1) DNA unzips - hydrogen bonds between base pairs are broken by special enzymes.

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1 Biology 12 Cell Cycle To divide, a cell must complete several important tasks: it must grow, during which it performs protein synthesis (G1 phase) replicate its genetic material /DNA (S phase), and physically split into two daughter cells (M phase) Cells perform these tasks in an organized, predictable series of steps that make up the cell cycle. DNA Replication: Steps 1) DNA unzips - hydrogen bonds between base pairs are broken by special enzymes. 2) New complementary DNA nucleotides (present in nucleus) attach to each 1/2 of DNA strand. Base pairs join by hydrogen bonding 3) Adjacent nucleotides join - phosphate to sugar - forming sides of DNA ladder 2 identical DNA molecules are produced Final Result: Two identical DNA molecules are produced, this allows exact DNA copies to be incorporated into new daughter cells Protein Synthesis: DNA controls the production of proteins in the cell. The DNA is found in the nucleus and carries the codes for the construction of the proteins. A section of DNA that contains the code to produce 1 polypeptide is called a gene. The construction of a polypeptide will take place in the cytoplasm. There are two stages in the process of protein synthesis: A. Transcription occurs in the nucleus where a messenger RNA (mrna) molecule is made on a template of an exposed DNA molecule (gene). The mrna molecule actually transcribes the codes for the construction of protein. B. Translation the mrna leave the nucleus and travels to a ribosome. It is read by the ribosome and the correct number and order of amino acids is determined. The amino acid chain is assembled at the ribosome. The properly folded polypeptide is called a protein Mutation: A change in the base pairs of DNA eg. by deletion or insertion of base pairs. Effects of Mutation: Mutations may cause changes in mrna made during transcription and so may change amino acid sequence of polypeptide produced during translation.

2 Metabolism In this unit we will be concentrating on protein enzymes that can be secreted from the cell or used within the cell. Enzymes are catalysts that cause chemical reactions to occur at lower activation energy allow chemical reactions to occur at lower temperatures, like 37 C in the human body. Metabolism = refers to all of the chemical reactions within a cell or organism. Metabolic Pathway A series of enzyme driven chemical reactions that control the steps by which products of one reaction become substrates for the next reaction. A is the substrate for the 1 st reaction and B is the product of the 1 st reaction. B becomes the substrate for the 2 nd reaction and C is the product of the 2 nd reaction. C becomes the substrate for the 3 rd reaction and D the end product of this metabolic pathway. The numbers refer to specific enzymes for each reaction. Enzymes (called catalysts) help speed up a given reaction by lowering the energy of activation for that reaction. Energy of activation - the energy that must be supplied to cause molecules to react with one another is called the energy of activation

3 Some of the most important chemical reactions in the body are those called CELLULAR RESPIRATION that produce ATP. The overall reaction for cellular respiration is: 38 ATP is the theoretical limit for ATP production from 1 glucose molecule. C 6 H 12 O 6 + 6O 2 38 ATP + 6CO 2 + 6H 2 O Remember that ATP (Adenosine triphosphate) is a compound containing adenine and three phosphates, two of which are high energy phosphates. ATP is the "common currency" of energy for most cellular processes. A burst of energy will be released by removing the last phosphate group - this means that ATP can act as an energy store for the cell. Countless ATP's move randomly around the cell so that they are available when needed. ATP ADP + P + energy Cellular Respiration: The simplified metabolic pathway C 6 H 12 O 6 Mitochondrion B O 2 No O 2 available C D E F H 2 O 38 ATP 4 ATP Lactic acid CO 2 Lactate H + Fatty acids Amino acids Carbohydrate NH 3 Urea Follow the Possible Reactions: (ALL of these reactions are catalyzed by enzymes) 1. Reactions from C 6 H 12 O 6 B C D E F These reactions run if O 2 is available in the cell (called aerobic cellular respiration). They produce a maximum of 38 ATP + 2 wastes products (H 2 O + CO 2 ) 2. If O 2 is not available then glucose will be metabolized to lactic acid. This reaction produces a maximum of 4 ATP and is called anaerobic cellular respiration. The waste product lactic acid causes ph to drop in the surrounding tissue and blood. The point at which lactic acid begins to accumulate in the blood is directly related to the lactate threshold because lactic acid is converted to lactate. The drop in ph causes a drop in athletic performance as muscle proteins begin to denature (the burn). 3. Fatty acids can be added as a substrate to produce ATP. The enzymes responsible for metabolizing fat can be increased through exercise and diet BUT not by reducing calories. This is a complex topic and one that requires further research. Becoming a fat burner is very desirable because of the huge energy store in fat as well as other health benefits associated with reducing body fat. 4. Under some circumstances, (over exercising or poor diet), amino acids can be added as a substrate to produce ATP. The problem here is that these amino acids will be stripped away from muscle and immune system proteins to provide emergency energy. The amino acids are deaminated by removing the amine group. This leaves a carbohydrate like substance that can be used as a substrate to produce ATP. The waste product NH 3 (ammonia) is toxic and is converted to urea in the liver. Both NH 3 and urea need to excreted from the body in urine and sweat.

