Ground Rules of Metabolism Chapter 4 Part A

Metabolic Reactions Metabolic reactions are orderly, enzyme-mediated sequences that build, rearrange, or breakdown molecules

Metabolic Reactions Terms used for metabolic reactions Reactants or Substrates: starting molecules Intermediates: molecules formed during a reaction sequence End Products: molecule(s) at the end of the reaction sequence Substrate Intermediates Product

Metabolic Reactions Some metabolic pathways are linear Runs straight from the substrate to the end product Substrate Intermediates Product

Metabolic Reactions Some metabolic pathways are cyclic The substrate reacts with the last intermediate of the cycle The end product exits the cycle The last step regenerates the last intermediate ready for the first step Substrate Product Intermediates

Metabolic Reactions Reactions can occur in both directions Synthesizing or breaking down Products become the substrate Substrates become the products

Energy Metabolic reactions may require or produce energy Energy is the capacity to do work Various forms of energy include Kinetic: energy of movement Potential: stored energy Chemical: potential energy stored in chemical bonds Heat Light

Energy Energy is defined by the Laws of Thermodynamics 1st Law Energy cannot be created or destroyed, but can be converted form one form to another

Energy Energy is defined by the Laws of Thermodynamics 2nd Law Entropy tends to increase Entropy is a measurement of how much the energy in a system has become dispersed

Energy Energy is defined by the Laws of Thermodynamics 2nd Law Entropy tends to increase Energy flows form more usable forms (low entropy) to less usable forms (high entropy) Least usable / highest entropy is heat energy

Energy Energy is defined by the Laws of Thermodynamics 2nd Law Entropy changes can cause some reactions to occur spontaneously or to require energy input

Energy Energy release or use in metabolic reactions Determined by free energy of the molecules Free energy = bond energy and entropy level of a molecule High free energy: Low entropy plus high bond energy Low free energy: High entropy plus low bond energy

Energy Energy release or use in metabolic reactions Endergonic reactions Energy is required Reactants that have less free energy than the products need an energy input High free energy: Low entropy plus high bond energy Low free energy: High entropy plus low bond energy

Energy Energy release or use in metabolic reactions Exergonic reactions Energy is released Reactants that have more free energy than the products will release energy High free energy: Low entropy plus high bond energy Low free energy: High entropy plus low bond energy

Energy Activation energy The minimum amount of energy required to start a chemical reaction Even exergonic reactions require activation energy

Energy ATP (Adenosine triphosphate) Used by cells to store and transfer energy Bonds between the phosphate groups hold a lot of energy

Energy ATP (Adenosine triphosphate) Contributes energy to endergonic reactions Similar to using a battery The mechanism ATP  ADP + phosphate group (Pi) Releases energy when the bond holding the phosphate group is broken Phosphate groups can be released free in the cytoplasm or attached to a substrate/intermediate in a metabolic pathway reaction requiring energy

Energy ATP (Adenosine triphosphate) Receives energy from exergonic reactions Similar to charging a battery The mechanism ADP + phosphate group (Pi)  ATP

Energy ATP (Adenosine triphosphate) ATP and ADP + Pi cycle between endergonic and exergonic reactions driving most metabolic reactions ATP ADP + phosphate group (Pi)

Enzymes Enzymes are used for most steps of metabolic reactions

Enzymes Enzymes are catalysts: molecules that make chemical reactions occur much faster than they would on their own

Enzymes Nearly all enzymes are proteins The polypeptide folds into a specific shape Creates an active site A pocket where substrates bind and a reaction occurs Induced fit The substrate doesn’t start out fitting perfectly As the enzyme and substrate interact, they change shape slightly resulting in the interactions that will promote the chemical reaction Impacted by any factors that affect proteins Denaturation, temperature, pH, etc.

Enzymes Enzymes help reactions occur faster by lowering the activation energy Forcing substrates together Brings two or more substrates close together More likely to react Orienting substrates Positioned so they align for a reaction Normally the odds of two substrates colliding randomly in the correct orientation are very low

Enzymes Enzymes help reactions occur faster by lowering the activation energy Inducing a fit between the enzyme and substrate Causes the substrate to change shape putting pressure on its bonds Shutting out water molecules Changes some of the chemical interactions internally in the substrate (hydrophobic/hydrophilic)

Enzymes Enzymes are not consumed or altered by the reaction and can work again and again

Enzymes Enzymes are helped by cofactors and coenzymes Metal ions Stabilize the structure of an enzyme Functional role by readily losing or gaining electrons

Enzymes Enzymes are helped by cofactors and coenzymes Coenzymes Small organic molecules Many vitamins are cofactors (or precursors for them) Coenzymes are often modified during a reaction, but they are regenerated elsewhere

Enzymes Enzymes are helped by cofactors and coenzymes Coenzymes NAD+ is a coenzyme Derived from niacin Accepts electrons and hydrogen ions becoming NADH Then donates the electrons and hydrogen ions forming NAD+ again NAD+ + electrons + H+ NADH NAD+ + electrons + H+

Control of Metabolic Pathways Cells control their metabolic pathways to control amounts of various reactants, intermediates, and products

Control of Metabolic Pathways Control enzyme activity Temperature Enzymes have optimal ranges of temperature Too low slows enzymes down Too high results in denaturation Adapted to environment Arctic verses hot springs

Control of Metabolic Pathways Control enzyme activity Denaturation Destroys the three-dimensional shape of the active site Environmental causes High temperature pH Salinity Enzymes have optimal ranges

Control of Metabolic Pathways Control enzyme activity Regulatory molecules Binding of an allosteric regulator alters the shape of the enzyme Can either inhibit or enhance the enzyme’s function

Control of Metabolic Pathways Feed-back inhibition

Control of Metabolic Pathways Feed-back inhibition The pathway produces a lot of the end product Excess product binds to the first enzyme inhibiting its action The cell uses the remaining product Product levels decrease and release the first enzyme The pathway is active again

Summary Metabolic Reactions Energy Enzymes Control of reactions Terminology Linear and cyclic Energy ATP Enzymes Control of reactions