H2 Biology 4 - 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.

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.

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).

A peptide bond is broken between 2 amino acids in a hydrolysis reaction with the addition of 1 water molecule, catalysed by enzymes(protease).

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)

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.

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.

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.

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)

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.

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.

1^o, 2^o, 3^o, 4^o

1^o: 4 polypeptide chains; 2 a chains, 2, b chains

2^o: each polypeptide chain coils into a-helices, maintained by intramolecular H bonds b/w C=O and -NH groups of different amino acids

3^o: 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

4^o: 4 protein subunits pack closely together, maintained by intermolecular H, ionic bonds and hydrophobic interactions; results in nearly spherical Hb molecule.

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

1^o, 2^o, 4^o

1^o: 3 pp chains, 1000 aa residues. aa sequence is repetitive(Glycine-X-Y, X proline, Y hydroxyproline/hydroxylysine)

2^o: each pp coils into a loose helix

4^o:

- 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

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.

1^o, 2^o, 3^o

1^o: single polypeptide chain

2^o: single polypeptide chain coiled into 7 transmembrane a-helices

3^o: 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.

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

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