Lecture 2: Protein Structure And Function

Question 0

Describe the structure of amino acids.

Answer 0

Central (alpha) carbon with amine and carboxylate acid groups, plus a variable side chain (R group).
The asymmetrical alpha carbon of all AAs (except glycine) allows the to exist in L or D conformation.
The L conformation is almost always used in the synthesis of proteins.

Question 1

List some types of proteins.

Answer 1

Structural (eg cytoskeleton or bone)
Enzymes and hormones
Plasma membrane proteins
Antibodies
Fibres

Question 2

Describe special amino acids.

Answer 2

CYSTEINE: reactive sulphydryl (SH) group in side chain can form a disulphide bond with another cysteine residue upon oxidation.
GLYCEINE: R-group is simply an H atom. It’s small size allows it to fit into very tight spaces upon protein folding.
PROLINE: Has cyclic ring which makes it very rigid. Responsible for fixed kinks in protein.

Question 3

Describe the polypeptide backbone and it’s steric limitations.

Answer 3

Peptide bonds join the carboxylate acid group of one AA with the amine group of another.
Side chains project from either side of the backbone
Has N and C terminals
STERIC LIMITATIONS
each AA contributes 3 bonds to the backbone
Peptide bond does not permit rotation
Rotation can occur around the C(alpha)-C bond, and the N-C(alpha) bond.
Steric limitations of he polypeptide backbone allow for a series of planes, hinged at C(alpha) and few conformations.

Question 4

Describe forces influencing protein folding.

Answer 4

NON-COVALENT INTERACTIONS
van der waals attractions: weak bonding interactions due to fluctuating electric charges.
Hydrogen bonds: electropositive h atom is partially shared by 2 electronegative atoms.
Ionic interactions
Hydrophobic force: depends on distribution of polar and non-polar amino acids (projection of side chains) in an aqueous environment, a protein will fold so that the core region contains the non polar side chains, and so that the polar side chains are on the outside of the molecule (allows formation of hydrogen bonds with water.
COVALENT INTERACTIONS
covalent crosslinking- only occurs in an oxidative environment. Disulphide bonds may attach 2 separate polypeptide chains, or stabilise the internal folded structure of one polypeptide chain.

Question 5

Describe the protein folding pathway and the role and mechanism of action of chaperone proteins.

Answer 5

The newly synthesised protein spontaneously folds as it grows from the ribosome. It quickly folds into the molten globule state. Subsequent folding is significantly slower. Protein folding is catalysed by chaperone proteins.
CHAPERONE PROTEINS
H shaped proteins (2 bottom to bottom barrels)
Misfolded protein is initially captured by hydrophobic interactions along one rim of the barrel.
Subsequent binding of ATP plus a protein cap increases the diameter of the barrel rim, which may partially stretch or unfold the client protein.
The protein now has the opportunity to refold into the correct conformation.
ATP hydrolysis ejects the new protein and the cycle repeats.
Only one half of the chaperone protein operates at one time.
Chaperones add reliability to the spontaneous folding of the protein, and are required due to the small size of the cytoplasm and the large number of proteins being synthesised at any one time.
Chaperone proteins prevent hydrophobic regions of newly synthesised proteins from aggregating with each other.

Question 6

What are the 4 conformations of the secondary structure of proteins?

Answer 6

Alpha helix
Beta sheets
Loops and turns
Motifs

Question 7

Describe alpha helices.

Answer 7

hydrogen bonding links C=O and N-H groups of AAs
These bonds allow the peptide backbone to twist into a helix, with 3.6 AAs per turn.
Side chains point out wards and determine the hydrophobic nature of the helix.
The polar groups of the backbone are engaged in H bonding in the helix and therefore are not involved in determining the hydrophobic/Philic nature of the helix

Question 8

Describe beta pleated sheets.

Answer 8

Formed by hydrogen bonding between backbone atoms in adjacent strands. Can be parallel (run in same direction) or antiparallel.
Side chains may project from both sides of the sheet.

Question 9

Describe loops and turns.

Answer 9

Part of secondary structure of proteins.
Connect alpha helices and beta sheets.
Turns are highly ordered structures with 4-5 AAs looped into U shape and stabilised by H bonds.
Loops are unstructured areas.

Question 10

Describe motifs.

Answer 10

Part of secondary protein structure.
Grouping of elements of regular secondary structure (alpha helices, beta sheets and loops and turns)
Same motif often appears in different proteins with similar functions.
May be combinations of alpha helices and beta sheets, or zinc finger motifs (involved in DNA Or RNA binding).
Eg calcium binding motif = helix-loop-helix

Question 11

Describe tertiary protein structure.

Answer 11

Involves the interactions between R groups which determines the final 3D conformation of the protein.
May be globular or fibrous.
The tertiary structure of proteins includes domains, which are a molecular unit associated with a particular function.
Domains are usually 40-350aa

Question 12

Describe the degradation of misfolded proteins.

Answer 12

If incorrect protein folding cannot be corrected by chaperone proteins, the protein will be degraded via the ubiquitin-proteosome pathway.

1. Ubiquitin is conjugated to proteins that are destined for degradation. A chain of 5 Ub molecules is sufficient for the complex to be recognised by the proteosome.
2. The tagged protein binds to the cap of the proteosome.
3. The protein becomes linearised, and moves through the central cylinder where it is digested into peptides.
4. These peptides are further broken down into AAs in the cytoplasm, where they can be used in the synthesis of new proteins.