LO 2 – amino acids bonds and protein structural classification

N terminus

Amino group (-NH₃⁺)

= start

C terminus

Carboxyl group (-COO^-)

= end

Primary protein structure

numerous amino acids forming a polypeptide

linear sequence of amino acids

sequence determines higher orders of structures

Polypeptide

many amino acids strung together

Primary protein structure - bonds

covalent peptide bonds linking amino acids - very strong

Which protein structure?

Primary protein structure

Secondary protein structure

backbone of polypeptide

linear sequence folded on itself

contains alpha helix, beta-sheet or random coils

Secondary protein structure - bonds

Peptide and hydrogen bonds

Two variations of Hydrogen bonds in secondary structures

Intermolecular (between CO and NH groups of amino acids on different polypeptides)

Intramolecular (between CO and NH groups of amino acids on same polypeptide)

Which protein structure

Secondary structure

Alpha helix

spiral shape; coils around itself; flexible, stretchy and dynamic

spiral turn has 3.6 aa (4th aa close to 3rd and 5th aa)

some aa disrupt bonds in alpha helix (known as helix breaker), as lack H, only found in beginning or end

Alpha helix - bonds

Hydrogen bonds (CO group binds to NH group of peptide bond, 4 aa downstream)

Beta Sheet

sheet like conformation

forms when 2 parts of a polypeptide chain lie side by side/across each other

intramolecular, stabilised by H bonds

Motifs

combinations of alpha helices and beta sheets

connected via looped regions of varying length (random coils, sequences of aa together)

Motifs - examples

b-a-b, hairpin loop and helix-turn-helix motifs

Tertiary structures

higher order of folding (polypeptide chain folded back on self to form a condensed structure)

depends on interaction between the side chains

Tertiary structures - bonds

Hydrogen bonds, peptide bonds, disulphide bonds, ionic bonds, London dispersion forces, hydrophobic interactions

Which protein structure?

Tertiary structure

Tertiary structures - fibrous

extended and filamentous

repetitive aa sequence

structural (e.g collagen, hair, elastin, silk)

only small amount present in cell

Tertiary structures - globular

compact

different aa sequence

many functions

most proteins in cell

e.g. enzymes, haemoglobin

Peptide bond

linking 2 amino acids

condensation reaction: water removed - O from carboxyl group, 2 H from amino group of another aa. Carboxyl carbon and amino nitrogen: linked by peptide bond

Covalent bond (sharing electrons)

What bond?

peptide bond

Hydrogen bonds

non-covalent (not sharing electrons)

weak bond

donors (amine or hydroxyl group in aa) have H-atom linked to a more electronegative atom of an acceptor (e.g. carbonyl and sulfhydryl groups of aa)

abundant in proteins: one is weak, many is strong

Which bond is (b)

Hydrogen Bond

Disulphide bonds

between sulphur atoms of 2 cysteine aa residues by covalent bonding through oxidation (removal of H atoms)

disruption denatures proteins through reduction (addition of 2 H atoms to regenerate the sulfhydryl groups SH)

Which bond is (a) ?

Disulphide Bond

Which stage disulphide bond?

oxidation - formation of bond between sulphur bonds due to removal of H

Ionic bonds

R groups may be +ve or -ve

electrostatic interactions between R groups, +ve and -ve attract, similar charges repel

high/low pH affects ionic bonds, results in denaturation

Which bond is c?

Ionic bond

London Dispersion Forces/van der Waals interactions

attraction of 2 non-polar molecules

weak

only effective if molecules are close, not when R group far away

Hydrophobic interactions

hydrophobic molecules excluded from water interaction

Which bond is (d)?

London dispersion forces, hydrophobic interactions