Lecture 5-8 Flashcards
Seven essential function carried out by proteins, and an example of a protein for each?
Enzymatic, e.g. trypsin Transport, e.g. haemoglobin Structural, e.g. collagen Movement, e.g. actin Signalling, e.g. insulin Defence, e.g. antibodies Storage, e.g. ferritin.
What must happen to proteins after synthesis?
They must fold properly.
What are proteins synthesised as?
Long unbranched chains of amino acids.
What is a protein’s primary structure?
The sequence in which the amino acids are arranged.
How many amino acids are used to make proteins?
20.
What are the 4 functional groups found in 19/20 amino acids?
Hydrogen atom, amino group, carboxyl group, R group.
What 5 properties do side chains vary in?
Size Shape Charge Hydrophobicity/hydrophilicity Chemical reactivity.
Are there optical isomers for amino acids? If so, why?
All but glycine.
4 different groups attached to the central atom.
What isomers are incorporated into proteins?
L-isomers.
Why is glycine not chiral?
2 hydrogen atoms attached to carbon.
At pH 7, are amino acid groups ionised? What name can you give them?
Yes.
Zwitterions.
What is pKa?
The pH at which an ionisable group is one-half charged and one-half neutral.
Which amino acid’s side chain has a pKa around physiological pH?
Histidine (pKa 6.8).
What is the pKa of CH3COOH, and what does this mean?
50% molecules = CH3COOH,
50% molecules = CH3COO-.
What type of bond joins amino acids together?
Peptide bonds.
How do peptide bonds work?
Carboxyl group of the first amino acid reacts with amino group of the second.
What type of reaction is the formation of a peptide bond?
Condensation reaction.
What do proteins have at either end?
Free amino group (N terminus) at start, free carboxyl group (C terminus) at end.
Which direction are proteins written in?
N->C direction.
How would you describe the bonding in a peptide bond? What effect does this have?
Partial double bond character.
Rotation is restricted - peptide unit rigid and planar.
Is the peptide unit sys or trans?
Trans.
What is the rotation around Cα-C denoted as?
Psi (ψ)
What is the rotation around the N-Cα denoted as?
Phi (φ)
Why are most phi and psi angles not allowed?
Steric collisions between side chains and main polypeptide chain.
What determines the shape of the entire protein regarding angles?
ψ and φ bond angles for each amino acid.
What is the main driving force in protein folding?
Attaining an energetically stable structure.
The main polypeptide chain is hydrophilic due to C=O and N-H groups. How does the protein combat this, enabling a hydrophobic core?
Structures must be assumed that neutralise these groups by hydrogen bonding.
2 types of secondary structure?
Alpha helix (α-helix) Beta sheet (β-sheet).
α-helices formed from how many amino acids typically?
5-40.
What happens to the N-H and C=O groups in the α-helix?
H-bonded to one another along the axis of the helix.
How many amino acids per turn of α-helix?
3.6.
How far does each amino acid turn the α-helix?
100º.
What’s the vertical distance from one amino acid to the next? Therefore, what’s the pitch of the helix?
Vertical distance = 0.15nm.
Pitch = 0.54nm.
To what is the C=O group of amino acid n bonded to?
N-H group of amino acid n+4.
Do amino acid side chains project into or out of the α-helix?
Project out.
What type of plot can an α-helix be plotted on?
Helical wheel diagram.
What are β-sheets formed from?
Non-continuous regions of the polypeptide chain. A.K.A.β-strands.
How do the β-strands bond to one another?
Form hydrogen bonds between C=O groups of one strand, and N-H groups of another.
Do β sheets always run continuously in one direction?
No. If all N->C, PARALLEL.
If opposite directions, ANTI-PARALLEL.
How do hydrogen bonds change between parallel and anti parallel βsheets?
Hydrogen bonds evenly spaced within parallel β sheet, but narrowly spaced separated by a larger gap in anti-parallel sheet.
What is another name for β sheets? And why?
β-pleated sheets.
Because Cα carbons lie successively above and below plane of sheet.
