Proteins and Enzymes PDF

DNA & Proteins Proteins and Enzymes  SACE Key Ideas – by the end of this chapter you should know… Science Understandings The folding of a polypeptide to form a protein with a unique three-dimensional shape is determined by its sequence of amino acids. Describe the factors that determin...

DNA & Proteins Proteins and Enzymes  SACE Key Ideas – by the end of this chapter you should know… Science Understandings The folding of a polypeptide to form a protein with a unique three-dimensional shape is determined by its sequence of amino acids. Describe the factors that determine the primary, secondary, tertiary, and quaternary structure of proteins. Proteins are essential to cell structure and function. Examples of proteins with specific shapes include enzymes, some hormones, receptor proteins, and antibodies. Explain why the three-dimensional shape of a protein is critical to its function. Enzymes are specific for their substrate and increase reaction rates by lowering activation energy. Describe the induced-fit model of enzyme–substrate binding. Enzymes have specific functions and are affected by factors including: – temperature – pH – presence of inhibitors. The rate of an enzyme-controlled reaction is affected by: – concentrations of reactants – concentration of the enzyme. Three-dimensional structure of proteins Each protein has a unique sequence of amino acids that results in a unique shape for the protein. This shape is complementary to the shape of the molecule to which the protein will bind. Primary structure Is the sequence of amino acids in the polypeptide chain. This is determined by the sequence of bases on the mRNA, which is in turn determined by the sequence of bases on the DNA that was transcribed – the gene! Changing just one amino acid may result in a significant change in the shape of the protein. Secondary structure The coiling ( helix) or folding ( pleated sheet) of the polypeptide chain  helix Due to hydrogen bonding between amino acids. The primary structure determines where the hydrogen bonds will occur, and therefore if coils or sheets are produced. Tertiary structure Cooking an egg The 3-D shape of the Egg-white contains the proteins ovalbuminovotransferrin and ovamucoid. polypeptide chain. When the egg is cooked the proteins denature This is often held in place by turning the egg white from an clear aqueous heat-sensitive disulfide bonds. solution into a white gel. Raising the temperature above Ovalbuminovotransferrin denatures at 61oC, approx. 45oC may cause the ovamucoid at 70oC. shape of the protein to change/denature. Quaternary structure Some proteins consist of two or more polypeptide chains. The bonding of the polypeptide chains is called the quaternary structure. Human haemoglobin in red blood cells is formed by the interaction of two alpha chains and two beta chains Protein Function: Many diseases are the result of cells producing proteins which have an abnormal 3D shape Each protein has a unique amino acid sequence which doesn’t allow them to bind to their correct substrate molecule. As a result, the protein has a unique 3-dimensional structure. Eg Cystic Fibrosis, Haemophilia, Sickle Cell Anaemia A protein’s structure determines its function. Most proteins carry out their functions by recognising and binding to other molecules The sequence of amino acids therefore indirectly determines the function of a protein – ultimately, the sequence of bases on the DNA molecule determines the function of the protein. (Protein Synthesis!) Protein Function: Function Example Structural Cytoskeleton, hair, nails, and ligaments Catalyse reactions Enzymes Contraction Fibres in muscle cells (eg actin) Transport Transport proteins in cell membranes, carrying oxygen (haemoglobin) Defence Antibodies produced by white blood cells (immunoglobulins) Coordination Hormones (eg insulin, thyroxine) and receptor proteins Storage Albumin in eggs, ferritin (stores iron in your cells) Which statement about proteins is correct? J. The primary structure of a protein is composed of many branched chains. K. Subunits of proteins are fatty acids. L. The tertiary structure of proteins is temperature independent. M. The quaternary structure of proteins is the result of the interactions of two or more independent polypeptide chains. Changing one amino acid in a particular protein would not change the: J primary structure of the protein K tertiary structure of the protein L activity of the protein M the number of amino acids in the protein Induced-fit model of enzyme-substrate binding. A cell is a microscopic chemical factory in which many (>1000) reactions occur, each catalysed by a different enzyme. The reacting molecules in a enzyme-controlled reaction are called substrates.  Enzymes are not used up in Enzymes are protein molecules reactions, but are released The groove on the surface of the enzyme unaltered to catalyse more to which the substrate binds is called the reactions. active site. The active site is complementary to the An enzyme may catalyse 106 shape of its substrate. “Lock and Key” reactions per second. Different enzyme, different amino acid sequence, different shape of active site. Active site Enzymes are biological catalysts They increase the rate at which the reactions occur. Substrate The reaction occurs on the bound to surface of the enzyme. enzyme Induced fit model The binding of the substrate to the active site often causes changes to the shape of both the enzyme and the substrate (induced fit). The chemical bonds in the substrate are stressed and break more easily, thus increasing reaction rate. Enzymes participating in a chemical reaction usually J are not specific for their substrate. K breakdown during the reaction. L are not consumed in the reaction. M react more readily as the reaction progresses. Summary - Enzyme Facts ALL ENZYMES ARE GLOBULAR PROTEINS ENZYMES ARE SPECIFIC FOR A PARTICULAR REACTION - every step in a metabolic pathway (chain of reactions) ENZYME NAMES END IN –ASE (most! Eg