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CHAPTERS 19 AND 20 CONCURRENT ENROLLMENT AMINO ACIDS Alpha-amino acids – An organic compound containing both an amino group and a carboxylate group, with the amino group attached to the carbon next to the carboxylate group – Overhead There are 20 natural proteins, they are alpha because the amino group is attached to the carbon Page 595 common amino acids 594 has general structure L-amino the amino group is on the left The amino acids found in living systems exist in the L form ZWITTERIONS A dipolar ion that carries both a positive and a negative charge as a result of an internal acidbase reaction in an amino acid molecule Amino acid structures varies with the changes of pH Pages 596-597 Isoelectric point - the pH at which the zwitterion forms Learning check 19.1 Oxidation of cysteine – The -SH on two cysteines lose the hydrogen's through oxidation to form a -S-S-(disulfide bond) and water PEPTIDE FORMATION Peptide linkage – The amide linkage between amino acids that results when the amino group of one acid reacts with the carboxylate group of another – Page 599 Dipeptide – A compound formed when two amino acids are bonded by an amide linkage – Notice that both amino acids are zwitterions page 599 Peptide – An amino acid polymer of short chain length Polypeptide – An amino acid polymer of intermediate chain length containing up to 50 amino acids Continue Protein – An amino acid polymer made up of more than 50 amino acids Amino acid residue – An amino acid that is a part of a peptide, polypeptide, or protein chain N-terminal residue – An amino acid on the end of a chain that has an unreacted or free amino group C-terminal residue – An amino acid on the end of a chain that has an unreacted or free carboxylate group – Page 600 learning check 19.2 IMPORTANT PEPTIDES Disulfide bridge – A bond produced by the oxidation of -SH groups on two cysteine residues. The bond loops or holds two peptide chains together – Insulin has three disulfide bridges Prion – A protein infectious particle capable of causing disease like mad cow disease Size of proteins – Very large 6000 to millions amu’s – Proteins are too large to pass through cell membranes and are contained inside the normal cells, when trauma or disease damage the cell membrane the proteins leak out, when protein is found in the urine, this indicates kidney damage Continue The tendency for large molecules like proteins to remain in solution or form a stable colloidal dispersion depends on the repulsive forces acting between molecules These the repulsive forces are smallest at the isoelectric point, when the net molecular charges are essentially zero Protein molecules tend to clump together and precipitate from solutions in which the pH is equal to or close to the isoelectric point PROTEIN FUNCTION Catalytic function – Nearly all reactions in living organisms are catalyzed by proteins called ENZYMES Structural functions – Plants have cellulose for structural materials – Animals structural materials (other than the skeleton) are composed of proteins. Collagen found in skin and bone. Keratin found in hair, skin and fingernails Storage functions – Proteins provide a way to store small molecules or ions – Ovalbumin is a stored form of amino acids found in embryos of bird eggs – Ferritin, liver protein, stores iron ions Continue Protective function – Antibodies - a substance that helps protect the body from invasion by foreign materials known as ANTIGENS – Antigens - a foreign substance that can stimulate the production of antibodies – Blood clotting is another protective process carried out by the proteins thrombin and fibrinogen Regulatory function – Body processes are regulated by hormones, many that are proteins – Growth hormone - regulates the growth rate of young animals Continue Nerve impulse transmission – Some proteins behave as receptors of small molecules that pass between gaps (synapses) separating nerve cells Movement function – Proteins, actin and myosin, are used in the movement of a muscle. These long-filament proteins slide along each other during muscle contraction Transport function – Small molecules and ions are transported through the body by binding with proteins – Hemoglobin carries oxygen – Ferrin carries iron in blood plasma CLASSIFICATION Fibrous protein – A protein made up of long rod-shaped or stringlike molecules that intertwine to form fibers Globular protein – A spherical-shaped protein that usually forms stable suspensions in water or dissolves in water Simple protein – A protein made up entirely of amino acid residues Conjugated protein – A protein made up of amino acid residues and other organic or inorganic components Prosthetic group – The non-amino acid parts of conjugated proteins PRIMARY STRUCTURE Linear sequence of amino acid residues in a protein chain Every protein has the same backbone of peptide bonds page 607 Overhead of insulin Small changes in the amino acid sequence can alter the function of the protein. This is what happens if you change a few amino acids in hemoglobin you cause sickle-cell anemia. The sixth amino acid glutamate is replaced with valine SECONDARY STRUCTURE The arrangement of protein chains into patterns as a result of hydrogen bonds between amide groups of amino acid residues in the chain. α -helix and β -pleated sheet α -helix – Discovered by Pauling and Corey – A