Amino acids, Peptides and Proteins - Chapter 1 - 2024-2025 PDF

AMINO ACIDS PEPTIDES AND PROTEINS Pr. Fatima Azzahra LAHLOU Chapter 1 Module: Biochemistry Academic Year : 2024-2025 www.um6ss....

AMINO ACIDS PEPTIDES AND PROTEINS Pr. Fatima Azzahra LAHLOU Chapter 1 Module: Biochemistry Academic Year : 2024-2025 www.um6ss.ma Learning Objectives  Describe the general structure of an amino acid  List the 22 proteinogenic amino acids and classify them based on their side chains characteristics  Identify D and L forms  Know their biological functions  Know chemical reactions where amino acids are involved in  Define how a peptide bond forms  Differentiate between an amino acid, a peptide and a protein  Differentiate between the four levels of a protein structure FACULTY OF MEDICINE – UM6SS – CASABLANCA  Introduction to biochemistry Biochemistry :  Science that integrates life with chemistry  Study of structure, properties and functions of biomolecules  Study of chemical processes in living organisms  Applications : medical, pharmaceutical, cosmetic, food industry, agriculture, environmental… 3  Introduction to biochemistry Biochemistry Structural Metabolic Clinical Analytical biochemistry biochemistry biochemistry biochemistry 4  Introduction to biochemistry Inorganic biochemical molecules :  Water  Oxygen  Carbon dioxide  Calcium  Iron  Sodium  Clhorine  … 5  Introduction to biochemistry Organic biochemical molecules :  Amino acids/peptides/proteins 6  Introduction to biochemistry Organic biochemical molecules :  Carbohydrates :  Simple  complex 7  Introduction to biochemistry Organic biochemical molecules :  Lipids : 8  Introduction to biochemistry Organic biochemical molecules:  Nucleotides/Nucleic acids: 9  Amino acids General structure: Carboxyl/Carboxylic acid group α Side chain 10  Amino acids About 500 amino acids in nature:  Organic molecules  22 proteinogenic: 20 standard and 2 non standard aas 11 Proteinogenic amino acids 12  Amino acids About 500 amino acids in nature:  Organic molecules  22 proteinogenic: 20 standard and 2 non standard aas  Non proteinogenic  9 essential amino acids 13 Essential amino acids 14  Amino acids About 500 amino acids in nature:  Organic molecules  22 proteinogenic: 20 standard and 2 non standard  Non proteinogenic  9 essential amino acids  Alpha amino acid : biochemical designation : start from α-carbon and go down the R-group 15  Asymmetric carbon  = Chiral carbon/chiral center  Attached to 4 different groups * 16  Asymmetric carbon  Glycine doesn’t possess an asymetric carbon * Glycine Smallest aas 17  Asymmetric carbon  = Chiral carbon/chiral center  Attached to 4 different groups  Enantiomers = non-superimposed mirror image/stereoisomers  D and L (all amino acids except for glycine) 18  Amino acids : L or D Natural amino acids are in L configuration 19  Amino acids Amino acids are amphoteric At physiological pH (pH= 7.3-7.4): amino acids are in ionized form/dipolar ion/Zwitterion form 20  Amino acids Nomenclature : Aas are encoded by three letter or one letter 21  Amino acids Classification:  Proteinogenic/non proteinogenic  Standard/non standard  Essential/non essential  D/L form  Side chain structure 22  Amino acids Classification:  Side chain structure : aliphatic or cyclic The largest aas 23  Amino acids Classification:  Proteinogenic/non proteinogenic  Standard/non standard  Essential/non essential  D/L form  Side chain structure  Side chain nature 24  Amino acids Classification:  Side chain nature : hydrocarbon 25  Amino acids Classification:  Side chain nature : alcohol 26  Amino acids Classification:  Side chain nature : sulfur 27  Amino acids Classification:  Side chain nature : acid group 28  Amino acids Classification:  Side chain nature : basic group 29  Amino acids Classification:  Side chain nature : amide group 30  Amino acids Classification:  Side chain nature : aromatic 31  Amino acids Classification:  Side chain nature : aromatic aas absorb UV light 32  Amino acids Classification:  Proteinogenic/non proteinogenic  Standard/non standard  Essential/non essential  D/L form  Side chain structure  Side chain nature  Polarity : polar/non polar 33  Amino acids Classification:  