The Working Cell Chapter 5. Overview Energy Metabolism Enzymes Metabolic Pathways.

The Working Cell

Chapter 5

Overview

• Energy

• Metabolism

• Enzymes

• Metabolic Pathways

Energy

The capacity to do work

In living organisms, chemical bonds are made & broken so that energy can be

exchanged or transformed

Energy of motion

Work needed to accelerate an object

from rest to its current velocity

Includes light, sound, electricity, & heat energy

Kinetic Energy

Potential Energy

The stored energy of position

The work done by a certain force (e.g. gravity) on an object relative to its position

Includes chemical & battery energy

Kinetic and Potential Energy as a Pair

Potential energy is converted into kinetic energy & vice versa

Imagine a rubber band:

When you stretch a rubber band, you give it potential energy

When you release it, it has kinetic energy

Thermodynamics

The study of the effects of work, heat, & energy on a closed system

Energy can be exchanged between physical systems as heat or work

1st Law of Thermodynamics“Energy can not be created or destroyed”

A finite amount exists in various forms, which can be converted to other forms of

energye.g. from work to heat, from heat to light, from

chemical to heat, etc.

e.g. The chemical energy released from burning a substance is converted into light & heat energy

In the conversion of energy from one form to another, some energy is lost as heat

(i.e. not 100% efficient)

Therefore, energy is unavailable to do work

Heat is a disordered form of energy

Release of heat makes universe more random & disorganized

energy conversions ↓ order & ↑ entropy

2nd law of thermodynamics“Energy tends to flow from concentrated to

less concentrated forms”

Goes from being localized to being spread out

(why hot things cool down when removed from heat, why air in a tire will escape from a small

hole, etc.)

Entropy

The magnitude that concentrated energy has been dispersed after an energy change

= how much energy is spread out or how widely it spreads out

Unavailable energy(in a closed system, entropy can not decrease)

Measure of disorder of a system(nature tends to go from order to disorder in closed

systems)

Time’s Arrow

All energy spontaneously spreads out from a localized area to a more dispersed

pattern

(opposite does not occur spontaneously)

In a closed system, everything will become more simple (i.e. will degenerate) over

time

Evolution’s basis is that simple organisms diversified into highly complex organisms

So why don’t highly ordered living organisms violate the 2nd law of thermodynamics?

Thermodynamics = closed system

Earth = open system(earth exchanges heat, light, matter with its

surroundings, including the sun)

Organisms have low entropy and use energy to fight entropy

If stop using energy → die

Energy Flow Through The Biosphere

Solar radiation is the ultimate source of energy in all food webs

(captured by photoautotrophs)

Glucose produced by each level is used up by level above

At all levels, respiration occurs

(releasing CO2, H2O, and energy from glucose)

Energy is lost as heat between each level

= 1-way flow where energy is used and dispersed

90% of energy lost

between each level

Metabolism and Energy

Chemical reactions convert reactants to products by making or breaking bonds

that hold atoms together

Requires net inputs of energy to combine small molecules into larger ones that are

more concentrated forms of energy

Larger molecules can spontaneously degrade into smaller molecules, which

ends with a release of energy

Components of a Metabolic Reaction

Reactant: Starting substance

Intermediates: Formed before reaction ends

Product: Substance remaining at end of reaction

Some rxns are linear:

Products formed directly from reactants

Some rxns are cyclic:

Final rxn regenerates the reactant molecule from the 1st step of the rxn;

rxn then runs again

Some rxns are branched:

Intermediates or reactants are directed into 2 or more different series of rxns

Most are reversible:

Run spontaneously towards chemical equilibrium

Rxn rate is about equal in both directions

Allows cell to change activities via control of enzymes that enable steps of reversible metabolic pathways

e.g. when cells need energy, glucose is split into 2 pyruvates via glycolysis (a 9-step

pathway)

When cells need glucose, they reverse the pathway & make glucose from pyruvate and

other molecules

If reversible pathway did not exist, cells would not be able to compensate for starvation

episodes when glucose is low

= cell death

Endergonic Reactions

Require energy

Do not occur spontaneously

(activation energy barrier is relatively high)

Usually anabolic: A + B → AB(products have higher potential energy than

reactants)

Most reactions in cells are endergonic so cells have to store energy until it is needed

e.g. biosynthesis of proteins

Exergonic Reactions

Generate energy (end with release of energy)

Usually occur spontaneously

(activation energy barrier is very low)

