Unit 3 Protein Structure, Enzymes & Metabolism PDF

Unit 3: Protein Structure, Enzymes & Metabolism B1.2.6-12 C1.1.11-17 Grab a whiteboard, marker and eraser!  Draw a diagram of a generalized amino acid showing the alpha carbon atom with amine group, carboxyl group, R- group and hydrogen attached.  Write the word eq...

Unit 3: Protein Structure, Enzymes & Metabolism B1.2.6-12 C1.1.11-17 Grab a whiteboard, marker and eraser!  Draw a diagram of a generalized amino acid showing the alpha carbon atom with amine group, carboxyl group, R- group and hydrogen attached.  Write the word equation for condensation reactions between amino acids to form dipeptides. Word equation: amino acid + amino acid → dipeptide + 1 water molecule Draw a generalized dipeptide:  Explain the difference between essential and non-essential amino acids. Essential amino acids are the amino acids that your body cannot produce and therefore you must obtain them from the food that you eat. Non-essential amino acids can be produced by the body from other amino acids or by the breakdown of proteins.  How many amino acids are coded for in the genetic code of life? 20 Review: The amino acid sequence determines the three-dimensional conformation of a protein. Review: The amino acid sequence determines the three-dimensional conformation of a protein. Proteins are commonly described as either being fibrous or globular in nature. Fibrous proteins have structural roles whereas globular proteins are functional (active in a cell’s metabolism). In globular proteins the hydrophobic R groups are folded into the core of the molecule, away from the surrounding water molecules, this makes them soluble. In fibrous proteins the hydrophobic R groups are exposed and therefore the molecule is insoluble. The sequence and number of amino acids in the polypeptide is the primary structure. The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding. AND The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups. The quaternary structure exists in proteins with more than one polypeptide chain. There are four levels of protein structure. Which level a protein conforms to is determined by it’s amino acid sequence. (Polypeptide) The chains of amino acids The polypeptide folds The interaction The order / sequence of the fold or turn upon and coils to form a between complex 3D shape multiple amino acids of which the themselves Caused by interactions protein is composed Held together by polypeptides between R groups (H- Formed by covalent hydrogen bonds or prosthetic bonds, disulphide between (non-adjacent) groups peptide bonds between bridges, ionic bonds A prosthetic adjacent amino acids amine (N-H) and and hydrophilic / hydrophobic group is an Controls all subsequent carboxylic (C-O) groups interactions) inorganic levels of structure H-bonds provide a level of Tertiary structure may be compound structural stability important for the involved in a Fibrous proteins function (e.g. specificity protein (e.g. the of active site in  Primary -peptide bonds Secondary -hydrogen bonds (alpha helices & beta pleated sheets) Tertiary -hydrophobic/hydrophilic interactions -Ionic bonds -Disulfide bridges -hydrogen bonds Quaternary -multiple polypeptide chains -prosthetic groups(non-protein component)=conju gated protein  Explain the form and function of insulin and collagen. Form: Insulin is an example of a globular protein that consists of two polypeptide chains: the ɑ-chain and β-chain. They are arranged in a specific three-dimensional shape that is held together by hydrogen bonds, hydrophobic interactions and disulfide bonds. Function:Insulin is a hormone that regulates the amount of glucose in the blood. It is produced by the pancreas and released into the bloodstream in response to high blood sugar levels. Insulin binds to specific receptors on cells, allowing glucose to enter the cells and be used for energy or stored for later use.  Explain the form and function of insulin and collagen. An example of a fibrous protein is collagen the most abundant protein in the body, forming the main component of connective tissue in animals, including skin, bone and cartilage. It is made up of three polypeptide chains that are twisted together in a triple helix structure Each chain is rich in the amino acid glycine, and it contains many proline and hydroxyproline residues. These residues allow the chains to twist together into a tight helix that is held together by hydrogen bonds and van der Waals forces provides structural support to tissues, helping them to maintain their shape and integrity. Guiding Questions What do we mean by “metabolism”? How do enzymes change the activation energy to speed up reaction rates? If each enzyme is substrate specific how can enzymes perform complex reactions like DNA replication? Which enzyme has the product acetaldehyde? Which enzyme has the substrate acetaldehyde? How do the enzymes link together to form a metabolic