Polarity : polar/non polar  Polar = hydrophilic “water loving”  Non polar = hydrophobic “water hating” 34  Amino acids Classification:  Polar/hydrophilic amino acids : ionized/ charged (+/-) 35  Amino acids Classification:  Polar/hydrophilic amino acids : non ionized/uncharged 36  Amino acids Classification:  Non polar/hydrophobic amino acids 37  Amino acids Exceptions: Proline makes exception to the common structure Glycine the smallest aa/ makes exception to the classification and no asymmetric carbon 38  Amino acids Amino acids reactions:  Decarboxylation Histidine: histamine (Allergic reaction/inflammation) Glutamic acid: GABA (neurotransmitter) 39  Amino acids Amino acids reactions:  Amidation Glutamic acid: glutamine (precursor for muscle growth/ acid-base balance in the kidney) Aspartic acid: aspragine (lack of Asp = hyperreflexia/weak muscle tone) 40  Amino acids Amino acids reactions:  Oxidative deamination Urea cycle 41  Amino acids Amino acids reactions:  Transamination 42  Amino acids Amino acids reactions:  Post-translation modifications: Tyr, Ser, Thr 43  Amino acids Amino acids reactions:  Post-translation modifications: N/O-glycosylation 44  Amino acids Amino acids biological roles:  Structural 45  Amino acids Amino acids biological roles:  Structural  Metabolic and functional 46  Amino acids Amino acids biological roles:  Structural  Metabolic and functional  Energetic Energy Energy 47 Peptide and protein 48  Peptide and protein Amino acid: 1 unit/monomer/residue Peptide: more than 2 aas  Oligopeptide: between 2 and 10 aas  Polypeptide: between 10 and 100 aas Protein: over 100 aas 49  Peptide and protein Peptide Bond 50  Peptide and protein Peptide Bond (properties):  Orientation: N-terminal end/C-terminal end  Strong (partial double bond character)  Stable and planar  Lack of rotation 51  Peptides Examples:  Glutathione (antioxidant): Cys-Glu-Gly 52  Peptides Examples:  Insulin:  Pancreas (beta cells)  Hormone  51 aas  Hypoglycemic: lowers blood glucose level 53  Proteins Protein synthesis = translation 54  Proteins Biological roles:  Structural  Transport  Defense  Enzymatic  Hormonal  Storage … 55 Proteins 56  Proteins Levels of protein structure:  Primary structure: aas sequence determined by an order and stabilized by peptidic bonds 57  Proteins Levels of protein structure:  Secondary structure: hydrogen bonds stabilization N terminus C terminus Antiparallel Beta sheets parallel Alpha Helix 58  Proteins Levels of protein structure:  Secondary structure: beta reverse bend/turn  Reverse the direction of a peptide chain  Proline and glycine [+++] Changes of direction 59  Proteins Levels of protein structure:  Tertiary structure: 3D folding of the protein/interaction between aas residues/ Function is determined by 3D structure 60  Proteins Levels of protein structure:  quaternary structure: subunits 61  Proteins Examples:  Keratin: hair, nails, skin/Fibrous Cross section of a hair/structure of intermediate filament of inter62  Proteins Examples:  Collagen: skin, muscles, bones, tendons, ligaments/Fibrous Young skin VS old skin 63  Proteins Examples:  Elastin: lungs, aorta, skin/extend and recoil 64  Proteins Examples:  Hemoglobin: Transport of O2 and CO2/globular 65  Proteins Classification:  Shape: o Fibrous (keratin/collagen) o Globular (hemoglobin)  Composition: o Simple: Albumin and globulins o Conjugated: Protein + non protein part (prosthetic group):  Glycoproteins (blood group antigens)  Lipoproteins (LDL/HDL)  Nucleoproteins (histones)  Phosphoproteins (casein)  Metalloproteins (hemoglobin/cytochrome) 66  Proteins Denaturation :  Alteration of protein structure: loss of secondary, tertiary and quaternary structure  Folded/unfolded  Breakdown of bonds  Loss of biological activity 67  Proteins Denaturation :  Temperature: above 41°C (body temparture is around 37°C/this demonstrates how a high fever can be dangerous)  pH:  Acidic: between 2-5  Basic: 10 or higher  Chemical solvants:  Exposure to ethanol  High concentration of NaCl  Reaction with reducing and oxidizing agents  Detergents  Heavy metal ions (Ag+, Pb2+, Hg2+)  Strong agitation 68  Proteins Denaturation :  Examples: 69 THANK YOU ! 70