Usually catabolic: AB → A + B(products have lower potential energy than

reactants)

e.g. hydrolysis, cellular respiration

Coupled Reactions

Reactions that require energy are paired with reactions that release energy

e.g. sun releases energy that is needed to drive photosynthesis

More energy is released from exergonic reactions than is used in endergonic reactions

(extra energy is lost as heat)

Coupled reactions often occur in different regions of the cell

Living organisms require a mechanism for transporting energy released by exergonic

reaction to site of endergonic reaction

Energy-Carrier Molecules

Are rechargeable

Used only for short-term energy storage (unstable)

Used only within a cell(not between cells)

Most common energy-carrying molecule is ATP

ATPStores & releases chemical energy for all

life processes

Energy released during breakdown of nutrients (glucose, etc.) is captured as

ATP

ATP is coupling agent/energy carrier for most metabolic reactions

When ATP gives up P, ADP forms

Exergonic reaction = releases energy

Energy can be used in endergonic reactions

ATP reforms when ADP binds to inorganic phosphate or phosphate group from

different molecule

Endergonic reaction = requires energy

Uses energy from other exergonic reactions

ATP/ADP CYCLE

P

P P

PP

Energy via glucose

ADENOSINE

ADENOSINEenergyP

So essentially:

P energyATP ADP +

+

+

EXERGONICENDERGONIC

Some of energy at each step is lost as heat

This heat warms living bodies

Heat also provides activation energy for chemical reactions

Electron Carriers

Also transport energy within cells

Play important role in metabolism

During glucose breakdown & photosynthesis, some of energy is transferred to e-s

E- carriers transport these high-energy e-s to other parts of cell

Include NAD+ & FAD

NADHFAD

Electron Transfer Chains

Membrane-bound groups of enzymes / molecules

Accept & give up e-s in sequence

E-s enter chain at higher energy level than when they leave it

Lose energy at each descending step of chain

Oxidation-Reduction (Redox Rxns)

Stepwise electron transfers

One molecule gives up e-s = oxidizedOne molecule gains e-s = reduced

H+ atoms released simultaneously(are attracted to negative charge of e-s)

Coenzymes pick up e-s & H+ from substrates and deliver to e- transfer

chains

If glucose was broken down all at once, all of the released energy would be lost

as heat= Inefficient! Can’t be used to do work!

Redox reactions allow efficient energy release

Energy can be used to do cellular work e.g. ATP formation

MetabolismAll of the chemical reactions that occur within living

cells

Allow growth, reproduction, responsiveness, etc.

Necessary for maintenance of life

Metabolic pathways are series of linked reactions

Photosynthesis

Light energy converted into glucose

12H2O + 6CO2 6O2 + C6H12O6 + 6H2O

Glycolysis

Glucose converted into ATP

Glucose → 2 pyruvate + 2 NADH + 2 ATP

Cellular respiration (aerobic)

Glucose converted into ATP in presence of O2

Glucose + 6O2 → 6CO2 + 6H2O + 36 ATP

Fermentation

Glucose converted into ATP in absence of O2

Glucose → 2 pyruvate + 2 NADH + 2 ATP

Many interrelated chemical reactions & pathways

= cells need mechanisms to control, coordinate, & connect these reactions

1. Enzymes act to ↑ rxn rate

2. Cells couple exergonic & endergonic rxns

3. Cells make energy-carrier molecules for short-term storage & transport of energy from exergonic rxns to endergonic rxns

Reactions occur slowly

Activation energy required for reactions to occur

Rxn rate generally ↑ with ↑ heat

Body temperature not enough to meet activation energy needs of most chemical rxns

Cells use enzymes to ↓ activation energy needed

= allows rxns to occur at body temperature

Activation Energy= Minimum amount of energy required for a

reaction to run

Molecules have to collide with enough energy and in the correct orientation in order

for molecules to react

Overcomes repulsion between e- clouds of molecules so that bonds can be rearranged

Cells can control when & how fast reactions occur by controlling energy inputs into

reactions

Catalysts

Speed up rxn rates(lower the activation energy required to

run a rxn)

Are not used up

Are not permanently altered

Can be re-used

Enzymes

= biological catalysts

Bind to molecules in ways that make it more likely that bonds will break & reactants will

interact in the right way

Usually proteins

Structurally stable

Substrate-specific (based on structure)

Can be regulated

Structure of an EnzymeActive site:

