CHAPTER 3 – BIOCHEMICAL PATHWAYS

CELLULAR METABOLISM Different types of cells carry out particular specialised functions, but certain basic processes must be performed by all cells. Cells must obtain nutrients, grow, maintain and repair themselves, provide energy for movement and metabolism, and eliminate wastes. These activities require the production of a variety of biological molecules (biomolecules), which are then assembled into new organelles or used for repair and maintenance of cells.

THIS CHAPTER….. Particular proteins called enzymes control the synthesis of these various biomolecules and many other cellular processes, such as cellular respiration, which keep the cells alive. This chapter is about how enzymes are used in the metabolism of the cell, and about the production and handling of biomolecules.

METABOLISM Metabolism is the overall chemical activity of cells. It includes the manufacture (synthesis) of organic molecules, various energy transforming and recycling processes, and the breakdown of unwanted substances. These chemical reactions involve hundreds of enzymes working in ‘chains’, where the product of one reaction is the substrate for the next enzyme. These chains of reactions are known as metabolic pathways. enzyme acts.

Enzymes are biological catalysts Enzymes act as catalysts for chemical reactions in the body. A catalyst speeds up (catalyses) chemical reactions that would otherwise take place, but much more slowly. They help reactions progress from the beginning to the end. If there is no enzyme present, a reaction would still run to completion but would take much longer.

ENZYMES are substrate specific can be reused over and over again are needed in small amounts and are neither reactants nor products make a reaction take place more easily (they reduce the activation energy) can catalyse a reaction in either direction (most chemical reactions are reversible) do not change the direction of a reaction do not change the final amount of product.

ENZYMES Enzymes are not used up in the reaction and they remain the same at the end of the reaction, although they may have been temporarily altered during the reaction. Enzymes can therefore be used over and over again. Enzymes are proteins and their actions are generally specific, meaning that each enzyme usually catalyses only one type of reaction.

ENZYMES This specificity is related to the three-dimensional structure of the molecules. The active site on an enzyme is the part of the molecule that interacts with the substrate. It has a shape that complements the shape of the binding site of the substrate; that is, they ‘fit together’ like pieces of a jigsaw puzzle.

ENZYMES The mechanism of an enzyme binding with a substrate has been refer red to as a ‘lock-and-key’ interaction, though more recent evidence supports an ‘induced-fit’ mechanism

Enzyme structure

HOW ENZYMES WORK.. In the lock-and-key mechanism, substrate molecules have the right shape to fit an enzyme. In the induced-fit mechanism, the actual interaction between substrate and enzyme changes the shape of the enzyme to produce the right fit.

ACTIVATION ENERGY AND ENZYMES Chemical reactions involve breaking and remaking chemical bonds. The molecules involved require a certain amount activation energy to get the reaction started, even if the reaction eventually releases energy Enzymes act by reducing the amount of activation energy required for a particular reaction to occur, allowing the reaction to take place more easily.

Factors affecting enzyme activity Enzyme action involves specific binding between enzyme and substrate molecules. Because of this, any condition that changes the shape of an enzyme molecule will affect the activity of the enzyme and therefore the rate of the reaction.

TEMPERATURE Enzymatic reactions are affected by temperature. Warming increases the rate of most chemical reactions, including enzyme- catalysed reactions. This is because the extra heat energy is taken up by the molecules so they move faster, which increases the rate of interaction between substrate and enzyme. However, too much heat can damage the structure of an enzyme. Enzymes are proteins, and all proteins are denatured by heat when a certain critical temperature is reached

DENATURATION Denaturation is an irreversible change in protein structure (often a loss of the correct folding of the molecule). Boiling denatures most enzymes. Most enzymes have an optimum temperature range, which is the temperature at which the enzyme’s catalytic activity is greatest. This is the range immediately below the critical temperature at which denaturation of enzyme molecules begins to occur.

Optimal temperatures for particular enzymes may vary in different species and are related to the normal body temperature of the organism

pH The three-dimensional structure of proteins is affected by pH. In the case of enzymes, altering the pH may change the shape of the binding (active) site and so alter the ‘fit’ between enzyme and substrate. The optimal pH is that at which the fit is best and so the enzyme’s activity is greatest.

Regulating enzyme affinity Cells can regulate the affinity of certain key enzymes for their substrate molecules. Affinity is the ease with which an enzymes binds with its substrate. Cells do this by attaching other molecules to the enzyme to alter the shape of its active site. This allows cells to increase or decrease the rate of a reaction in particular circumstances.