4 What are Enzymes? Most enzymes are globular proteins either tertiary or quaternary structure proteins. Therefore, they are strings of amino acids that bend and fold into a particular 3d shape A quaternary protein When a protein folds it creates a shape that is called an active site. Substrates fit into the active site. Each enzyme is specific for one and ONLY one substrate (one lock - one key) Active site: part of the enzyme that fits with the substrate Note that the active site has a specific fit for this particular substrate and no other. This theory has some weaknesses, but it explains many basic things about enzyme function.

5 How Do Enzymes Work? Enzyme, Substrate and Product Enzyme: a protein based catalyst that speeds up a specific reaction or type of reaction. An enzyme is left unaltered by the reaction. Substrate: a reactant in a reaction controlled by an enzyme. Product: the end result of a chemical reaction. Lock and Key Theory of Enzyme Action Where: E= Enzyme, S= Substrate, ES= Enzyme/substrate complex, P=Product. Active site - This is where the substrates attach to the enzyme to become the enzyme- substrate complex. Here they are changed (joined, split or molecularly rearranged) without the enzyme being changed itself. Following disengagement, the new product is formed. Protein portion of enzyme The portion of an enzyme that deals with its specificity (the ability of the enzyme to speed up only one particular reaction). Co-enzyme The non-protein helper of an enzyme. A molecule that aids in the action of an enzyme, to which it is loosely bound. They may be large molecules that the body is incapable of synthesizing. All well known vitamins are parts of co-enzymes. Example of co-enzymes = B vitamins like Niacin (B3), Thiamine (B1) etc. Protein enzyme + Coenzyme Active Enzyme Non protein component

6 Types of Enzymes: 1. Hydrolytic Enzymes - used to digest (break apart) large molecules by hydrolysis. All enzymes found in the digestive tract and in lysosomes are hydrolytic enzymes. An Example of Lock and Key Theory 2. Dehydration Synthesis Enzymes - used to put molecules together by dehydration synthesis An example of this process occurs in the liver and muscles where enzymes connect glucose unit molecules together to produce glycogen. An Example of Lock and Key Theory