What links secondary structures?
Loop regions.
What are long loops called, and what is a key property?
Random coils - very flexible.
What are short loops called, and what do they connect?
Hairpin loops or β turns.
Connect anti-parallel β strands.
What are the 2 amino acids often found in loops, and why?
Proline - locked ring structure introduces kink to polypeptide chain.
Glycine - small side chain enables it to form turns where others couldn’t.
What are parallel β-strands often connected by, and how?
Also, what is this called?
α-helices, by crossing β-sheet from one edge to the other.
Called β-α-β motif.
What is a tertiary structure?
Association of secondary structure into complex domains.
What is a disulphide bridge?
Sulphydryl on one cysteine forming a crosslink with another sulphydryl on another cysteine near to it in space.
What benefit does cysteine’s disulphide bridge confer to proteins?
Stabilises tertiary structure, making proteins more resistant to degradation and denaturation.
What is a quaternary structure?
Multiple polypeptide chains (subunits) associating into a multimeric complex held together by electrostatic, hydrogen and van der waals bonds (sometimes disulphide bridges).
Why is polypeptide backbone usually shown as line/ribbon?
Diagrams usually very complex when representing all atoms.
How is an α-helix depicted in diagrams?
Spiral/cylinder.
How are β-strands depicted in diagrams?
Thick arrows, pointing from N to C terminal end.
What are the 2 major classes of proteins?
Globular - arranged in compact domains.
Fibrous - protein chains arranged into fibres.
What is the typical role of globular and fibrous proteins?
Globular proteins usually active components of cellular machinery.
Fibrous proteins usually structural role.
3 main groups of fibrous proteins?
And how are they defined?
coiled-coil (e.g. keratin, myosin).
β-sheets (e.g. amyloid fibres, silks).
triple helix (e.g. collagens).
Defined by secondary structure.
Where are keratins found, and why?
Hair, nails, feathers, etc.
Mechanically durable.
How many amino acids are repeated in α-keratin? What does this form?
- (a-b-c-d-e-f-g).
Forms α-helix.
Which 2 residues of α-keratin lie on the same side of the helix? What’s notable about them?
a and d.
Both are hydrophobic residues.
How are the 2 α-keratin helices associated?
What is this structure called?
Both twist around each other, associated by hydrophobic faces of helices.
COILED-COIL.
When 2 coiled coils in α-keratin line up with one another, how are they referred to?
Staggered antiparallel tetramer.
What are staggered antiparallel tetramers the foundation of?
Foundation of protofilaments, which form protofibrils, forming microfibrils.
What do long stretches of silk fibroin contain?
A six amino acid repeat (Gly-Ser-Gly-Ala-Gly-Ala), forming an antiparallel β-sheet.
Where do glycine, alanine and serine side chains protrude in silk fibroin? What benefit does this confer?
Glycine protrudes on one side.
Serine and alanine protrude on the other side.
Enables β-sheets to stack into an array with alternating layers.
Why is silk strong yet flexible?
Strong because stretching would require breaking of covalent bonds.
Flexible because β-sheets interact via weak van der Waals bonds.
What is the most abundant vertebrate protein?
Collagen.
Nearly one third of the amino acids in collagen are which amino acid?
Another 15-30% are which other amino acids?
~1/3 = glycine. 15-30% = proline or hydroxyproline (Hyp).
What’s the primary amino acid sequence in collagen?
repeating tripeptide
Gly-X-Y.
X often proline.
Y often Hyp.
Why can collagen not form an α-helix? What does it form instead?
Pro and Hyp residues prevent collagen from forming α-helix.
Forms loose helix instead, with around 3 residues per turn.
Three collagen peptides wind around each other. What does this form?
Triple helix. (Trimer)
What is the only residue that can fit through the centre of the triple helix? (every 3rd amino acid).
Gly.
What do the Hyp and Pro residues do in collagen?
Confer rigidity.
What bonds do the polypeptide chains form?
Inter-chain hydrogen bonds.
What can trimers do in collagen?
Associate, building large, strong fibres.
