Proteins and Enzymes: Structure, Function, and Activity

Proteins Enzymes Amino acids and polypeptides Amino acids have a central carbon atom with four different atoms or groups linked to it: hydrogen atom amine group (-NH2 ) carboxyl group (-COOH) R group or radical (R). Amino acids (each...

Proteins Enzymes Amino acids and polypeptides Amino acids have a central carbon atom with four different atoms or groups linked to it: hydrogen atom amine group (-NH2 ) carboxyl group (-COOH) R group or radical (R). Amino acids (each of the twenty amino acids in proteins has a different R group) AMINO ACID DIVERSITY The R-group of amino acids is variable. Amino acids with hundreds of different R-groups could be produced in the laboratory. Most living organisms include only twenty of them in the polypeptides synthesized by their ribosomes. The use of the same repertoire of amino acids is one of the pieces of evidence supporting the theory that all living organisms share common ancestry. There are two extra amino acids that are considered extra variations rather than a falsification of the theory that there are twenty basic amino acids in all organisms. PEPTIDE BONDS AND POLYPEPTIDES Amino acids are linked together by condensation reactions Condensation reactions The new bond formed between the amine group of one amino acid and the carboxyl group othe next is a peptide bond. POLYPEPTIDES AND PROTEINS A molecule consisting of two amino acids Chains of fewer than 40 amino acids are linked together is a dipeptide. usually called peptides rather than Polypeptides consist of many amino polypeptides or proteins. acids linked by peptide bonds. Is an The amino acid sequence of a polypeptide unbranched chain of amino acids. is coded or by a gene. The number of amino acids is very The sequence of bases in the DNA of the variable and can be over 10,000, though gene determines the sequence of amino most have between 50 and 2,000 amino acids in the polypeptide. acids. A protein consists either of a single Over two million polypeptides have so far polypeptide or more than one polypeptide been discovered in living organisms. linked together. PROTEINS AND PROTEOMES A proteome is all of the proteins produced by a cell, a tissue or an organism. The genome is all of its genes. Whereas the genome of an organism is fixed, the proteome is variable because different cells in an organism make different proteins. Even in a single cell the proteins that are made vary over time depending on the cell's activities. Protein structure and function The conformation of a protein is its three-dimensional structure. The polypeptides of most proteins are folded up to produce a globular shape. The sequence of amino acids in a polypeptide determines how this folding is done and so determines the conformation of a protein. Each time a polypeptide with a particular sequence of amino acids is synthesized on a ribosome, the conformation will tend to be precisely the same. The structure is stabilized by intramolecular bonds between the amino acids in the polypeptides that are brought together by the folding process DENATURATION The conformation of most proteins is delicate and it can be damaged by various substances and conditions. This is called denaturation. Heat causes vibrations within protein molecules that break intramolecular bonds and cause the conformation to change. Heat denaturation is almost always irreversible. DENATURATION Every protein has an ideal or optimum pH at which its conformation is normal. If the pH is increased by adding alkali or decreased by adding acid, the conformation of the protein may initially stay the same but denaturation will eventually occur when the pH has deviated too far from the optimum. This is because the pH change causes intramolecular bonds to break within the protein molecule. FUNCTIONS OF PROTEINS Rubisco is the enzyme that catalyses the Rhodopsin is the pigment that makes the rod photosynthesis reaction. cells of the retina light- sensitive. Insulin is the hormone that is carried Collagen is a structural protein. Is used in skin dissolved in the blood and causing the to prevent tearing, in bones to prevent fractures cells to absorb glucose and lower the and in tendons and ligaments to give tensile blood glucose concentration. strength. Immunoglobulins are antibodies that bind to antigens on pathogens. The Spider silk is a structural protein that is used to immune system can produce a huge make webs or catching prey and lifelines on range of immunoglobulins. which spiders suspend themselves. Enzymes SUBSTRATES AND ACTIVE SITES Catalysts speed up chemical reactions without being changed themselves. Living organisms make biological catalysts called enzymes to speed up and control the rate of the reactions of metabolism. Enzymes are globular proteins. A reactant in an enzyme-catalysed reaction is known as a substrate. Enzymes catalyse reactions using a special region called the active site.  Collisions can result in binding as the shape and chemical properties of the active site complement those of substrates. They are chemically attracted to each other and fit together. Molecules other than the substrate do not fit or are not attracted so do not bind, making enzymes substrate-specific. The binding of substrates to the active site reduces the energy needed for them to be converted into products. The products detach from the active site, https://www.youtube.com/watch?v=qgVFkRn8f10 leaving it free for more substrate to bind. IMMOBILIZED ENZYMES Enzymes are widely used in industry for 1. Catalysis can be controlled by adding or catalysing specific reactions.The enzymes are removing enzymes promptly from the reaction usually immobilized, by attachment of enzymes mixture. to another material or into aggregations to 2. Enzyme concentrations can be higher. restrict their movement. 