Metabolism Chapter 8 PDF

Campbell and Reece 8 Chapter 8 Page An Introduction to Metabolism I. Metabolism, Energy and Life Metabolism Metabolism is all of an organism's chemical processes (an emergent property that arises from interactions of molecules i...

Campbell and Reece 8 Chapter 8 Page An Introduction to Metabolism I. Metabolism, Energy and Life Metabolism Metabolism is all of an organism's chemical processes (an emergent property that arises from interactions of molecules in the orderly environment of the cell) Metabolism is very important for the management of cellular material and energy resources Metabolic reactions Metabolic reactions are organized into pathways of enzyme controlled chemical reactions. Cells need a supply of molecules (food) and energy Cells need to get rid of waste products 1. Catabolic pathways: Catabolic pathways release energy by breaking down complex molecules into simple molecules Energy stored in complex molecules is made available to do work or transformed into readily usable chemical forms (i.e., ATP) small molecules resulting from the catabolism of complex energy rich molecules may be used by the cell to build new molecules Examples of catabolic reactions: Digestive enzymes breaking down food Cellular respiration, the breakdown of glucose in the presence of oxygen Energy stored in compounds (potential energy) can be used to do WORK Types of cellular work  i. mechanical ii. transport iii. chemical - [i.e., endergonic reactions] 2. Anabolic pathways Anabolic pathways use energy to synthesize complex molecules from simple molecules. The synthesis of protein from amino acids is an example of anabolism Bioenergetics is the study of how organisms manage their energy resources Energy extracted from the environment is used to create order and carry out life processes (Bioenergetics – the study of energy flows through living organisms) II. Laws of Energy Transformations or Thermodynamics 1st Law - Energy can be transferred and transformed but cannot be created or destroyed. 2nd Law - Every energy transfer or transformation increases the entropy (i.e., randomness) of the universe. III. Free Energy and Metabolism Energy = capacity to do work or cause change Free energy (G) - portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system Biologists want to know which reactions occur spontaneously and which require input of energy To do so, they need to determine energy changes that occur in chemical reactions Change in free energy (DG) o DG = G final state - Ginitial state (spontaneous) &XCgOR O Re E (non-spontaneous) endergonic energy) (Absorption of Reactans-> Products P energy - Release ↓-  reactant- > High release of > energy - low product - > AGLf enege rata - It started energy why woudded that's reactant > absorb > low energy - - IV. ATP and Energy Coupling > - High product- > 1078 Energy coupling - energy released by catabolic processes is used to drive anabolic processes ATP (adenosine triphosphate) ATP powers cellular work by coupling exergonic (i.e., energy releasing) reactions to endergonic (i.e., energy storing) reactions ATP mediates most but not all energy coupling in cells ATP stores energy in unstable “high energy” bonds that can be hydrolyzed to release energy ATP + H2O ® ADP + Pi DG= -7.3 kcal/mole in test tube  exergonic reaction - proceeds spontaneously with a net release of free energy energy released through the hydrolysis of ATP is coupled through production of phosphorylated intermediates The phosphorylated intermediate is more reactive than the original unphosphorylated molecule endergonic reactions - stores energy ATP is regenerated by energy coupling (ATP cycle) ADP + Pi ® ATP + H2O DG= 7.3 kcal/mole in test tube V. Chemical Reactions Chemical reaction Breaking and reforming of bonds resulting in the change in composition of matter The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy. Steps involved in a chemical reaction 1. Absorption of Activation Energy (EA)  Activation energy is the energy required to break bonds in reactants - usually obtained in the form of heat from the environment Bonds of reactants only break when molecules have absorbed enough heat from environment to become unstable Many exergonic reactions will not occur at a noticeable rate because of a significant EA barrier 2. Transition state Unstable state Enough energy has been absorbed to break chemical bonds 3. Reaction occurs Energy is released as new bonds are formed How can you increase the rate of a chemical reaction? Overcoming the EA barrier catalysts - chemical agents that increase the rate of a chemical reaction without being permanently changed in the process. Examples of biological catalysts Protein enzymes VI. Enzymes Biological catalysts made of proteins Enzymes  speed up reactions by allowing the transition state to be reached at cellular temperatures, they accelerate reactions that would occur eventually Enzymes catalyze reactions by lowering the EA barrier but cannot change ∆G They are very selective and therefore they determine which chemical processes will be going on in the cell at any particular time (unlike an increase in temperature which would increase the rate of every reaction in a cell) Features of Enzymes 1. Enzymes are substrate specific The reactant(s) that an enzyme acts upon is referred to as the enzyme's substrate(s) The 3-dimensional conformation of an enzyme determines its substrate specificity enzyme Substrate(s) ⇄ Product(s) 2. Catalysis occurs in the enzyme's active site The active site binds the substrate and is the enzyme's catalytic centre The active site is usually a pocket or groove on the surface of the enzyme Substrate entering the active site induces the enzyme to change its shape slightly so that there is a better fit between substrate and enzyme - This is known as induced fit. 3. Catalytic cycle Substrate + enzyme ® ES complex ® product + enzyme a. Substrate binds to active site residues by weak interactions (e.g., H-bonds, ionic interactions) b. Induced fit around substrate ® catalysis Mechanisms for lowering EA Proper positioning of two or more reactants Distort chemical bonds Provides appropriate microenvironment – e.g., pH Participation of R-groups in the reaction c. Product departs the active site. d. Enzyme may take part in another reaction Factors affect Enzyme Activity Enzyme activator i. An enzyme’s activity can be affected by – General environmental factors, such as temperature and pH – Chemicals that specifically influence the enzyme ii. Each enzyme has an optimal temperature in which it can function iii. Each enzyme has an optimal pH in which it can function iv. Optimal conditions favor the most active shape for the enzyme molecule 2+ 2+ 2+ 2+ v. Cofactors are nonprotein enzyme helpers (metal ions – Mg , Mn , Zn , Ca ) vi. An organic cofactor is called a coenzyme ,Coenzymes include vitamins, and electron carriers such as NADH. Enzyme Inhibitors a) irreversible - covalently bound to enzyme b) reversible competitive noncompetitive Note: Not all inhibitors are toxins - naturally occurring molecules regulate enzymatic reactions by acting as inhibitors Control of Metabolism Selective regulation occurs in metabolic pathways (i.e., molecular traffic lights) Example of enzyme regulation Feedback inhibition - A metabolic pathway is switched off by its end product, which acts as an inhibitor of an enzyme in the pathway. In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed