Lecture 3 Flashcards
Another name for peptide bond
Amide bone
What is a peptide bond
- bond between carboxyl group of 1 molecule reacts with the amino group of the other molecule, releasing a molecule of water
- amino group becomes deprotonated and attacks carbonyl
Polypeptide synthesis is a ______ rxn
Condensation
What is the name when polypeptide is less than 20
Oligopeptide
What is the name when polypeptide is greater than 20
Polypeptide
What direction is the peptidyltransferase rxn
5’ to 3’
N to C
What atoms are in the mainchain atoms?
- N
- Calpha
- C (of carbonyl)
- O (of carbonyl)
Describe the nomenclature for identifying residues w/in a polypeptide
i-2, i-1, i, i+1, i+2…. nomenclature
- naming the carbon side chains
What is the pattern of H bonding?
i to i+4
What is the peptide bond length? Normal C-N length? C=N bond?
- Peptide (N-C) = 1.33 A
- Normal C-N = 1.45 A
- C=N = 1.25 A
What ___% double bond character does the peptide bond have?
40%
Why is the peptide bond length different than a normal C-N bond?
The peptide bond length is due to resonance (keto-enol tautomerization)
How does resonance affect the stability of the peptide bond?
The resonance translates to greater stability for the bond. Amides are the most stable of all carbonyl fxnal groups.
Draw the dipole moment in the peptide bond
N/A Lecture 3 Slide 8
Describe the peptide bond’s stereochemistry
- re/si
- re face is right handed orientation (Ser/Lys proteases)
- si face is left handed orientation (Ser/His/Asp proteases)
Mainchain bond angles are dictated by ____
steric constraints/clashes
What is the torsion angle?
In a chain of 4 bonded atoms: A-B-C-D, you measure the dihedral angle between the plane containing the atoms A,B,C and the plane containing the atoms B,C,D.
What is the
1) Phi bond
2) Psi bond
3) Omega bond
1) Phi bond: rotation about N-Calpha bond
2) Psi bond: rotation about Calpha-C
3) Omega bond: Cn-Nn+1
A list of the Phi (Φ) and Psi (ψ) values for each amino acid in the protein defines the ____ structure
tertiary structure (3D structure) of the protein.
Describe what atoms are involved in the phi bond angle and how to find it. E.g. on residue 2
- The phi bond for residue 2 is defined by atoms C, N, CA, C (atoms 2, 3, 4, 5)
- Look down bond N-CA (atoms 3,4), bond just before CA
- Measure relative position of C (atom 2) and C (atom 5) aka the backbone carbonyl carbon atoms
- To get the correct value you need to put the Carbonyl (atom 2) at 12-oclock, and look for the direction of the C=O behind.
Describe what atoms are involved in the psi bond angle and how to find it. E.g. on residue 2
- The psi bond angle for residue 2 involves the N, CA, C, N (atoms 3, 4, 5, 6)
- Look down the CA-CO bond, bond just after CA
- Measure relative position of N (atom 3) and N (atom 6) aka position of backbone amide nitrogen atoms
- To get the correct value you need to put the amide nitrogen (atom 3) at 12-oclock, and look for the direction of the N behind.
Describe what atoms are involved in the omega bond angle and how to find it.
- The omega bond angle is defined by atoms CA, N, CO, CA (atoms 1, 2, 3, 4)
- Looking down the CO – N bond (atoms 2, 3)
- Measure relative position of the Cα atoms (atom 1 and atom 4)
- To get the correct value you need to put the Cα at 12-oclock, and look for the direction of the Cα behind.
What degree is the omega angle usually?
This is the main chain amide or peptide bond torsion angle, and it is almost always 180°. In other words, the trans form is favored energetically because of steric effects.
The X-Pro bond is more likely to be ___ than standard X-X peptide bonds
cis
The cis isomer of X-Pro can exist ____% of the time, depending on the amino acid preceding the Pro (X residue).
0-40%
Why do all cells have the essential enzymes prolyl isomerase (also called peptidylprolyl isomerase or PPIase).
On the ribosome all the X-Pro peptide bonds are trans, so if the cis is required in the native 3D structure, cis-trans isomerization of the X-Pro omega bond can be a rate-limiting step.
Draw a ramachandran plot
a plot of Φ vs. Ψ angles
- N/A Lecture 3 Slide 21
What % combination of Φ, Ψ angles are not allowed?
