangles.
- MUTATION OF APP AND TAU causes familial AD.
- Aging causes sporadic AD formation
What causes Parkinson’s disease (PD)?
Aggregation of alpha-synuclein (AS).
-forms insoluble fibrils which deposit Lewy bodies in dopaminergic neurons in substantial Nigra which causes death of neurons and reduced availability of dopamine
- mutations of AS = familial PD
- aging = sporadic PD
What neurotransmitter is responsible for motor control
Dopamine
-Parkinson’s is caused by reduced availability of dopamine
What causes Huntington’s Disease (HD)?
- mutation in Huntington gene results in expansion of CAG repeat.
- CAG repeat causes polyglutamine repeats in HTT protein and forms intramolecular H-bonds that misfold and aggregate protein
- causes selective death of basal ganglia cells
**20-26 repeats is normal >36 is HD
What causes Creutzfeldt-Jakob disease?
- caused by misfolding of prion proteins
- it is transmissible (infective) and can cause infection which converts normal proteins to misfolded ones
- relates to Transmissible spongiform encephalopaties (TSEs)