Where substrate (reactant) enters enzyme

Has right shape, size, & charge environment for substrate

Allows for specificity

Substrate

The molecule upon which an enzyme acts

Substrates have some structure that is complementary to an enzyme’s active site

= allows for substrate recognition

Substrate binds with active site

Forms enzyme-substrate complex

Both change shape due to binding

Interactions between substrate & enzyme cause bonds to break and / or be formed

Products produced do not fit in active site so are released from active site

Enzyme returns to original shape & can be re-used

Induced-Fit ModelSubstrate is not exactly complementary to

active site

Enzyme molds substrate into specific shape that moves substrate to transition state

= point at which colliding reactant molecules will always go on to form products

Activation Energy

Energy required to line up reactive chemical groups, destabilize electric

charges, & break bonds

Substrate reaches a transition state where bonds break & the reaction runs

How Enzymes Work to Lower Activation Energy

Enzyme binds weakly to substrate & energy is released

Transition state is stabilized:

Enzymes & substrate are kept together so reaction can run

Other Helpful Enzymatic ThingsHelp substrates get together

Localize concentrations so that molecules can react

Position substrates so reaction is favouredBonds at active site put reactive groups close together so more directed collisions can occur

Shut out water moleculesActive sites have non-polar (hydrophobic) amino

acids that repel water so that unwanted H-bonding doesn’t occur

Controls over Enzymes

Chemical reactions must be controlled

Regulation of enzymes is 1° mechanism for controlling rxn rate

Can be regulated via:• Adjusting speed of enzyme synthesis• Maintaining, increasing, or decreasing

substance concentrations• Activating / inhibiting enzymes

• Feedback inhibition• Allosteric regulation

• Competitive inhibition

Note:

There is a point of saturation where all

active sites are bound to substrate &

reaction rate levels off

Effects of Concentration

Increased substrate concentration increases enzymatic activity

Activation of Enzymes

e.g. pepsin

Can digest any protein

Produced in non-active form

Activated only in gastric fluid (pH 1 - 2)

If activated pepsin leaked out of the stomach, would digest proteins in

tissues

Feedback InhibitionMaintains homeostasis in a cell by slowing metabolic

pathways when products begin to accumulate

Product produced as result of enzyme activity acts to reduce function of enzyme

(if you already have enough of the product, why waste energy making more?)

InhibitorsDecrease enzyme activity

Irreversible:Changes enzyme chemically so can’t be used anymore

Usually involves formation of covalent bonds

Reversible:Non-covalent bonds that do not change enzyme

Differential effects depending on what part of enzyme or enzyme-substrate complex is bound

Allosteric Regulation

A molecule binds at site other than active site

= allosteric site

Shape of enzyme is changed

Active site is hidden (inhibited) or exposed (activated)

Competitive InhibitionInhibitor has similar structure as substrate so has

affinity for active site of enzyme

Competes with substrate for access to active site

Increased concentration of substrate helps it out-compete inhibitor

Many toxins / poisons act as competitive inhibitors

Enzymatic rates depend on environmental conditions

Conditions that denature proteins will decrease or stop enzymatic activity

Enzymes are affected by:– Temperature

– pH– Salinity

– Coenzymes

Environmental Controls of Enzymes

TemperatureAs temperature , reaction rate

(increased probability of collisions between molecules)

Increase in substrate’s internal energy pushes reaction closer to activation energy

At extreme temperatures, weak bonds are broken

= alters enzyme shape (denaturation)

Substrate can’t bind to active site, so reaction rate decreases / stops

pH

Most enzymes work best at pH 6 - 8

If not at optimal pH, rxn rate may decrease / stop

Extreme pH values can cause denaturation of enzymes

Coenzymes

Organic compounds that may or may not have vitamin group

Bind to enzymes

Are necessary for enzyme function but are not part of the enzyme

itself

Are modified during the reaction but are regenerated elsewhere

NADH

Concept CheckEnzymes catalyze the many reactions in a cell. There are hundreds of different enzymes in a cell—each with a unique three-dimensional shape. Why do cells have so many different enzymes?

a. Each enzyme molecule can only be used once.

b. The shape of an enzyme’s active site generally fits a specific substrate.

c. The substrate molecules react with enzymes to create new enzymes.

d. Enzymes are randomly produced. With thousands of different shapes, one is likely to work.

Concept Check

In order to start an exergonic reaction, a certain amount of energy must be absorbed by the reactants. This is called the energy of activation. Which of the following is the normal energy of activation?

– A

– B

– C

Concept Check

Which of the following represents the energy of activation that is modified by an enzyme?

– A

– B

– C