Describe the test for proteins.
Biuret test
1. Add 2cm3 sodium hydroxide solution to 2cm3 of sample in test tube.
2. Add 1% copper(II) sulfate solution drop by drop.
3. Shake the mixture after each drop.
+ve result -> blue solution turns purple.
What does an amino acid consist of?
Amino acid contains 4 groups bonded to a C atom -
1. H atom
2. Amino group(-NH2)
3. Carboxylic acid group(-COOH)
4. R group - confers basic(-NH2), acidic(-COOH), neutral(uncharged) properties.
Describe formation of peptide bond.
A peptide bond is formed between the amino group of one amino acid and the carboxylic group of another amino acid, in a condensation reaction with the loss of 1 water molecule, catalysed by enzymes(peptidyl transferase).
Describe breakage of peptide bond.
A peptide bond is broken between 2 amino acids in a hydrolysis reaction with the addition of 1 water molecule, catalysed by enzymes(protease).
Define the primary structure of a protein.
It is the precise number, type and sequence of amino acids linked by peptide bonds in a linear polypeptide chain.
(contains information that determines the conformation of the protein)
Define the secondary structure of a protein.
It is when the polypeptide chain coils and folds into geometrically regular repeating structures, mainly a-helices and b-pleated sheets. These structures are maintained by intramolecular hydrogen bonds between C=O and -NH groups in the main chain of polypeptide.
Define the tertiary structure of a protein.
It is when the polypeptide chain is further bent, coils and folds to form a precise 3D conformation. It is maintained by intramolecular hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between the R groups of amino acids.
Define the quaternary structure of a protein.
It is the aggregation of 2 or more polypeptide chains(subunits), subunits held together by intermolecular hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between R groups of amino acids on different polypeptide chains, forming a protein.
How are bonds in proteins formed?
hydrogen bonds
-intramolecular; between O atom of C=O and H atom of -NH of amino acids, between R-groups of polar & polar/basic/acidic R groups of amino acids on same ppc
-intermolecular; between R-groups of polar & polar/basic/acidic R groups of amino acids on diff ppc
ionic bonds
-between R-groups of positively-charged & negatively-charged amino acids, in same ppc or b/w diff ppc.
disulfide bonds(strongest, only broken by reducing agent)
-between -SH groups of 2 molecules of cysteine, in same ppc or b/w diff ppc.
hydrophobic interactions
-between non-polar R groups of amino acids.
(in (aq) medium, hydrophilic R groups of amino acids face outwards towards (aq) medium; hydrophobic R groups of amino acids face inwards, shielded from (aq) medium -> protein is soluble)
Describe the effect of temperature on the structure of protein.
When temperature increases, kinetic energy of the protein increases.
High heat disrupts the weak hydrogen bonds & hydrophobic interactions that maintain the secondary, tertiary structures of the protein.
This results in the loss of specific 3D conformation of protein, leading to denaturation.
Describe the effect of pH on the structure of protein.
When pH increases, more H+ ions present -> combine with COO- R groups to form COOH
When pH decreases, less H+ ions present -> NH3+ R groups donate H+ to form NH2
Ionic bonds, hydrogen bonds that maintain tertiary structure are disrupted, results in the loss of specific 3D conformation of protein, leading to denaturation.
Describe the structure of haemoglobin.
1o, 2o, 3o, 4o
1o: 4 polypeptide chains; 2 a chains, 2, b chains
2o: each polypeptide chain coils into a-helices, maintained by intramolecular H bonds b/w C=O and -NH groups of different amino acids
3o: each polypeptide chain further bent, folded into globular protein subunit maintained by intramolecular H, ionic bonds, hydrophobic interactions b/w R groups of amino acids
4o: 4 protein subunits pack closely together, maintained by intermolecular H, ionic bonds and hydrophobic interactions; results in nearly spherical Hb molecule.
Relate structure to function; haemoglobin(w.r.t polypeptide)
4 protein subunits pack closely together -> Hb is compact, allows for packing of more Hb into rbc -> more O2 can be carried & transported
Hb in contact w/ (aq) medium, hydrophilic R groups of a.a faces outwards, interacting w/ (aq) medium -> Hb is soluble in (aq) medium -> allows mobility around body thru bloodstream as Hb can bind & transport O2 dissolved in blood
Hydrophobic R groups face inwards, shielded from (aq) medium -> hydrophobic interactions b/w hydrophobic R groups hold molecule in precise 3D conformation
Describe structure of collagen.
1o, 2o, 4o
1o: 3 pp chains, 1000 aa residues. aa sequence is repetitive(Glycine-X-Y, X proline, Y hydroxyproline/hydroxylysine)
2o: each pp coils into a loose helix
4o:
- 3 helical pp chains wind tightly, bound by H bonds between C=O and -NH of aa on diff. pp, forms tropocollagen. every 3rd aa is glycine - small size allows 3 pp to lie closely & coil tightly.
- ends of parallel tropocollagen are staggered, covalent cross-links form between C=O end of 1 tropocollagen and the -NH end of another tropocollagen; forms collagen fibril, assemble to form collagen fibres
Relate structure to function; collagen.
amino acid sequence is repetitive(Glycine-X-Y) -> small size of glycine allows 3 helical polypeptide chains to lie close together & coil tightly
ends of parallel tropocollagen molecules are staggered, covalent cross-linking forms between C=O end of 1 tropocollagen & -NH end of another -> cross-links are out of step with each other, confers greater tensile strength
tropocollagen form covalent-cross links w/ other tropocollagen, forms collagen fibril which further assembles to form collagen fibres -> confers a flexible, inelastic structure for support -> high tensile strength, can withstand large pulling forces.
Describe structure of GPLR.
1o, 2o, 3o
1o: single polypeptide chain
2o: single polypeptide chain coiled into 7 transmembrane a-helices
3o: polypeptide chain further bent, folded and coiled into tertiary structure, maintained by intramolecular H, ionic, disulfide bonds & hydrophobic interactions between R groups of amino acids on same polypeptide.
Relate structure to function; GPLR.
single polypeptide chain coiled into 7 transmembrane a-helices -> allows GPLR to be embedded in & span cell surface membrane (hydrophobic R groups form weak hydrophobic interactions w/ hydrophobic fatty acid tails)
has extracellular region -> serves as specific binding site for ligand which can't pass thru CSM
has intracellular region -> serves as specific binding site for G-protein
Relate structure to function; haemoglobin(w.r.t molecules)
Each subunit contains prosthetic haem group w/ Fe2+, reversibly binds to O2, allows O2 to be readily released to respiring tissues -> 4 subunits, 4 haem groups; Hb can carry, transport 4 O2 molecules @ once, enables more efficient transport of O2 around body
allosteric in nature, can undergo conformational changes -> binding of O2 to 1 haem group results in binding of O2 to other haem groups -> easier binding & release of O2