3. Enzymes can be reused, saving money. Enzyme immobilization has benefits: 4. Enzymes are resistant to denaturation over greater ranges of pH and temperature. 5. Products are not contaminated with enzymes There are many methods of enzyme immobilization: 1. attachment to surfaces such as glass (adsorption) 2. entrapment in a membrane or a gel (e.g. alginate) 3. aggregation by bonding enzymes together into particles of up to 0.1 mm diameter. PRODUCTION OF LACTOSE-FREE MILK Lactose is the sugar in milk. It can be This process can be performed in the laboratory hydrolysed into glucose and galactose by the by making alginate beads containing lactase enzyme lactase. and putting them into milk. The lactose concentration othe milk drops and the glucose concentration rises Lactose-free milk is produced either by adding free lactase to the milk or by using lactase that has been immobilized on a surface or in beads of a porous material. The enzyme is obtained from microorganisms such as Kluveromyces lactis, a yeast that grows in milk. Lactose-free milk has advantages 1. Many people are lactose intolerant and cannot drink more than about 250 ml of milk per day unless it is lactose-reduced. 2. Galactose and glucose are sweeter than lactose, so less sugar needs to be added to sweet foods containing milk, such as milk shakes or fruit yoghurt. 3. Lactose tends to crystallize during production of ice cream, giving a gritty texture. Because glucose and galactose are more soluble than lactose they remain dissolved, giving a smoother texture. 4. Bacteria ferment glucose and galactose more quickly than lactose, so the production of yoghurt and cottage cheese is faster. Factors affecting enzyme activity Wherever enzymes are used, it is important that they have the conditions that they need to work effectively. Temperature, pH and substrate concentration all affect the rate at which enzymes catalyse chemical reactions. Lab practice Action of catalase on hydrogen peroxide Explore Sustrate: hydrogen peroxide Enzyme: catalase Analysis Conclusions Describe the effect of enzyme concentration on Relationship of results to initial purpose of enzyme activity. the lab Compare your hypothesis with the data Describe the effect of temperature on enzyme you recorded. activity. What could have gone wrong? , What Describe the effect of acidity on enzyme activity. were some mistake made? Discussion of validity of results. What other factors could you test or modify? ONLY HL Chemical diversity of R groups in amino acids Diversity on functions and form of a.a. Primary structure of proteins A molecule of protein contains one or more polypeptides. A polypeptide is an unbranched chain of amino acids, linked by peptide bonds. Primary structure is the number and the linear sequence of amino acids in a polypeptide. Examples: beta-endorphin (31 a.a.) Insulin (51 a.a.) a.a. rotation Secondary structure of proteins Polypeptides have a main chain consisting of a repeating sequence of covalently bonded carbon and nitrogen atoms. Hydrogen bonds can form between the N - H and C = O groups in a polypeptide if they are brought close together. The structure that develops is called a beta- pleated sheet. The structure that develops is called an alpha helix. Silk, collagen, keratin Tertiary structure of proteins Tertiary structure is the three-dimensional conformation of a polypeptide. (Globular proteins) The conformation is stabilized by intramolecular bonds and interactions that form between amino acids in the polypeptide, especially between their R groups. Polar amino acids are on the surface where they bond to each other and come into contact with water. Hydrogen bonds, disulfide bonds, ionic bonds, hydrophobic bonds Example: Lysosyme, plasma proteins Effect of polar and non- polar amino acids on tertiary structures non-polar and therefore hydrophobic polar or charged and therefore hydrophilic. These proteins have hydrophilic amino acids on their surface where they are in contact with water and hydrophobic amino acids clustered in the centre where water is excluded. Quaternary structure of proteins Quaternary structure is the linking of two or more polypeptides to form a single protein. Haemoglobin Enzymes and activation energy ENERGY CHANGES IN CHEMICAL REACTIONS During chemical reactions, reactants are converted into products. Before a molecule of the reactant can take part in the reaction, it has to gain some energy. This is called the activation energy of the reaction. The energy is needed to break bonds within the reactant. Most biological reactions are exothermic - the energy released is greater than the activation energy. Enzymes reduce the activation energy of the reactions that they catalyse and therefore make The graph (right) shows energy changes it easier or these reactions to occur. during uncatalysed and catalysed exothermic reactions. Enzyme inhibition Competitive inhibition The substrate and inhibitor are chemically very similar. The inhibitor binds to the active site of the enzyme. While the inhibitor occupies the active site, it prevents the substrate from binding and so the activity of the enzyme is prevented until the inhibitor dissociates. The activity of an enzyme is reduced if a fixed low concentration of a competitive inhibitor is added, but as the substrate concentration rises, the effect of the inhibitor becomes less and less until eventually it is negligible. Non-competitive inhibition The substrate and Inhibitor are not similar. The inhibitor binds to the enzyme at a different site from the active site. The inhibitor changes the conformation of the enzyme. The substrate may still be able to bind, but the active site does not catalyse the reaction, or catalyses it at a slower rate. The activity of the enzyme is reduced at all substrate concentrations if a fixed low concentration o non-competitive inhibitor is added and the percentage reduction is the same at all substrate concentrations.