Structure of proteins Primary structure: is amino acids sequence or the covalent structure (50-2500) amino acids M.Wt. of amino acid=110 Dalton (56 110=5610 Dalton). Single chain or more than one polypeptide chain. Gly-Ala-Val Gly-Val-Ala Both the tripeptides shown above contain the same amino acids, but their sequence is altered.when the sequence is changed, the polypeptide is also different. Insulin: Hormone secreted by β- cell of pancreas (facilitate glucose entery to the cell for metabolism) Proinsulin: single polypeptide chain of 86 amino acids. Biologically active insulin consist of (2 chain) A.chain: consist of 21 amino acids. B.chain: consist of 30 amino acids. C peptide: connecting peptide 3-disulfide bonds of cysteine 1
Primary structure of insulin Secondary structure: conformation of polypeptide chain is based on rotational angels about covalent bonds. α helix β- plated sheet Collagen helix 1-α-helix: coiled single chain, spiral. 2
P = d n P = helix pitch, n = no. of a.a. residues per 360 turn, d= distance between α- carbon of adjacent a.a. characteristic of α- helix: 3.6 a.a. per turn d= 1.5 A, P= 5.4 A Peptide bond β plated sheet: 1-Sheet like 2-The poly peptide chains is almost fully extended. The distance between adjacent amino acids is 3.5 A. 3- Stabilized by H- bonds between N-H and C=O groups of different polypeptide chain 4- Parallel β- sheet or anti parallel 5-Side chain group are projected above and below. 3
Collagen helix: Three dimensional structure Tertiary structure: In this structure the protein chain or polypeptide chain form a- 3- dimensional conformation stabilized by non-covalent bonds: hydrogen bonds, hydrophobic bonds, van der walls, electrostatic interaction. Quaternary structure: Is seen only when protein is formed from more than four subunits. Its spatial arrangement of different subunits in the space. Hydrogen bond: is the interaction or bond (non-covalent) formed between the carbonyl oxygen and amide group of polypeptide chain, H- bond could form between not only oxygen and hydrogen, but also between these tow atoms and polar R- groups.the side chain could partisepitate in hydrogen bond formation and according to hydrogen bonds potentiality, we can classify hydrogen bond into 3 groups: 4
1-The side chain in amino acid residue could act as hydrogen bond donar. 2-Could act both as H- bond donar and acceptor regardless to PH. 3-Vary with the PH of the medium, they could act at certain PH as hydrogen bond donar and acceptor, if the PH is changed this will make these residue act as donar or acceptor, therefore H-bond varies with the PH of medium. Electrostatic bond: forms between polar side group on the surface of the protein or between two subunits, if protein is formed of more than one subunit, so it will stabilize the quaterally subunit. Could be seen when the electron density of two molecules is high in a close distance, at this distance there will be a conformation between these two atoms. Normally is seen in protein inside it (core of protein not on it surface). Hydrophobic interaction: happens between the non-polar groups of both aliphatic or aromatic amino acid residues. They come in close inside the core of protein and forms this form of interaction. The most abundent conformation is hydrogen and hydrophobic interaction. The energy that partisepitates in the interaction formation is very small to that which forms the covalent bond, but because of the large number of these bonds in protein conformation the stability will be confined the energy difference. 5
Collagen Helix: is a triple helix, collagen is abundant in skin, oarta, cartilage.etc. Synthesized by special cells (e.g.: osteoblast, fibrocytes and chondroblast in cartilage). It is rich in amino acids and derived amino acids like proline, glycine, hydroxy proline (OH- proline) and hydroxy glycine (OH-glycine). Hydroxylation is carried out by enzyme hydroxlase in presence of vitamine C and succinate and α- keto glutarate. Addition of carbohydrates (in form of glucose and galactose) prior to the collagen secretion forms its primary structure. When it is formed by 3 polypeptide chains the helix is called tropo- collagen. According to the 3 polypeptides we have five tybes of collagen depending on amino acids sequences. Type II, III and IV have similar amino acids sequence in their 3 polypeptides. Type I and V have only two identical polypeptides chains in the amino acids sequence. Every turn of the helix carry three amino acids and the 3 rd amino acid is always glycine on the same side of the helix. The three helices will be coiled on each other and form the super coiled structure of tropocollagen, the coiling will be always on the 3 rd position (on glycine) to facilitate the conformation. The coiling is stabilized by achieving two bonds: 1-Hydrogen bond 2- Hydrophobic interaction. Deficiency of vitamine C in the body causes scurvey characterized by the break down of RBCs. 6
Cross linking: the amino acids will be first oxidized into aldehydes by an enzyme called lysyl oxidase and then will be pass into chain of reactions in covalent bond cross linkage between these helices, this is important in the stability of collagen fiber. The protein is classified according to the quaternary structure into: Fibrous and globular proteins. Fibrous proteins: Have a rode shape structure for example: collagen, they have low solubility in water, vary in molecular weight, have a high tensile structure important in matrices for certain tissues, have high amount of regular secondary structure. Globular proteins: Spherical in shape, water soluble, have secondary and tertiary and quaternary structures, for example: haemoglobin and myoglobin Haemoglobin: Formed by four polypeptide chain, each two of identical primary structure. Binds with O 2 and CO 2 from lungs and tissues. Types: 1-Adult haemoglobin (HbA). 2-Infant haemoglobin (HbF) 3-HbA 2. 7
Myoglobin: Oxygen binding protein in muscles, made of a single polypeptide chain, has only on oxygen binding site. 8