7 Factors That Can Affect the Rate of an Enzyme Driven Reaction = yield factors Certain factors influence the yield of enzymatic reactions 1. Genetic factors inheritance, mutations and gene expression 2. Denaturation 3. Concentrations of enzymes and substrates 4. Competitive inhibition 1. Genetic factors the ability to make protein enzymes is determined genetically. a. Inheritance and mutation enzyme production can be determined by the genes inherited from your parents. The one gene one enzyme theory suggests that each enzyme is produced by one gene. This hypothesis has been proven for many enzymes but does not explain the production of all enzymes in the body. Some enzymes require multiple genes for their production but we can understand the basics by understanding the one gene, one enzyme theory. Lactose intolerance - A simple example of gene inheritance and mutation. Lactase is an enzyme that breaks down the disaccharide lactose (a sugar found in milk and other dairy products). Lactase is produced by the lactase (LCT) gene. Lactose lactase Glucose + Galactose Where is the LCT gene located? The LCT gene is located on the long (q) arm of chromosome 2 at position 21. More precisely, the LCT gene is located from base pair 135,787,845 to base pair 135,837,180 on chromosome 2. Since everyone has 2 of each chromosome, each person will have 2 copies of the LCT gene. There are 2 forms (alleles) of the LCT gene the wild type gene that produces active lactase enzyme (label as A ) and the mutated gene that produces mutated non-active lactase enzyme (label as a ). Label this allele as A Label this allele as a Possible genotype (Type of genes inherited) AA homozygous wild type Aa heterozygous aa heterozygous aa homozygous mutated Phenotype (trait) Can digest lactose Can digest lactose but may be reduced Can digest lactose but may be reduced Lactose intolerant Enzyme production 2 wild type genes means person has the ability to produce sufficient lactase enzyme. 1 wild type gene and 1 mutated gene means person has ability to produce some lactase enzyme. 1 wild type gene and 1 mutated gene means person has ability to produce some lactase enzyme. 2 mutated genes means person does not have the ability to produce lactase enzyme.

8 In the simplest sense, you can think of mutations as affecting the amount of particular proteins including enzymes. b. Gene expression and epigenetics To complicate the gene inheritance picture even further there are a number of factors that can affect gene expression. These factors are called epigenetic factors. Epigenetics means above the level of the genome (gene). For example, diet, exercise (activity), stress and other environmental factors can influence how often a gene is read (transcribed and translated) and so affect the amount of enzyme produced. This genetic picture is even more complicated when you consider that the production of many enzymes require multiple genes. Also, consider that metabolic pathways require many enzymes to catalyze the chemical reactions in the body. At this stage in your biology career, it is important to recognize the concept of BIOCHEMICAL INDIVIDUALITY. The uniqueness of each individual can be attributed to the combination of genetic and epigenetic factors that influence the a person s metabolism.

9 2. Enzyme denaturation the protein loses its normal shape and usually loses its function Active (functional) protein Denatured (non-functional protein Denaturation of an enzyme = alters active site so that substrate can no longer fit. Therefore, less ES complexes can be formed and fewer products produced Enzyme Denaturation Factors a. Heavy Metals - e.g. Lead and Mercury- These bond with the protein in enzymes and thereby inactivate them. b. Temperature - Extremes, high temperatures will change the shape of proteins and therefore, will damage an enzyme. Within certain limits higher temps will speed up enzyme action and cooler temperatures will slow down the action. Every enzyme has its own optimum range of action. Most human enzymes work best around 37 C. Initially, the increase in enzyme activity is due to increasing molecular movement of both substrate and enzyme. c. ph - This affects ionic bonding between the side chains of molecules, particularly the "R" groups of the proteins. This will change the shape of the mol. and therefore affect its performance. Each enzyme has its own optimum range of ph to work efficiently. environment Pepsin works in the acidic of the stomach. Trypsin works in the slightly basic environment of the small intestine

10 3. Concentrations If the concentration of the substrate is increased, the amount of the product increases; that is, the more S or E available, the more P there is within a certain amount of time. In many instances, the substrate is plentiful within the cell, but the enzyme is present only in small amounts. The amount of enzyme limits the overall rate of reaction. In other words, if there is only a small amount of enzyme present, there will be fewer products in a given unit of time. Enzymic reactions Are faster but they reach a saturation point when all the enzyme molecules are occupied. If you increase the concentration of the enzyme then reaction rate will increase too. 4. Competitive Inhibition Reduction in rate of a reaction due to the presence of a compound that competes with the enzyme for the reactant (s) so that less of the desired product is produced per unit time. Competitive inhibitors block the active site so that few ES complexes can be formed Hydrogen cyanide is an inhibitor for cytochrome oxidase (enzyme) - lethal effect on the human body.