Chapter 6 An Introduction To Metabolism

Metabolism/Bioenergetics

• Metabolism: The totality of an organism’s chemical processes; managing the material and energy resources of the cell

• Catabolic pathways: degradative process such as cellular respiration; releases energy

• Anabolic pathways: building process such as protein synthesis; photosynthesis; consumes energy

Complexity of Metabolism

Thermodynamics• Energy (E)~ capacity to do work; • Kinetic energy~ energy of motion; • Potential energy~ stored energy• Thermodynamics~ study of E transformations• 1st Law: conservation of energy; E transferred/transformed, not created/destroyed• 2nd Law: transformations increase entropy (disorder,

randomness)

• quantity of E is constant, quality is not

Stability, Spontaneous Change, Equilibrium and Work

Free Energy• Free energy: portion of system’s E that can perform work (at a

constant T)• Exergonic reaction: net release of free E to surroundings• Endergonic reaction: absorbs free E from surroundings

Free Energy Equation

Organisms live at the expense of free energy.The amount of energy available to do work.

G = H - TS

G = free energyH = enthalpy or total energyT = temperature in 0KS = entropy (disorder/randomness)

Significance of Free EnergyIndicates whether a reaction will occur spontaneouslyor not.

In a spontaneous reaction, G decreases, G<0 (negative)

EXERGONIC REACTION ENDERGONIC REACTIONProducts have less G Products have more GReaction is ‘downhill’ Reaction is ‘uphill’Spontaneous Require energy inputG is negative G is positive

Metabolic Disequilibrium

Many metabolic reactions are reversible and reach equilibriuim.

At equilibrium a cell is dead!

Disequilibrium is maintained by the continual use/removal of products e.g. respiration

Free Energy Gradient Keeps Metabolism away from Equilibrium

Energy Coupling & ATP

• E coupling: use of exergonic process to drive an endergonic one (ATP)

• Adenosine triphosphate• ATP tail: high negative charge• ATP hydrolysis: release of free E• Phosphorylation (phosphorylated intermediate)~

enzymes

Energy Coupling

by Phosphate Transfer

The ATP Cycle

Chemical Reactions

Animation 6.1.1

An Energy Profile of a Reaction

Enzymes

• Catalytic proteins: change the rate of reactions w/o being consumed

• Free E of activation (activation E): the E required to break bonds

• Substrate: enzyme reactant• Active site: pocket or groove on enzyme that

binds to substrate• Induced fit model binding of substrate changes

shape of the active site so that the substrate can bind

Enzyme Properties•Are proteins

•Lower the activation energy of a reaction – transition state can be reached at cellular temperatures.

•Do not change the nature of the reaction – only speed up a reaction that would have occurred anyway.

•Are very selective for which reaction they will catalyze

Substrate + enzyme enzyme-substrate complex

product + enzyme

The Catalytic Cycle of an Enzyme

How an Enzyme Lowers Activation Energy

• Active site holds 2 or more reactants.

• Induced fit distorts bonds-less E required to break them.

• Active site may produce a micro-environment.

• Side chains of amino acids may participate.

How Enzymes Work

Animation 6.1.6

http://www.chem.ufl.edu/~itl/2045/lectures/lec_m.html

Initial Substrate Conc. Determines Rate of an Enzyme-Controlled

Reaction

• The higher the substrate conc. the faster the reaction

• If the substrate concentration is high enough – the enzyme may become saturated, reaction will slow

• Reaction rate may be increased by adding more enzyme.

Effects on Enzyme Activity

• Temperature• pH• Cofactors:

inorganic, nonprotein helpers; e.g. zinc, iron, copper

• Coenzymes:organic helpers;

e.g. vitamins

Enzyme Inhibitors

• Irreversible (covalent); Reversible (weak bonds)

• Competitive: competes for active site (reversible); mimics the substrate

• Noncompetitive: bind to another part of enzyme (allosteric site) altering its conformation (shape); poisons, antibiotics

Allosteric Regulation

Allosteric enzymes have two conformations, one catalytically active, the other inactive.

Binding of an activator to the allosteric site stabilizes the active conformation of the enzyme

Binding of an inhibitor to the allosteric site stabilizesthe inactive form of the enzyme (non-competitive)

Allosteric Inhibition

Feedback Inhibition

Cooperativity

Binding at one site enhances binding at other sites

Enzyme Catalysis Lab

Each enzyme is specific for the reaction it will catalyze. In this laboratory,

Enzyme = catalase Substrate = hydrogen peroxide (H2O2)Products = water and oxygen H2O2 H2O + O2

If a small amount of catalase is added to hydrogen peroxide, you will be able to observe bubbles of oxygen forming.

To determine the amount of hydrogen peroxide that remains after the reaction, you will do a titration with KMnO4.

In such a titration, you slowly add a chemical (KMnO4) that will cause a color change until a target is achieved.

To determine how much hydrogen peroxide (substrate) has been broken down by catalase at varying times, you measure the amount of peroxide remaining in each flask.

Reading the Burette

Analysis of Results Enzyme Action Over Time We can calculate the rate of a reaction by measuring, over time, either the disappearance of

substrate or the appearance of product.

For example, on the graph above, what is the rate, in moles/second, over the interval from 0 to 10 seconds?

Rate = Dx = 7-0 moles = 7 = 0.7 mols/sec Dy 10-0 seconds 10

Calculate the rate in moles/second between 40 and 50 seconds.

After 40 seconds there were no more substrate molecules. The curve becomes flat at this point, and the rate is zero.

During what time interval is the enzyme working at its maximum velocity?

a. 0–30 secondsb. 60–120 secondsc. 120–180 secondsd. Over the entire time course

In order to keep the rate constant over the entire time course, which of the following should be done?

a. Add more enzyme.b. Gradually increase the temperature after 60 seconds.c. Add more substrated. Add H2SO4 after 60 seconds.e. Remove the accumulating product.

Which of the following graphs represents the rate of the reaction shown above? Notice that in the graphs below,

the y-axis is number of molecules/sec.

What is the role of sulfuric acid (H2SO4) in this

experiment?

a. It is the substrate on which catalase actsb. It binds with the remaining hydrogen peroxide during titrationc. It accelerates the reaction between enzyme and substrated. It blocks the active site of the enzymee. It denatures the enzyme by altering the active site

A student was performing a titration for this laboratory, and accidentally exceeded the endpoint. What would be

the best step to obtain good data for this point?

a. Estimate the amount of KMnO4 that was in excess, and subtract this from the resultb. Repeat the titration using the reserved remaining sample.c. Obtain data for this point from another lab groupd. Prepare a graph of the data without this point, and then read the estimated value from the graph.