PROTEINS

Consist of: C, H, O, N and sometimes S Basic structural unit: amino acid Proteins differ from Carbs: ALWAYS CONTAIN NITROGEN AMINO ACIDS >100 naturally occurring, only 20 used in biosynthesis Consists of: o -carbon atom (which is bonded to) o Hydrogen atom o Amino group (-NH2) o Carboxyl group (-COOH) o Variable R group (aka side chain) Different amino acids have different R groups Classification of amino acids (A) Based on human nutrition a. Essential amino acids i. Cannot be synthesized from simple substances by human ii. Must be obtained from diet b. Non-essential amino acids i. Can be synthesized from simpler substances (B) Properties of R group a. Neutral amino acids i. Have non-polar (hydrophobic) or polar (hydrophilic) side chains ii. Sum of +ve and ve charges are equal b. Electrically-charged amino acids i. Negatively-charged: acidic amino acids (hydrophilic) ii. Positively charged: basic amino acids (hydrophilic) Properties of amino acids (I) Exists as zwitterions (aka dipolar ion) a. Not ALL the time though! b. In solution, ionized a.a. carry both +ve and ve charges i. Protonated: (-NH2) receives H+ (-NH3+) ii. Deprotonated: (-COOH) dissociates H+ (-COO-) (II) Amino acids as buffers a. Amphoteric: can act as both acids and bases good buffer quality b. Buffer: prevents changes in pH when small amt of acid/alkali is added by accepting or donating H+ i. When acid (H+) is added to the solution, COO- of zwitterion accepts a H+ to neutralize the H+, and becomes COOH Thus preventing a change in pH of the solution, a.a. becomes positively charged (III) Based on R groups of amino acids a. Physical & chemical properties determine uniqueness of a.a. Charge/size/shape/reactivity POLYPEPTIDES Monomers: amino acids o Dipeptide (2 residues) o Tripeptide (3 residues) o Oligopeptide (3-10 residues) o Polypeptides (>10 residues) Formed through condensation/dehydration o Links carboxyl group to amino group, removes water molecule o Peptide bond! Backbone: regularly repeating part, main chain Variable part: distinctive vatiable R groups

Amino-terminal (N-terminal) start of polypeptide chain Carboxyl-terminal (C-terminal) end of polypeptide chain Folds into specific 3-D shape

STRUCTURE OF PROTEINS Primary Structure Refers to sequence and number of amino acids in a polypeptide chain. Bond: peptide bonds between successive a.a. Each polypeptide chain has unique sequence/number/type of a.a. o Sequence determines type and location of cross linkages pattern of folding unique 3-D conformation o NOT random! linking of a.a. determined by nucleotide sequences in genes Important in determining the function of the protein o One amino acid alteration in the primary structure can alter the entire structure of the protein o Sequence of nucleotides in the gene + sequence of amino acid residues = important in determining shape and function o E.g. sickle cell anaemia glutamic acid (6th a.a.) replaced with valine results in abnormal -globin polypeptide alters entire structure of the haemoglobin altered property (haemo molecules aggregate together at low oxygen concentrations causes red blood cells to change shape Primary structure remains unaffected during denaturation Secondary Structure Refers to spatial arrangement formed by regular coiling and pleating of a single polypeptie chain Bond: H bonds at regular intervals (between CO and NH grps of backbone) -helix: single polypeptide chain coiled into an extended spiral spring o CO groups of one turn linked to NH grps of the next turn (ALL CO & NH are involved stability) at every 4th peptide bond o 3.6 amino acid residues in every turn o E.g. keratin (structural protein of hair), wool, nails -pleated sheet: when 2 or more regions/segments of a single polypeptide chain lying side-by-side are linked by H-bonds o NH & CO grps of one chain will form bonds with NH & CO grps from adjacent chain (ALL involved structure is stable and rigid) o Runs parallel (same) or anti-parallel (opposite) forms a flat sheet which becomes folded o R-groups are not involved in bonding project above or below the plane o E.g. Fibroin (silk produced by silkworms and spiders) Tertiary Structure Refers to the structure formed by extensive folding of a single polypeptide chain compact shape, gives overall 3-D shape of protein Bond: 4 types of interaction o Hydrophobic interaction (weakest) Between non-polar R-grps which interact and cluster at the core of the protein (mutual exclusion from water) Polypeptide folds to shield hydrophobic R-grps from aqueous environment (hydrophobic point inwards; hydrophilic face outwards) o Hydrogen bond Between polar R-groups Electropositive (H of NH or OH) and electronegative (O of C=O, N of N-H) atoms form H bonds Individually H bond is weak; but collectively it is strong o Ionic bond Between oppositely-charged groups of amino acids COO- (acidic) and NH3+ (basic) found on R groups or at the ends of a polypeptide chain Change in pH alter the changes and hence ionic bonds

Bonds are weak under aqueous conditions charged groups are surrounded by H20 molecules o Disulphide bond (strongest) Between 2 cysteine amino acid residues brought together by folding of polypeptide Strong covalent bonds contribute to toughness (increase in bonds, increase stability of protein to heat denaturation) Steric/spatial relation of residues that are far apart on chain as well as those which are adjacent

Quarternary structure Polypeptide = subunit Bonds: ionic boncs, hydrogen bonds, disulfide bonds & hydrophobic interactions Constituent chains may be identical or different 2 subunits = dimers more than 2 subunits = oliomers Not all proteins have quarternary structure E.g. lysozome, myoglobin and albumin Fibrous protein Long polypeptide chaings forming long strands Length of polypep/sequence of a.a. may very slightly between 2 samples of same protein Insoluble in H20 has hydrophobic R groups on the exterior of their molecules Repetitive regular sequence of amino acids Functions as structural and contractile proteins COLLAGEN Structural protein; essential component of connective tissue in tendons, bone, skin and teeth (most abundant fibruous protein) Structure helical polypeptide chain tropocollagen fibril fibres 3 helical polypeptide chains wound around each other like a rope tropocollagen H bonds further stabilize it and increase rigidity and tensile strength each helical polypeptide: about 1000 a.a. (glycine-X-proline/hydroprline) o glycine (smallest a.a.) fits restricted space @ centre of triple helix (3 chains come together) tropocollagen forms inelastic tight coil o proline bulky/inflexible confers rigidity unique secondary structure tropocollagen cross-links (covalent bonds involving lysine residues) with neighbouring tropo running parallel Forms fibrils fibrils unite to form fibres o staggered/overlapping minimizes points of weaknesses along length Globular protein Long polypeptide chains folded into spherical shape Length of polypep/sequence of a.a. are always identical between 2 samples of the same protein Soluble in H20 have hydrophilic R groups on exterior of molecules which interact with H20 Irregular sequence of amino acids Functions in a variety of metabolic roles. (e.g. haemoglobin, enzyme) HAEMOGLOBIN Transport protein; pigment which transports 02 found in rbc Structure Quarternary structure: 4 polypeptide subunits (2 -globin + 2 -globin) Each subunit = polypeptide component ( globin) + prosthetic/non-protein component ( haem group) o Haem group: poryphin ring an Fe2+ (which binds to O2, so 1 Hb can carry up to 4 O2) Bonds: weak hydrophobic interactions and hydrogen bonds allows subunits to move, allowing a change in position that influences its affinity for O2 Cooperative binding of O2 1 O2 molecule + 1 Hb subunit = structural change in remaining 3 subunits so that their affinity for O2 increases (results in rapid uploading of O2 onto other subunits) and vice versa