Amino Acids and Protein Structure 2024 PDF

Amino Acids and Protein Structure Caner GEYİK [email protected] 2024  HSF101 - Biochemistry/ 2023 2 Learning Objectives List the functions of proteins Describe the structure of amino ac...

Amino Acids and Protein Structure Caner GEYİK [email protected] 2024  HSF101 - Biochemistry/ 2023 2 Learning Objectives List the functions of proteins Describe the structure of amino acids Calculate isoelectric point Describe the bonds forming proteins Recognise the primary, secondary, tertiary, and quarternery structures in proteins Explain protein denaturation  HSF101 - Biochemistry/ 2023 3 Proteins Biomacromolecules that consists of amino acids and responsible for various important duties! (Image: © Jason McLellan/Univ. of Texas at Austin) HSF101 - Biochemistry/ 2023 4  HSF101 - Biochemistry/ 2023 5 Protein Functions Catalysis (Enzymes) They increase the reaction rate of metabolic chemical reactions by decreasing the needed activation energy  HSF101 - Biochemistry/ 2023 6 Protein Functions Transport Transport in circulatory system (Hemoglobin, lipoproteins …) Transport from extracellular media to cytoplasm or vice versa (Ions, water, monosaccharides…)  HSF101 - Biochemistry/ 2023 7 Protein Functions Signalling Hormones direct and regulate metabolism in the body Receptors receive the signals and play role in cellular response  HSF101 - Biochemistry/ 2023 8 Protein Functions Structural Elements Cytoskeleton Muscle Hair, Nail  HSF101 - Biochemistry/ 2023 9 Protein Structure HSF101 - Biochemistry/ 2023 10  HSF101 - Biochemistry/ 2023 11 Amino Acids  HSF101 - Biochemistry/ 2023 12 Amino Acids NH2 COOH C Amino acids have a common structure Central Carbon Atom (α-Carbon) Carboxylic acid group Amino group Radical group (side chain)  HSF101 - Biochemistry/ 2023 13 Amino Acids NH2 COOH C  HSF101 - Biochemistry/ 2023 14 Amino Acids More than 300 amino acid can be found in nature. But only 20* found as constituents of proteins (proteinogenic amino acids) *20 is directly coded by DNA. But with special translation mechanisms another 2 amino acids can also be used for protein synthesis in different organisms In eukaryotes: (Selenocysteine, 21st amino acid)  HSF101 - Biochemistry/ 2023 15 Amino Acids Amino acids in protein structure are always in L- conformation  HSF101 - Biochemistry/ 2023 16 Amino Acids  HSF101 - Biochemistry/ 2023 17 Amino Acids  HSF101 - Biochemistry/ 2023 18 Amino Acids  HSF101 - Biochemistry/ 2023 19 Amino Acids Every amino acid have a «three letter» and «one letter» abbreviation Example 1 Q6V mutation: The 6th amino acid is glutamine in normal, but it changed with valine in mutant Example 2 Phosphorylated from Tyr368 : Phosphate groups is added to tyrosine in 368th position  HSF101 - Biochemistry/ 2023 20 Essential Amino Acids These amino acids cannot be synthesized in mammals, thus we need to obtain them from diet. Otherwise, all amino acids are essential ☺  HSF101 - Biochemistry/ 2023 21 Amino Acids and pH Amphoteric molecules Weak alkaline α-amino group and weak acidic α-carboxyl group Asidic amino acids have an additional carboxyl group Basic amino acids have an additional amino group NH2 COOH NH3+ COO-  HSF101 - Biochemistry/ 2023 22 Asidic environment = Low pH = Many H+ in medium  HSF101 - Biochemistry/ 2023 23 Alkaline environment = High pH = Less H+ in medium  HSF101 - Biochemistry/ 2023 24 Amino Acids and pH Asidic environment = Low pH = Many H+ in medium Alkaline environment = High pH = Less H+ in medium Point that net charge is 0 = Isoelectric point  HSF101 - Biochemistry/ 2023 25 Protein Structure HSF101 - Biochemistry/ 2023 26  HSF101 - Biochemistry/ 2023 27 Primary Structure Polypeptide chain: dipeptide, tripeptide,... Oligopeptide, protein  HSF101 - Biochemistry/ 2023 28 Peptide Bond One molecule of water is released during peptide bond formation in polypeptide synthesis (dehydration, condensation)  HSF101 - Biochemistry/ 2023 29 Secondary Structure Local hydrogen bonds between amino acids α-helix β-sheet (β-pleated sheet) β-turns Random coils, loops  HSF101 - Biochemistry/ 2023 30 Tertiary Structure Compact structures formed by interaction of R groups Distant amino acids may come near Function gain Hydrophobic amino acids are inside in aqueous media Hydrophobic amino acids are on the surface in membrane  HSF101 - Biochemistry/ 2023 31 Tertiary Structure Peptide bonds Disulfide bonds Hydrogen bonds Ionic bonds Hydrophobic interactions van der Waals interactions  HSF101 - Biochemistry/ 2023 32 Disulfide Bonds Between two cysteine Hydrogens leave when -SH and –SH groups meet S-S bond is formed  HSF101 - Biochemistry/ 2023 33 Quaternary Structure Many proteins may consist of two or more polypeptide chains. These chains are called subunit, protomer or monomer Subunit number: Dimer, pentamer,..... Subunit types: Homo- , Hetero-, HSF101 - Biochemistry/ 2023 34  HSF101 - Biochemistry/ 2023 35 Summary Amino acid sequence, primary structure Hydrogen bonds between -NH and -CO in backbone, secondary structure R group interaction, tertiary structure More than 2 tertiary structures, quaternary structure  HSF101 - Biochemistry/ 2023 36 Denaturation Primary structure does not change! (Peptide bonds are preserved) Loss of biological activity  HSF101 - Biochemistry/ 2023 37 Denaturation Temperature pH Organic solvents Chaotropic agents (Urea, guanidin HCl) Heavy metals UV Ionic detergents (SDS)  HSF101 - Biochemistry/ 2023 38 Renaturation Gaining natural form after denaturation