Biochemistry Lecture Notes - Almaaqal University PDF

Almaaqal University Chemistry of Protein and Amino Acids Dr/ Wael Sobhy Darwish Biochemistry PhD Lec-10  Proteins Proteins: Proteins are macromolecul...

Almaaqal University Chemistry of Protein and Amino Acids Dr/ Wael Sobhy Darwish Biochemistry PhD Lec-10  Proteins Proteins: Proteins are macromolecules formed of amino acids united together by peptide bonds. Proteins account for more than 50% of the dry mass of most cells. There are 20 amino acids from which all protein molecules are made. Some proteins contain just a few amino acids in a chain, other proteins are chains of thousands of amino acids. Polymers of proteins are called polypeptides. A protein consists of one or more polypeptide chain. Structure of amino acid Amino acids are organic molecules at the center of an amino acid is an asymmetric carbon atom called the alpha (α) carbon. 1- Amino group: (NH2). 2- Carboxyl group: (COOH). 3- Hydrogen atom (H). 4- Side chain or radical group (R) The 20 amino acids are distinguished by their R-group. Structure of amino acid  Amino Acid Polymers Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen atom from the amino group of another. The resulting covalent bond is called a peptide bond. Repeating the process over and over creates a polypeptide chain. At one end is an amino acid with a free amino group (the N-terminus), and at the other end is an amino acid with a free carboxyl group (the C-terminus).  Amino Acid Polymers Peptide bond OH SH CH2 CH2 CH2 H H H N H C C N C C OH H N C C OH H O H O H O DESMOSOMES (a) H2O OH DESMOSOMES ESMOSOMES OH SH Side chains Peptide CH2 CH2 bond CH2 H H H H N C C N C C N C C OH Backbone H O H O H O Amino end Carboxyl end (b) (N-terminus) (C-terminus) Classification of amino acids into Essential and nonessential amino acids  Essential and nonessential amino acids Essential amino acids: are amino acids which are not synthetized by the body and must be obtained by the diet. Nine essential amino acids, including:- phenylalanine, valine, tryptophan, threonine, isoleucine, methionine, histidine, leucine, and lysine. Function: Serves to build and repair muscle tissues. Also, it forms precursor molecules for the formation of neurotransmitters in the brain  Non essential amino acids Non essential amino acids : The human body can synthesize these amino acids using only the essential amino acids. 11 of the 20 amino acids are non-essential Function: 1- Removal of toxins 2- Integral in the synthesis of RBC and WBC 3- Promotes brain function. Some non-essential amino acids (e.g. Arginine, Cysteine, and Tyrosine) are called semi- essential because the body cannot synthesize them in sufficient quantities during certain physiological periods of growth, including pregnancy, adolescent growth, or recovery from trauma  Classification of amino acids : Amino acids are classified into three groups: 1. Neutral amino acids: are the largest group which are divided into: a. aliphatic amino acids ( glycine, valine, alanine, leucine, isoleucine). b. aromatic amino acids ( tyrosine, phenylalanine). c. heterocyclic amino acids ( tryptophan, histidine). d. sulpher containing amino acid (cysteine , methionine ) 2. Acidic amino acids ( aspartic acid , glutamic acid ) 3. Basic amino acids (Lysine , arginine).  Classification of proteins 1- Classification based on protein function of proteins i) Catalytic proteins, e.g. enzymes. ii) Structural proteins, e.g. collagen, elastin, keratin. iii) Contractile proteins, e.g. myosin, actin. iv) Transport proteins, e.g. hemoglobin, myoglobin, albumin, transferrin. v) Regulatory proteins or hormones, e.g. ACTH, insulin, growth hormone. vi) Genetic proteins, e.g. histones. vii) Protective proteins, e.g. immunoglobulins, clotting factors.  Classification Based on Composition Simple proteins: A protein that contains amino acids only. Examples: albumin, globulins & histones. Conjugated Proteins: A protein that have some non-protein moiety in its structure along with protein part: lipoprotein, glycoprotein. Derived proteins: Proteins derived from simple and conjugated proteins by physical or chemical treatment. Examples: peptones peptides and denatured proteins. Classification of protein based on structure  Structures of protein There are four orders of protein structures. 1- Primary structure of protein. Referred to the number, type and sequence of amino acids in the chain. The main bond in this structure is peptide bond.  Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Secondary structure result from hydrogen bonds between the repeating constituents of the polypeptide backbone Includes the  helix and the  pleated sheet.  Tertiary structure Secondary structures are arranged to form final functional 3D structure called domain. Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups  Forces Controlling Tertiary Protein Structure a. Hydrogen bond: between polar side chains of amino acids b. Hydrophobic forces: between the non-polar (R) groups of the amino acids c. Electrostatic forces (ionic bonds, salt bridges): between oppositely charged (R) of amino acids d. Disulfide bonds: (Strong covalent bonds) between sulfur amino acids (cysteine)  Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen  Chains Iron Heme  Chains Hemoglobin The four level of protein structure Protein denaturation Protein denaturation results in the unfolding and disorganization of the protein’s secondary and tertiary structures, which are not accompanied by hydrolysis of peptide bonds. Denaturing agents include: Heat, organic solvents, high pressure, mechanical mixing, strong acids or bases, detergents, and ions of heavy metals such as lead and mercury. Denaturation may be reversible or, more commonly, irreversible. Denatured proteins are often insoluble and, therefore, precipitate from solution.