pepsin, trypsin, rennin) Intracellular enzymes (majority) catalyse chemical reactions inside a cell. Extracellular enzymes catalyse reactions outside the cell. e.g the enzymes of the digestive system (sucrase, amylase, lipase etc) pH, temperature and chemical inhibitors can alter the binding of enzymes and substrates at the active site. Every enzyme has an optimum pH. Changing the pH away from the optimum can alter the shape of the enzyme’s active site, lowering its activity. Eg Salivary amylase pH 7 (neutral), pepsin in stomach pH 2 (acidic) Effect of temperature In general, increasing temperature increases reaction rate (particles move faster – more collisions). Explain this bit However, proteins denature above ~45o C, losing the specific shape …and this of their active site and are therefore unable to catalyse the reaction. Another graph for you to explain Inhibitors reduce the activity of enzymes Competitive inhibitors have a similar shape to the substrate. compete with the substrate for the active site. Non-Competitive inhibitors Bind to the enzyme at a site away from the active site. Cause the active site to change shape, preventing the enzyme working. Examples DDT (Pesticide) – inhibits enzymes in the nervous system, prevents messages from being transmitted causing paralysis Penicillin - inhibits enzymes that make cell walls in bacteria Glyphosate - It prevents the plants from making certain proteins that are needed for plant growth. Glyphosate stops a specific enzyme pathway. Cyanide – inhibits cytochrome oxidase, and enzyme in the mitochondria, preventing energy from being produced Methotrexate – used in chemotherapy, immune system suppressant Enzymes: J. are always most active at high pH. K. are present in all living cells. L. always increase in activity with increasing temperature. M. do not bind with inhibitors. Reactions require an initial input of energy to proceed. Chemical reactions involve the breaking and reforming of bonds that hold the atoms together in molecules. To start a chemical reaction reactant molecules must absorb energy for their bonds to break. The initial energy required to start a reaction is called the energy of activation. Enzymes lower the activation energy The induced-fit places stress on the bonds in the substrate molecule. This stress lowers the energy input needed to break the bonds and start the reaction. Enzymes bring the reactants together in the correct orientation Enzymes may make the reaction Small steps help to manage occur in many small steps, each the heat energy released at step only requires a small each stage of the reaction. amount of activation energy Refer to the following graph, which shows the change in energy during a biological reaction (2005 Q26) The graph shows the change in energy during a biological reaction that has not been catalysed by an enzyme. (a) Draw a line on the graph above to show the change in energy that would occur if an enzyme were present. (2 marks) Cell Membrane Receptors. Protein receptor molecules are either embedded in the lipid bilayer of the cell membrane (protein hormones bind to Cell membrane receptors (proteins or these) or within the cell (steroid hormones) glycoproteins) allow cells to recognise. and select molecules necessary for cell They have distinctive shapes. activities. The region of the receptor molecule that has as shape that is complementary to that of a specific hormone is called the binding site. Hormone-receptor complex triggers an effect. Glycoproteins allow cells to recognise each other – this helps cells form tissues Hormones bind to cell membrane receptors because they have complementary shapes Human Hormones: A cell may have 50 or more different cell membrane receptors, each specific for only one EPO – increases hormone production of red blood cells The binding causes specific changes to occur inside Insulin – initiates uptake the cell of glucose by cells Growth hormones – For example, when insulin binds to its cell increases muscle mass membrane receptor on a liver cell, it causes the cell to store glucose as glycogen Transport proteins span the entire width of the cell membrane. have a specific shape that is complementary to the substance that they transport across the membrane. For example, certain proteins assist in the transport of glucose molecules across the cell membrane. Glucagon is a hormone produced by the pancreas. It causes liver cells to convert glycogen into glucose. Glucagon does not affect brain cells. (2002 Q3) It is reasonable to conclude that glucagon J. can be transmitted to liver cells but not to brain cells. K. is a store of energy in human beings. L. is formed in response to high levels of blood glucose. M. receptors are found on liver cells but not on brain cells. Antibodies Antibodies are proteins (Immunoglobulins) All antibodies have the same basic structure with 2 regions called ANTIGEN BINDING SITES that have a specific shape. The antigen binding site has a shape that is complementary to surface molecules of specific antigens (virus/bacteria) Antibodies will therefore bind to specific antigens. Self and Non-self concept ALL CELLS CONTAIN SURFACE ANTIGENS. The immune system is able to distinguish between its own antigens and those that are foreign. This is established before birth, immune cells corresponding to your own antigens are destroyed The most important surface antigens are the blood group (ABO) antigens found on red blood cells and marker proteins on the membranes of other cells. Enzyme Animation  Websites Utah Genetics – Types of Proteins Types of Proteins (utah.edu) Khan Academy Introduction to proteins and amino acids (article) | Khan Academy CK12 Biology Proteins | CK-12 Foundation Lumen Learning Proteins | Boundless Anatomy and Physiology (lumenlearning.com) Videos Bozeman – Proteins 9:15 https://www.youtube.com/watch?v=2Jgb_DpaQhM Anytime Education – What are proteins? 8:59 https://www.youtube.com/watch?v=TiVgRVEeV4o Amoeba Sisters – Enzymes 5:46 https://www.youtube.com/watch?v=qgVFkRn8f10