pathway? Metabolism (AHL) Essential idea: Metabolic reactions are regulated in response to the cell’s needs. Many elements of the metabolism are controlled by negative feedback Intracellular and extracellular metabolic by end product inhibition. The end product acts as a non-competitive pathways are two types of biochemical inhibitor binding the allosteric site reactions that occur within and outside the on an enzyme which controls the cell, respectively, to carry out various production of an intermediate compound earlier in the pathway. metabolic reactions. Metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions. Metabolism: the sum total of all chemical reactions that occur within an organism. Metabolic pathways*: cycles or chains of enzyme catalyzed reactions. The chemical change from one molecule to another often does not happen not in one large* aka biochemical jump, but in a sequence of TREA small steps. TheInitial small steps togetherpathways form what is called a substrate BREA metabolic D pathway. DREE B BLEE D intermedia tes BLEN D BLIN D BLIN D end product http://highered.mheducation.com/sites/dl/free/0072437316/120070 Metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions. Metabolic pathways: cycles or chains of enzyme catalyzed reactions. Glycolysis, a part of The Calvin cycle, a part of respiration, is an photosynthesis, is an example of a example of a metabolic metabolic cycle chain http://www.ib.bioninja.com.au/higher-level/topic-8-cell-respiration/82-photosynthesis.htm lhttp://www.ib.bioninja.com.au/higher-level/topic-8-cell-respiration/81-cell-respiration.html Glycolysis- metabolic pathway According to the second law of thermodynamics, no transformation of energy is ever 100% efficient, that is, some energy is always ‘lost’ as heat. This also applies to metabolic reactions where there is always loss of energy as heat. Enzymes lower the activation energy of the chemical reactions that they catalyse. Activation energy: the initial input of energy that is required to trigger a chemical reaction. The key effect enzymes have upon reactions http://www.stolaf.edu/people/giannin i/flashanimat/enzymes/transition%2 0state.swf un-catalyzed reaction catalyzed reaction Enzymes benefit organisms by speeding up the rate at which reactions occur, they make them happen millions of times faster. Enzymes lower the activation energy of the chemical reactions that they catalyse. How do enzymes lower the activation energy of a reaction? The substrate binds to the enzymes’ active site and the active site is altered to reach the transition state. Due to the binding the bonds in the substrate molecule are stressed/become less stable. The binding lowers the overall energy level of the transition state. The activation energy of the reaction is therefore reduced. n.b. the net amount of energy released by the reaction is Enzyme inhibitors can be competitive or non-competitive. http://www.northland.cc.mn.us/biology/biology1111/animations/enzy Enzyme inhibitors can be competitive or non-competitive. When the concentration of substrate begins to exceed the amount of inhibitor, the maximum rate of the uninhibited enzyme can be achieved. However, it takes a much higher concentration of substrate to achieve this maximum rate. Enzyme inhibitors can be competitive or non-competitive. The binding of the non- competitive inhibitor prevents some of the enzymes from being able to react regardless of substrate concentration. Those enzymes that do not bind inhibitors follow the same pattern as the normal enzyme. Enzyme inhibitors can be competitive or non-competitive. End-product inhibition of the pathway that converts threonine to isoleucine. Isoleucine is an essential amino acid* Bacteria synthesize isoleucine from threonine in a series of five enzyme-catalysed steps As the concentration of isoleucine increases, some of it binds to the allosteric site of threonine deaminase Isoleucine acts as a non- competitive inhibitor to threonine deaminase The pathway is then turned off, regulating isoleucine production. If the concentration of isoleucine later falls (as a *Essential amino acids cannot be made result of its use) then the Mechanism based Inhibition Mechanism-based inhibition is caused by the irreversible binding of the inhibitor to the active site of a specific enzyme through a covalent bond. This produces a stable inhibitor–enzyme complex causing the enzyme to lose its catalytic activity permanently Example: Penicillin **** One interesting note is that Transpeptidase is an enzyme produced in bacteria and bacterial cells can become resistant maintains the rigidity of the cell wall by forming cross-links to penicillin by changing the between polysaccharide chains. Penicillin binds to structure of transpeptidase so transpeptidase irreversibly, thereby inhibiting its function. penicillin cannot bind to it As a result the cell wall is weakened and the bacterial cells burst and are killed.