Chemical inhibition Other chemical substances can inhibit enzyme function by binding to the active site of the enzyme, or by combining with another part of the enzyme in such a way that the shape of the binding site is altered. The antibiotic sulfanilamide is effective against bacteria because it binds to the active site of the bacterial enzyme involved in the formation of folic acid (a B- complex vitamin). It is able to do this because the molecular structures of sulfanilamide and the normal substrate for the enzyme are very similar

Competitive inhibition

Non-competitive inhibition

Amounts of reactants The rate of a reaction is also affected by the relative amounts of substrate or enzyme present and how much product has accumulated.

Coenzymes and cofactors Coenzymes are very small organic molecules—less complex than proteins— that are associated with particular enzymes and are essential for their activity. They usually donate electrons (negative particles) or protons (positive particles). Many coenzymes cannot be synthesised by animals and must be obtained from plants or microorganisms.

Anabolic reactions

Anabolic reactions

Catabolic reactions

Catabolic reactions

Chemical energy in compounds

Chemical energy in compounds

Cellular metabolism summary More complex organic compounds anabolism (synthesis) endergonic reactions (require energy) Organic compounds in cells catabolism (breakdown) exergonic reactions (release energy) digestion, absorption and assimilation Simple compounds (e.g. carbon dioxide and water) Organic food

Cellular respiration Is the process 100% efficient?

Aerobic respiration

Aerobic respiration Can be divided into three stages: Glycolysis Krebs Cycle Electron Transport

Glycolysis Occurs in cytosol 6-carbon glucose is broken down to form two 3-carbon pyruvate molecules. Energy is released to form 2 ATP loaded acceptor molecules 2 NADH

Kreb’s Cycle Inner compartment of mitochondria One pyruvate forms 3 CO2 Energy is released to form: 2 ATP loaded acceptor molecules 8 NADH 2 FADH2

Electron Transport Inner membranes of mitochondria Electrons and hydrogen ions (H+) unite with oxygen to form H20. Energy released to drive ATP production: 32 ATP

Stages of Aerobic Respiration Location ATP Output Glycolysis Cytosol of cells 2 ATP 2 pyruvate 2 loaded acceptors Krebs cycle Mitochondria 6 CO2 10 loaded acceptors Electron transport 32 ATP Water Acceptors returned to unloaded state

Anaerobic respiration Cellular respiration Aerobic vs. anaerobic Anaerobic respiration Aerobic respiration oxygen not required oxygen required rapid ATP production slower rate of ATP production mammals sustain over short time only sustain indefinitely less efficient energy transfer more efficient energy transfer 2 ATP produced per glucose used 36 ATP produced per glucose used (some tissues produce 38) various end products: lactate and water (humans) ethanol and CO2 (yeasts) butyl alcohol (some bacteria) end products are: CO2 and water

Putting photosynthesis and aerobic respiration together Photosynthesis converts radiant energy to chemical energy in organic molecules such as carbohydrates. The energy in these molecules is released by cellular respiration and ATP is produced. ATP provides energy for all cellular processes.

Chemical Structure of ATP Adenine Base 3 Phosphates Ribose Sugar

Energy

Summary of Photosynthesis

Summary of Photosynthesis chlorophyll 6CO2 + 12H2O C6H12O6 + 6O2 + 6H2O light energy

The Chloroplast

Photosynthesis Photosynthesis can be divided into two main stages: Light dependent stage (light reaction) Light independent stage (dark reaction)

Brief Summary of Photosynthesis

photosynthesis Light-dependent stage

photosynthesis Light-dependent stage Highly simplified diagram showing a summary of the light-dependent reaction of photosynthesis. Note the inputs and outputs of this stage of photosynthesis. Pi = inorganic phosphate.

Photosynthesis Light-dependent stage Light energy trapped by chlorophyll splits water to form high-energy electrons and protons, with oxygen as a waste product. The energy released from these electrons is used to drive the formation of ATP and ‘loaded’ carrier molecules of NADPH Note the inputs and outputs.

photosynthesis Light-independent stage

Photosynthesis Light-independent stage Carbon dioxide enters stroma where it begins a series of reactions that use the hydrogen and ATP from the light-dependent stage of photosynthesis. Note the inputs and outputs

Photosynthesis Light-independent stage Calvin Cycle (carbon reduction)

Photosynthesis Carbon reduction in C3 and C4 plants (light independent) C3 C4

Alternative pathways

Photosynthesis summary The outputs from the light-dependent reactions in photosynthesis (ATP and the ‘loaded’ acceptor molecule, NADPH) are used to drive the light-independent fixation of carbon. Because water ‘waste’ is recycled in the process, it is not considered an output of the total process, similarly for ADP and Pi.