The Ramachandran plot shows that 75% of the Φ/Ψ combinations are not “allowed” because of steric clashes.
On the Ramachandran plot, what does the following colours represent
1) green
2) blue
3) white
1) green: favourable regions (angles), no steric clashes
2) blue: allowed regions (angles)
3) white: disallowed regions (angles) steric clashes, unless Gly
What angle combination on the Ramachandra plot represents
1) alpha helix
2) beta sheet
1) alpha helix: Φ= ~-100°, Ψ= ~-60°
2) beta sheet: Φ= ~-100°, Ψ= ~-60°
The Ramachandran plot also serves as a _____ check on experimentally determined protein structures. There should always be ____ reasons for any residue that does not fall within the most favorable region in a Ramachandran plot.
The Ramachandran plot also serves as a QUALITY check on experimentally determined protein structures. There should always be STRUCTURALS reasons for any residue that does not fall within the most favorable region in a Ramachandran plot.
In lysine, χ1 is the torsion angle formed from what atoms?
N, Cα, Cβ and Cγ
In lysine, χ2 is the torsion angle formed from what atoms?
Cα, Cβ, Cγ and Cδ
What does the side chain bond angles depend on
the steric constraints imposed by the environment, but there are trends, due to steric restrictions with the main chain atoms
Draw the different cellular compartments of a bacteria cell and label the site of protein synthesis
- Cytoplasm
- Inner membrane
- Periplasm
- Outer membrane
- Extracellular environment
Draw the signal peptide (pre sequence)
N/A Lecture 3 Slide 26
Describe the 5 parts of the general secretion system in prokaryotics
- Sec B: targeting chaperone
- Sec A: ATPase - motor
- Sec YEG: channel (pore)
- Sec DFyajc: helps Sec YEG
- SPase: cleaves off signal peptide
Describe the 5 parts of the general secretion system in eukaryotics
- SRP: targeting chaperone
- Ribosome: motor
- Sec 61: channel (pore)
- SR: SRP receptor/adaptor
- SPC: cleaves off signal peptide
What is the main difference functionally between the prokaryotic and eukaryotic systems?
the prokaryotic protein translocation system occurs post-translationally and the eukaryotic protein translocation system occurs co-translationally.
What are post translational modifications?
- Enzyme catalyzed rxn
- Occur in different compartments as protein travel through the cell.
- Increases chemical diversity of proteins
- Activates / Deactivates etc…
What are the 4 main chain modifications?
- Signal peptide cleavage (via signal peptidase)
- Zymogen or pro-protein cleavage (via peptidases)
- Inteins (intramolecular cleavage and ligation)
- Viral polyproteins (via viral or host proteases)
Where and when does glycosylation occur? Involves which amino acid? Involves which enzymes?
- ER (co-translationally)
Enzymes:
- glycosyltransferase (forms sugar protein bond)
- glycosidases (breaks sugar proteins bonds)
- Asparagine (Asn) - Golgi (post translationally)
- glycosyltransferase (forms sugar protein bond)
- glycosidase (breaks sugar protein bond)
- Serine/threonine
What 3 amino acids compose glutathion?
Glu-Cys-Gly
What is a glutathion peroxidase rxn?
2 glutathion + H2O2 ->
2 H2O + glutathion disulfide
What is a glutathion oxidase rxn?
glutathion disulfide + NADPH + H+ ->
2 glutathion + NADP+
What is the most common PTM?
Phosphorylation
Which amino acids are most commonly phosphorylated? Prevalence?
- Serine 1000
- Threonine 100
- Tyrosine 1
- Histamine (only in bacteria; phosphorylates a amino group in pentamer)
What are the enzymes involved in phosphorylation?
- Kinases (catalyzes formation of phosphate protein bond)
2. Phosphatases (catalyzes breaking of phosphate protein bond)
What amino acid is sulfation most commonly done to?
Tyrosine
What enzyme is used during sulfation?
Sulfotransferase
What is tyrosine sulfation equation?
Tyrosine + 3’Phosphoadenosine-5’phosphosulfate (PAS) (sulfate donor) -> tyrosine sulfate
What is myristoylation?
Myristic acid (C14:0) added to N-terminal alpha amine (forms amide bond). Irreversible
In myristoylation, what amino acid is required?
The N-terminal residue modified by myristic acid has to be glycine, Therefore the initiation Met removal is required.
What enzyme is used in myristoylation?
N-myristoyltransferase (NMT)
Where is myristoylation catalyzed?
Cytoplasm
Fxn of myristoylation?
- Allows for weak interaction w/membrane and other proteins
- Myristoylation is important in: signal transduction, apoptosis, cancer, viral and other infections
What is palmitoylation?
Addition of a palmitic acid (C16:0) to a CYSTEINE side chain, forms a thiolester linkage. Rxn is reversible
What enzyme is used in palmitoylation?
Protein palmitoyltranserases (PATs)
What is prenylation?
C-terminal lipidation at a Cys side chain
Which residue does prenylation occur at
Cysteine
What enzymes are used in prenylation
- Farnesyltransferase
2. Geranylgeranyltransferase I
What is the recognition sequence motif at the C-terminus of the modified protein
- CAAX
- Where C is cysteine, A is an aliphatic residues, X is the C-terminal residue (one of 6 different residues, the identity of which dictates the type of prenyl group that is transferred.
What is methylation? Enzyme used?
- Adding methyl group to residues
2. protein arginine methyltransferase, lysine methyltransferase
Which amino acids does methylation usually occur on
- Arginine
2. Lysine
What is the methyl donor in methylation
S-adenosylmethionine Methyltransferase (SAM)
What is hydroxylation
Adding hydroyxl group to residue
Which amino acids does hydroxylation usually occur on
- Proline
2. Lysine
What is carboxylation
Adding carboxyl group to residue
What is the enzyme used in hydroxylation
Prolyl-4-hydroxylase
Lysyl-5-hydroxylase
What is carboxylation
Adding carboxyl group to residue
Which amino acid does carboxylation occur on
Glutamate
Fxn of carboxylation?
Allows for coorindation of Ca
Enzyme used in carboxylation
γ-glutamyl carboxylase
What is a schiff base/imine linkage composed of
Primary amine + aldehyde
-> schiff base
Example of schiff base in biology
The addition of retinal to opsin to form rhodopsin, an important signal transduction membrane protein involved in vision. Retinal forms a Schiff base with residue K296 of the protein opsin. The cis-trans isomerization initiates the signal.
Fxn of ubiquitination?
Ubiquitination labels proteins for recycling
What are isopeptide bonds?
peptide bonds between side chains of amino acids
What is ubiquitination?
(α-amino group in the C-terminal Gly of Ubiquitin is bonded to the ε-amino group of a lysine side chain on the substrate protein (the protein that is being recycled)
What are the 13 PTM?
- Glycosylation
- N linked via Asn
- O linked via Ser/Thr
- glycosidase
- glycosyltransferase - Disulfide bond formation
- Cys
- Reversible - Glutathion
- Glu-Cys-Gly
- Glutathion peroxidase
- Glutathion reductase - Phosphorylation
- Kinases
- Phosphatases
- Serine, Threonine, Tyrosine, Histamine
- Reversible - Sulfation
- Tyrosine sulfate
- PAPS (3-phosphoadenosine-5’-phosphosulfate) (donor
- Sulfotransferase
- Irreversible - Myristoylation (N-TERM)
- Myristic acid (C 14:0) added to N-terminal alpha-amine group (form amide bond) of GLYCINE. Within cytoplasm.
- N-myristoyltransferase
- Irreversible - Palmitoylation
- Palmitic acid (C16:0) added to CYSTEINE side chain, forms THIOESTER linkage
- Palmitoyltransferase
- Reversible - Prenylation (C-TERM)
- C-terminal lipidation to Cys side chain
- Recognition sequence motif @ C-term of protein: CAAX - Methylation
- On positively charged residues e.g. arginine, lysine
- Methyl donor = SAM (S-adenosylmethionine methyltransferase) - Hydroxylation (collagen)
- Proline, lysine
- prolyl-4-hydroxylase, lysyl-5-hydroxylase - Carboxylation (clotting cascade)
- glutamate
- gamma-glutaryl carboxylase - Schiff base
- primary amine + aldehyde
- retinal + opsin = rhodopsin - ubiquitination
- alpha carboxyl group of C-term glycine of ubiquitin and E-amino group of lysine side chain on protein to be recycled - GFP
- chromosome exists inside beta-barrel-like structure
- gives off green fluorescence, used for tracking