single protein chain twists so the it resembles a coiled helical spring – Proteins like α-keratin in hair, myosin in muscles, fibrin in blood clots β-pleated sheet – Protein chains are aligned side-by-side in a sheet-like array held together by hydrogen bonds – Only silk is made up of just β-pleated sheets – All other proteins with β-pleated sheet have α -helixes and random structures OVERHEAD TERTIARY STRUCTURES A specific three-dimensional shape of a protein resulting from interactions between R groups of the amino acid residues in the protein Disulfide bridges – Disulfide linkage between two cysteine residues found in different parts of the chain Salt bridges – Interactions that result in ionic bonds that can form from ionized forms of an acidic amino acid(-COO-) and a basic amino acid(-NH3+) Hydrogen bonds – Formed if you have a -OH, -NH2, or CONH2 – Two serine residues can form a hydrogen bond Hydrophobic interactions – When nonpolar groups are attracted or forced together by their mutual repulsion of water – This will form a globular protein because the polar groups will point outward and the nonpolar groups will point inward QUATERNARY STRUCTURE Overhead on globular protein The arrangement of subunits that form a larger protein – Subunit- a polypeptide chain having primary, secondary, and tertiary structural features that are a part of a larger protein Overheads showing the subunits of hemoglobin and hemoglobin Protein + water ----> smaller peptides ----> amino acids H+ or OHH+ or OHNative state – The natural three-dimensional conformation of a functional protein Denaturation – The process by which a protein loses its characteristic native structure and function Continue The change of egg whites from clear to white when heated This is why you pressure cook food it denatures the protein Clostridium botulinum that causes botulism Table 19.7 page 616 ENZYMES A biomolecule that catalyzes chemical reactions Catalytic efficiency – Increase rate of reaction without being used in reaction – Enzymes speed up the reaction by lowering the activation energy – Figure 20.2 page 624 Absolute specificity – The characteristic of an enzyme that is acts on one and only one substance Relative specificity – The characteristic of an enzyme that it acts on several structurally related substances Stereochemical specificity – The characteristic of an enzyme that it is able to distinguish between stereoisomers Regulation – The cell controls the rates of the reaction and the amount of product by regulating the enzymes ENZYME NOMENCLATURE Substrate – The substance that undergoes a chemical change catalyzed by an enzyme The name of the enzyme is the common name of the substrate and adding -ase Hydrolysis reactions the enzyme would be hydrolases Overhead Learning check page 627 Cofactor – A nonprotein molecule or ion required by an enzyme for catalytic activity Coenzyme – An organic molecule required by an enzyme for catalytic activity Continue Apoenzyme – A catalytically inactive protein formed by removal of the cofactor from an active enzyme Apoenzyme + cofactor --> active enzyme (coenzyme or inorganic ion) Typical inorganic ions are Mg2+, Zn2+, and Fe2+ (metals) Many coenzymes are formed from vitamins found in the body NAD+ is a coenzyme necessary part for some redox reactions, it is formed from the vitamin nicotinamide Table 20.2 page 628 Active site – The location on an enzyme where a substrate is bound and catalysis occurs Enzyme + substrate -> enzyme-substrate -> enzyme + product complex Continue Overhead Lock and key theory – A theory of enzyme specificity proposing that a substrate has a shape fitting tht of the enzyme’s active site, as a key fits a lock Overhead Induced-fit theory – A theory of enzyme actionproposing that the conformation of an enzyme changes to accommodate an incoming substrate ENZYME ACTIVITY The rate at which an enzyme catalyzes a reaction Turnover number – The number of molecules of substrate acted on by one molecule of enzymes per minute Factors affecting enzyme activity – Enzyme concentration -increase of enzyme will increase the ES which increases the rate – Substrate concentration - increase of substrate at first increases rate until it reaches saturation point – Temperature - enzymes are proteins, so there is a temperature limiting called the optimum temperature usually 25 °C to 40 °C – Effect of pH - more active in a narrow range of pH, becomes less active as the pH deviates from the optimum (usually around 7) – Overhead ENZYME INHIBITION A substance that decreases the activity of an enzyme Irreversible inhibitor - forms covalent bond with a specific functional group of the enzyme and renders the enzyme inactive – Cyanide ion interferes with the operation of an ironcontaining enzyme called cytochrome oxidase – Antibiotics - a substance produced by one microorganism that kills or inhibits the growth of other microorganisms - usually contains sulfur Reversible inhibitor - inhibitor can be removed from the enzyme by shifting the equilibrium Continue Competitive inhibitors can be reversed by increasing the substrate and letting LeChâtelier’s principle work Noncompetitive inhibitor – Binds to the enzyme at a location other than the active site Zymogen or proenzyme – Inactive precursor of an enzyme, when the enzyme is needed the zymogen is released from storage and activated Read 639-643 take notes will be on test