Chapter 3: Proteins

Structure of amino acid

Consists of an a-carbon atom bonded to 4 groups: H atom, amino group, carboxyl group, variable R group

Properties of amino acids

1. exist as zwitterions

2. act as buffers (can donate/ accept H+ → amphoteric)

Describe formation of a peptide bond

Amino acids are joined via peptide bonds during condensation reaction 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

Number and sequence of amino acids in a single polypeptide chain, linked by peptide bonds.

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 

• A hydrogen bond forms between the C=O group of one amino acid residue and the N-H group of another amino acid residue 4 amino acids away from the backbone of a single polypeptide

• 3.6 AA residues in every turn of the helix

ß-pleated sheets

• 2 or more segments of single polypeptide chain lying side by side linked by hydrogen bonds

• Hydrogen bonds formed b/w CO grp of an AA residue of 1 region and NH group of another amino acid residue on an adjacent segment

• Chains run parallel or antiparallel

• Form flat sheet which becomes folded

Tertiary structure of proteins

• Structure formed by 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 within a polypeptide

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

Quaternary structure

• Association of 2 or more polypeptide chains into 1 functional protein molecule.

• Maintained by all 4 types of interactions, formed between R groups of amino acid residues of different polypeptides

• Constituent chains of a multimeric protein can be identical or different

Structure and function of haemoglobin (subunits)

Structure:

• Quaternary structure made up of 4 subunits: 2 a-globin, 2 b-globin

• Each subunit consists of:

• Globin polypeptide

• Haem group (prosthetic component aka non protein)

  • Porphyrin ring

  • Iron ion (Fe2+)

Function:

• Fe2+ of each haem group binds reversibly to O2 -> 1 Hb molc can carry up to 4 O2 molcs -> form oxyhaemoglobin

Structure and function of Hb (R groups)

Structure

• AAs with hydrophilic R groups on external surface

• AAs with hydrophobic R groups buried in interior

Function

• Soluble in aq environment → can take place in chemical reactions in RBCs → Transport protein

Structure and function of Hb (ixns)

Structure:

• The 4 subunits held tgt by weak intermolecular ixns formed between R groups -> subunits can move wrt eo → allow change in position that influences Hb’s affinity for O2

Function:

• Binding of 1 O2 molc to Hb subunit induces a conformational change in remaining 3 subunits such that their affinity for O2 increases

• known as cooperative binding of O2

Structure and function of collagen (amino acids)

Structure:

• Each chain consists of 1000 AAs and contain a repeating sequence, usually glycine-X-Y

  • X: usually proline

  • Y: Usually hydroxyproline

• The tropocollagen molc can form a tight, compact coil as almost every 3rd AA is glycine (smallest AA)

• Allows R group to fit into the restricted space in the center of the triple helix

Function

• Bulky and relatively inflexible proline and hydroxyproline residues confer rigidity on the molecule.

Structure and function of collagen (H bonds)

Structure

• Extensive H bonds form between amino acid residues of the 3 polypeptides

Function

• Incr tensile strength due to stretching

Structure and function of collagen (staggering)

Structure

• Adjacent tropocollagen molecules are arranged in a staggered manner

Function

• Staggered arrangement minimizes points of weaknesses along length of fibrils

Structure and function of collagen (cross-links)

Structure:

• Covalent cross-links between lysine residues at C and N ends of adjcanet tropocollagen molecules results in formation of fibrils

Function:

• Incr tensile strength

Structure and function of collagen (fibres)

Bundles of fibrils unite to form long collagen fibrils → incr tensile strength