Protein Chemistry Lecture 2: Peptides & Protein Structures PDF

Prof. Rania Khalil 1  Peptides are compounds formed of less than 50 amino acids linked together by peptide bonds. 1. Dipeptide: 2 AA (Gly-Asp) 2. Tripeptide: 3 AA (Gly-Asp-Glu) 3. Oligopeptide: 3-10 AA (DIAK) 4. Poly peptide: 10-50 AA one amino acid substitution in the bond...

Prof. Rania Khalil 1  Peptides are compounds formed of less than 50 amino acids linked together by peptide bonds. 1. Dipeptide: 2 AA (Gly-Asp) 2. Tripeptide: 3 AA (Gly-Asp-Glu) 3. Oligopeptide: 3-10 AA (DIAK) 4. Poly peptide: 10-50 AA one amino acid substitution in the bonding sequence of a polypeptide can alter the final protein's shape and ability to function. 2 Amino acids are joined by the peptide bond which is a covalent chemical bond, via dehydration (condensation reaction). Peptide bond is created when COOH group of one amino acid molecule reacts with an HH2 group of another amino acid molecule *The polypeptide chain is referred to as the primary structure of the protein. 3 The primary structure of a peptide simply consists of its linear sequence of amino acids N terminal amino acid is the only free amino group and always to the left side. C terminal amino acid is the only free carboxylic group and always to the right side. 4  Peptide content Function Anserine β-Ala-(CH3)His Reduce muscle fatigue and have buffering capacity Aspartame Asp-phe Artificial sweetener (GSH) Glutathione Glu-cys-gly Defense mechanism against toxic compounds and antioxidant Bradykinin 9-AA Inflammatory mediator and vasodilator decrease blood pressure 5 1. Electrophoresis: It depends on the movement of charged particles towards one of the electrodes under the influence of electrical current 2. Ion exchange chromatography : It depends on the difference in net charges of proteins at a given PH 6  AA can be ionic with a positive and a negative charge at physiological neutral pH (pH= 7)  Carboxylic group is dissociated forming a negatively charged carboxylate ion (COO-)  Amino group is protonated forming positively charged ion (NH3+)  This character is known as Amphoteric: organic substance that acts as both an acid and a base 7 Zwitterions : It is the amino acid that carries both positive and negative charges. It is electrically neutral (net charge is zero) and cannot migrate in electric field. 8 Isoelectric point (PI): it is the PH at which zwitterion is formed. This PH is at midway between the pk values of COOH and NH2 groups 9  Calculate the PI of alanine in which pka1= 2.34; pka2=9.69 PI (PH)= (2.34+9.69)/2= 6.105 At this PI the net charge of alanine is zero, least soluble in water, not migrate in the electric field 10  If the side chain is acidic (asp and glu): average the side chain pKa with the α-COOH pKa.  If the side chain is basic (his, arg, and lys): average the side chain pKa with the α-NH3 pKa.  For other ionizable groups (tyr and cys), determine the middle pKa and average it with the α-COOH pKa. Calcluate the PI of glutamate in which pka1= 2.2; pka2=9.7, Pka side chain= 4.3 PI (PH)= (2.2+4.3)/2= 3.25 At this PI the net charge of glutamate is -1 11 AA Pka1 Pka2 Pka3 PI Gly 2.35 9.78 - 6.07 Asp 2.10 9.82 3.86 2.98 Lys 2.18 8.95 10.53 9.74 Cys 1.86 10.25 8 4.93 Tyr 2.2 9.11 10.07 5.66 12 13 14  Proteins are a very high molecular weight macromolecules which are formed from greater than 50 amino acids united together in different proportions that linked together by a peptide linkage  Some proteins are formed of 2 or more polypeptide chains. 15  Protein Function Protein Function Enzymes Catalytic function Lipoproteins Transport function Lysozyme as transporter of Ribonuclease lipids A Hemoglobin Transport function Glycoproteins Structural function as Carrier of oxygen in cell membrane Keratin Defense against Prothrombin Blood clotting mechanical and Fibrin chemical injury Insulin Hormonal regulation Ferritin Storage form of iron Collagen Structural function Antibodies Defense function in skin and bone 16 17 18  Definition: It is the number, types and arrangement of amino acids in the polypeptide chain  Types of bonds: Peptide bonds (amide bond)  Peptide bonds are resistant to conditions that denature proteins as heating  Forms: N.B it determined by the genetic information present in DNA  Examples: Lysozyme, insulin hormone 19  Lysozyme, is an enzyme that attacks bacteria, consists of a polypeptide chain of 129 amino acids. 20 21 Contain 3 disulfide bonds: one intra-chain , and 2 inter-chain disulfide bonds 22 Secondary structures of proteins are formed because of hydrogen bonding between hydrogen of NH- groups and oxygen of C=O- groups in the peptide backbone Types of 2ry structure: 1. α-helix 2. β-pleated sheet 3. β-Turn or loop Certain amino acids have a propensity to form an α- helix, while others have a propensity to form a β- pleated sheet. 23  Its shape is Coiled or spiral rod like  Each turn contains 3.6 amino acids  The α-helix is stabilized by intra chain hydrogen bonds formed between –N–H groups and –C=O groups that are four residues back, i.e., –N–H group of a 6th peptide bond is hydrogen bonded to –C=O group of 2nd peptide bond  The R-group of amino acids project outwards of the helix.  It has 2 types according to the direction of the rod which :  Clockwise, or anti-clockwise  It could be disrupted by helix breakers  Example: Keratin 24 25 AAs disrupt α- helix (helix breakers) 26  It is fibrous protein that is the major component of hair and skin Has defense against mechanical and chemical injury 27  It is 3 alpha helix chains woven together  It found in fibrous proteins as: 1. collagen: it present in connective tissue of tendon, bone, teeth, skin and cartilage. 2. Troponin: in heart muscle 3. Fibrillinin: in heart valve, blood vessels and ligament 4. Fibrin: component in blood clot 5. Fibronectin: component of extracellular matrix 28  It has Zigzag sheet like (fully extended)  It contains 2 or more of polypeptide chains  The hydrogen bonds are inter-chain hydrogen bonds which make the pleated sheet more stable than the helix.  It has the R groups above and below the sheet.  It not susceptible for disruption as helix  It has 2 types: 1. Parallel: 2 chains in same direction Ex: Myosin 2. Anti parallel: 2 chains in opposite direction Ex: silk fibroin 29 30  Myosin is one of motor proteins  Myosin plays a structural role in muscle contraction.  Myosin is a superfamily of proteins which bind actin, hydrolyze ATP and transduce force. Thus most are located in muscle cells. 31  α-helix β-pleated sheet Shape Coiled or spiral rod like Zigzag sheet like (fully extended) Number of 3.6/turn Not fixed amino acids Number of one 2 or more polypeptide chains Types Clockwise Parallel Anti-clockwise Anti parallel Disruption yes No Examples keratin Silk fibroin (the principal protein of silk worm fibers) 32  Turns or bends are short segments of amino acids that join two units of secondary structures, such as two adjacent strands of an anti-parallel β-sheet.  It generally composed of 4 amino acids, one of which is proline (cause a kink of polypeptide chain) and glycine (with its small R flexible group)  Generally, alpha helix and beta pleated sheet are located at the core of the protein, while the loops located in the outer region  Example of loop: Ribonuclease A 33 loop loop 34 35 Dr. Siham Gritly 36 37