Chapter 3: Proteins

Structure of amino acid

Properties of amino acids

1. exist as zwitterions

2. act as buffers

Describe formation of a peptide bond

Amino acids are joined via condensation that links the carboxyl group of one amino acid to the amino group of another, with the removal of one water molecule 

The sequence and direction of amino acids in a polypeptide does not matter. T/F?

F. They have a direction (N-terminus and C-terminus)

Primary structure of proteins

•  no. & sequence of AA in a single polypeptide chain

• peptide bonds

• Each chain unique in number, sequence, type of AAs

  • Sequence of AAs and R groups determine type and location of chemical interactions -> pattern of folding -> conformation and unique characteristic 

Secondary structure of proteins

• regular coiling and pleating of a single polypeptide chain

• hydrogen bonds b/w CO and NH groups of polypeptide backbone (R groups NOT involved)

• a helix and B-pleated sheets

a-helix

• Single polypeptide chain wound into coiled/spiral structure 

• Turns of helix linked by hydrogen bonds b/w CO grps of 1 turn and NH grps of next turn

  • H bonds form every 4th peptide bond (1-4, 2-6 etc)

  • H bond formed b/w O of CO grp of 1 AA and H of NH grp 4 AAs away

• All main chain CO and NH grps involved in H bond formation -> stability

• 3.6 AA residues in every turn

ß-pleated sheets

• 2 or more regions of single polypeptide chain lying side by side linked by H bonds

• H bonds formed b/w CO grp of 1 region and NH group of adjacent region

• Chains run parallel or antiparallel -> form flat sheet -> folded

Tertiary structure of proteins

• further extensive folding and bending of single polypeptide chain -> compact, globular molc -> specific conformation 

• H bonds, ionic bonds, hydrophobic interaction, disulfide bonds formed b/w R groups of AA residues

Hydrogen bond

• Formed b/w electronegative (δ-, eg. O of C=O and N of NH) and electropositive (δ+, eg. H)

• 3˚: Formed b/w R groups of polar AAs

• 2˚: Formed b/w -CO and -NH groups of peptide bonds

• ’Weak’ individually but strong collectively

Ionic bond

• Formed b/w oppositely-charged R groups of AAs

  • eg. B/w COO- and NH3+ (found on R groups of acidic and basic acids respectively)

  • Ends of polypeptide chain

• Relatively strong bond but change in pH -> change [H+] (alter charges) -> disrupt ionic bonds

  • excess [H+] or [OH-] may affect ionisation of R-groups of charged AA (eg. Excess H+: —COO- turn into -COOH; excess —OH-: -NH3 turn into NH2)

Hydrophobic interaction

• Formed b/w non-polar R groups (hydrophobic)

• Interact and gather at core of protein to avoid water -> polypeptide folds so  as many of hydrophobic R groups are shielded from aq environment as possible

  • Most hydrophobic R groups tend to point to centre

  • Most hydrophilic groups face outwards into aq environment -> protein soluble

• Weak interactions; easily disrupted 

Disulfide bond

• Formed b/w 2 cysteine AA by oxidation of sulfydryl (-SH) groups (contain sulfur)

• Strong covalent bond; strongest out of the 4 interactions -> stability

•  ⬆ disulfide bond ⬆ stability of protein to heat denaturation

What level of structure is this?

Tertiary