Proteins

Question 1

What are the different configurations of amino acids?

Answer 1

L (levulo) configuration
- amine group on the left side
D (dextro) configuration
- amine group on the right side

Question 2

What are the different side chains of an amino acid?

Answer 2

amino acids with positively charged (basic) side chains
amino acids with negatively charged (acidic) side chains
amino acids with hydrophilic (polar, but not charged) side chains
amino acids with hydrophobic (non-polar) side chains

Question 3

What are the bonds in a proteins joining the amino acids?

Answer 3

peptide bonds join amino acids

• peptide bonds are a type of covalent bond
• have partial double bond character = are planar and rigid (oxygen is trans to hydrogen attached to nitrogen)
• no freedom of rotation around the peptide bond

Question 4

What is a residue?

Answer 4

an amino acid in a peptide chain

Question 5

What are the different structures of an amino acid?

Answer 5

primary structure - sequence of amino acid residues in a polypeptide chain (N terminus to C terminus) = peptide (covalent) bonding between amino acids

secondary structure - local/regular folded structures of the polypeptide chain, stabilised by hydrogen bonds = alpha helix and beta sheet

tertiary structure - due to the bending and twisting of the secondary structure into a more compact 3D shape (disulphide bonds, ionic bonds, hydrogen bonds)

Quaternary structure: the combination of a number or different polypeptide chains and/or associated non-protein groups

amino acid sequence (sequence of the gene) determines secondary, tertiary and quaternary structure).

Question 6

What is the alpa helix structure?

Answer 6

right handed - 3.6 amino acid residues per turn

formed by the backbone of the protein chain, side-chains extend outwards

formed and stabilised by hydrogen bonds
- the oxygen of the CO group is hydrogen bonded to the hydrogen of the NH group that is situated 4 residues further towards the C terminus of the sequence

N terminus is at the top and C terminus is at the bottom

Question 7

What is the beta sheet structure?

Answer 7

sheet-like structure

formed by the backbone of the protein chain, side-chains extend above and below the sheet

formed and stabilised by hydrogen bonds
- oxygen of the CO group is hydrogen bonded to the hydrogen of NH group in different polypeptide chains or in the same chain further away

adjacent chains can run in the same direction
- parallel beta sheet
adjacent chains can run in the opposite direction
- antiparallel beta sheet

Question 8

What is the role of the tertiary structure (and quaternary) structure of proteins?

Answer 8

determines the shape of the molecule

globular proteins
- myoglobin, haemoglobin, cytochrome c, insulin, most enzymes (e.g. Lysozyme)

fibrous proteins: collagen, elastin, keratin

proteins that form filaments or tubes

• actin
• tubulin

Question 9

What are disulphide bonds?

Answer 9

are a type of covalent bond

• form between 2 sulphur atoms
• form by oxidation and are broken by reduction

Question 10

What are ionic bonds?

Answer 10

electrostatic attractions between oppositely charged atoms

Question 11

What is hydrogen bonding?

Answer 11

can be formed between uncharged molecules as well as charged ones

• a hydrogen atom is shared between two other atoms
• the partial negative charge on the hydrogen acceptor (-) attracts the hydrogen attached to the hydrogen donor (+)

Question 12

What are hydrophobic interactions?

Answer 12

unfolded polypeptide can become folded in aqueous environments
- hydrophobic region contains the non-polar side chains while the polar chains facing outward can form hydrogen bonds with water

Question 13

What is the loss of protein folding called and caused by?

Answer 13

loss of protein folding is called denaturation
it is caused by different factors including:
- heat, acids and alkalis, organic solvents, mechanical force