M 3.2 Protein PDF

M 3.2 (ii) Biological molecules - protein  Learning Outcomes: Describe amino acid structure and the nature of the peptide bond. Explain polypeptide primary, secondary and tertiary structure. Understand the role of structural and functional domains in protein tertiary structu...

M 3.2 (ii) Biological molecules - protein  Learning Outcomes: Describe amino acid structure and the nature of the peptide bond. Explain polypeptide primary, secondary and tertiary structure. Understand the role of structural and functional domains in protein tertiary structure. Explain the role of specialised proteins termed ‘enzymes’ in the body. PROTEINS..... Loading…  Proteins 100,000 different protein types in the human body Most versatile cell components Most enzymes are proteins Polymers Proteins largely determine what a cell looks like and how it functions Loading…  AMINO ACID- BUILDING BLOCK OF PROTEINS All Amino acids have a fundamentally similar structure, central (or a) Carbon and Hydrogen, an amino functional group, a carboxylic acid / or carboxylate functional group a distinctive side chain or R group R GROUPS  20 different amino acids POLAR Alpha carbo n R group Asparagin Glutamine Tyrosine Serine Threonin e Gin Tyr Ser e Asn Thr  20 different amino acids NONPOLAR Glycine Alanine Valine Leucine Isoleucine Gly Ala Val Leu lle Phenylalanine Tryptophan Proline Cysteine Methionine Phe Trp Pro Cys Met  20 different amino acids ELECTRICALLY CHARGED Aspartic acid Glutamic acid Arginine Lysine Histidine Asp Glu Arg Lys His  Levels of Protein Organisation/Structure Four levels of organisation: 1. Primary structure - amino acid sequence 2. Secondary structure - results from hydrogen bonding between amino acids Loading… 3. Tertiary structure - depends on interactions among side chains 4. Quaternary structure - results from interactions among polypeptides REVISION PEPTIDE BOND The amino group from one amino acid (with side group R) can react with the carboxylic acid from a 2nd amino acid (with side group R’) to form a dipeptide. The bond between the two amino acids is called the peptide bond Free N-terminal and C- terminal of dipeptide available to react with further amino acids to make larger polypeptides and eventually proteins Peptide bond is quite rigid but adjacent R groups etc can rotate Glucagon  Secondary Structure – a Helix and b Pleated Sheet a Helix b Sheet THE ALPHA HELIX Each hydrogen bond forms between an oxygen with a partial The a -helix negative charge and a hydrogen with a partial positive charge The oxygen is part of the remnant of the carboxyl group of one amino acid; the hydrogen is part of the remnant of the amino group of the fourth amino acid down the chain Thus, 3.6 amino acids are included in each complete turn of the helix Basic structural unit of some fibrous proteins that make up wool, hair, skin and nails. Elasticity due to helical shape and hydrogen bonding THE BETA PLEATED SHEET The hydrogen bonding takes place between different polypeptide chains or different regions of a polypeptide chain that has turned back on itself Each chain is fully extended as each has a zigzag structure The resulting “sheet” has an overall pleated conformation Strong and flexible but not elastic as the distance between the pleats is fixed. Fibroin, the protein of silk Tertiary Structure – Bonding between 2o Structure Quaternary Structure – More than 1 Polypeptide / Subunit WHY DO PROTEINS HAVE DIFFERENT CONFORMATIONS? Conformation is dictated by the amino acid sequence Environment – Conditions in a cell ‘in vivo’ may be different than outside i.e. test tube or ‘ex-vivo’ Specialised proteins – ‘molecular chaperones’ MOLECULAR CHAPERONES Proteins are assisted in folding by molecular chaperones Hsp60 (chaperonins) Hsp70 and Hsp90 are three main classes Hsp70 recognizes exposed, unfolded regions of new protein chains - especially hydrophobic regions It binds to these regions, protecting them until productive folding reactions can occur https://www.youtube.com/watch?v=b39698t750c  WHAT DETERMINES THE BIOLOGICAL ROLE / ACTIVITY OF A PROTEIN? Entire protein structure determines its role Different regions of a single protein can have different functions Many proteins are modular: 2 or more globular regions – domains connected by less compact regions of polypeptide chain In turn each domain can have different functions e.g. one domain could act as an enzyme while the other docks in a membrane CHANGES IN AMINO ACID SEQUENCE DENATURATION Changes in environment / conditions affect protein function Disrupts hydrogen and ionic bonding Leads to unfolding, change in shape Loss of biological activity Hea t Chemical Exposure pH Change Enzymes  How important are enzymes? – all chemical reactions in living organisms require enzymes to work building molecules enzyme – synthesis enzymes + breaking down molecules – digestive enzymes enzyme + – enzymes speed up reactions “catalysts”  Each enzyme is the specific helper to a specific reaction – each enzyme needs to be the right shape for the job – enzymes are named for the reaction they help sucrase breaks down sucrose proteases breakdown proteins lipases breakdown lipids DNA polymerase builds DNA  Enzymes are not changed by the reaction – used only temporarily – re-used again for the same reaction with other molecules – very little enzyme needed to help in many reactions substrate product active site enzyme  Lock & Key model – shape of protein allows enzyme & substrate to fit – specific enzyme for each specific reaction Loading…  Reading Chapter 3 ‘The Chemistry of Life’ Organic Compounds Solomon 11th Ed. p59-68