chapter 8: energy and metabolism why do organisms need energy? how do organisms manage their energy...

Chapter 8: Energy and Metabolism

Why do organisms need energy? How do organisms manage their energy needs?

Defining terms and issues: energy and thermodynamics metabolic reactions and energy transfers

Harvesting and using energy ATP is the main energy currency in cells energy harvesting (redox reactions)

Regulating reactions: Enzymes

• Discuss energy conversions and the 1st and 2nd law of thermodynamics.

– Be sure to use the terms • work• potential energy• kinetic energy• entropy

• What are Joules (J) and calories (cal)?

Energy and Thermodynamics

energy for work: change in state or motion of matter

expressed in Joules or calories 1 kcal = 4.184 kJ

energy conversion: energy form change potential / kinetic

Energy and Thermodynamics potential energy (capacity to

do work)

Energy and Thermodynamics potential energy (capacity to

do work)

kinetic energy (energy of motion, actively performing work)

chemical bonds: potential energy

work is required for the processes of life

• Discuss energy conversions and the 1st and 2nd law of thermodynamics.

– Be sure to use the terms • work• potential energy• kinetic energy• entropy

• What are Joules (J) and calories (cal)?

Laws of thermodynamics describe the constraints on energy usage…

• The laws of thermodynamics are sometimes stated as:

– In energy conversions, “You can’t win, and you can’t break even.”

Explain.

Laws of Thermodynamics

First law: the total amount of energy (+ matter) in a

closed system remains constant

also called conservation of energy

note: the universe is a closed system

living things are open systems

note: the universe is a closed system

living things are open systems

“You can’t win.”

Laws of Thermodynamics Second law: in every energy conversion

some energy is converted to heat energy

heat energy is lost to the surroundings

heat energy cannot be used for work

energy converted to heat in the surroundings increases entropy (spreading of energy)

thus, this law can also be stated as:

Every energy conversion increases the entropy of the universe.

Laws of Thermodynamics Second law:

Upshot: no energy conversion is 100% efficient “You can’t break even.”

Just to maintain their current state, organisms must get a constant influx of energy because of energy lost in conversions

• The laws of thermodynamics are sometimes stated as:

– In energy conversions, “You can’t win, and you can’t break even.”

Explain.

• Differentiate between:

anabolism and catabolism

exergonic and endergonic reactions

Metabolism: anabolism + catabolism

metabolism divided into anabolism (anabolic reactions)

anabolic reactions are processes that build complex molecules from simpler ones

Metabolism: anabolism + catabolism

metabolism divided into anabolism (anabolic reactions)

anabolic reactions are processes that build complex molecules from simpler ones

catabolism (catabolic reactions)

catabolic reactions are processes the break down complex molecules into simpler ones

• Differentiate between:

anabolism and catabolism

exergonic and endergonic reactions

Chemical Reactions and Free Energy

Chemical reactions involve changes in chemical bonds

changes in substance concentrations

changes in free energy free energy = energy available to do work in a

chemical reaction (such as: create a chemical bond)

free energy changes depend on bond energies and concentrations of reactants and products

bond energy = energy required to break a bond; value depends on the bond

left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and products is correct

forward and reverse reaction rates are equal; concentrations remain constant

left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and products is correct

forward and reverse reaction rates are equal; concentrations remain constant

cells manipulate relative concentrations in many ways so that equilibrium is rare

Chemical Reactions and Free Energy exergonic reactions – the products have less free

energy than reactants

the difference in energy is released and is available to do work

Chemical Reactions and Free Energy exergonic reactions – the products have less free

energy than reactants

the difference in energy is released and is available to do work

exergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on activation energy later)

catabolic reactions are usually exergonic

ATP + H2O ADP + Pi is highly exergonic

Chemical Reactions and Free Energy endergonic reactions – the products have

more free energy than the reactants

the difference in free energy must be supplied (stored in chemical bonds)

Chemical Reactions and Free Energy endergonic reactions – the products have

more free energy than the reactants

the difference in free energy must be supplied (stored in chemical bonds)

endergonic reactions are not thermodynamically favored, so they are not spontaneous

How to get energy for an endergonic reaction?

couple with an exergonic one!

together, the coupled reactions must have a net exergonic nature

reaction coupling requires that the reactions share a common intermediate(s)

EXAMPLE:

A B (exergonic)

C D (endergonic)

EXAMPLE:

A B (exergonic)

C D (endergonic)

Coupled: A + C B + D (overall exergonic)

EXAMPLE:

A B (exergonic)

C D (endergonic)

Actually: A + C I B + D

EXAMPLE:

A B (exergonic)

C D (endergonic)

Actually: A + C I B + D typically, the exergonic reaction in the couple is

ATP + H2O ADP + Pi

anabolic reactions are usually endergonic

EXAMPLE:

A B (exergonic)

C D (endergonic)

Actually: A + C I B + D typically, the exergonic reaction in the couple is

ATP + H2O ADP + Pi

anabolic reactions are usually endergonic

This will be explored in more detail in an example in a bit, but first some more about ATP…

Why is ATP so darned important?

What is a phosphorylated intermediate?

How much ATP is in a cell at any given time?

Why must cells keep a high ATP/ADP ratio?

ATP is the main energy currency in cells

One way that organisms manage their energy needs is to use ATP as a ready energy source for many reactions.

ATP – nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groups

last two phosphate groups are joined to the chain by unstable bonds; breaking these bonds is relatively easy and releases energy; thus:

hydrolysis of ATP to ADP and inorganic phosphate (Pi) releases energy

ATP + H2O ADP + Pi

hydrolysis of ATP to ADP and inorganic phosphate (Pi) releases energy

ATP + H2O ADP + Pi

the amount of energy released

depends in part on concentrations of reactants and products

is generally ~30 kJ/mol

Intermediates when ATP hydrolysis is coupled to a reaction to provide energy

often phosphorylated compounds

glucose glucose-6-phosphate

the inorganic phosphate is transferred onto another compound rather than being immediately released

a phosphorylated compound is in a higher energy state

EXAMPLE of a coupled reaction:

glucose + fructose sucrose + H2O (endergonic; requires ~27 kJ/mol)

ATP + H2O ADP + Pi (exergonic; provides ~30 kJ/mol)

coupled:

glucose + fructose + ATP + H2O sucrose + H2O + ADP + Pi

simplified:

glucose + fructose + ATP sucrose +ADP + Pi

with intermediates:

glucose + fructose + ATP + H2O glucose-P + fructose + ADP sucrose + H2O + ADP + Pi (net exergonic, releases ~3 kJ/mol)

coupled:

simplified:

coupled:

simplified:

with intermediates:

glucose + fructose + ATP + H2O glucose-P + fructose + ADP sucrose + H2O + ADP + Pi (net exergonic, releases ~3 kJ/mol)

Thus, energy transfer in cellular reactions is often accomplished through transfer of a phosphate group from ATP

Making ATP involves an endergonic condensation reaction

reverse of an exergonic reaction is always endergonic

ADP + Pi ATP + H2O

endergonic, usually requires more than ~30 kJ/mol

ADP + Pi ATP + H2O

endergonic, usually requires more than ~30 kJ/mol

must be coupled with an exergonic reaction; typically from a catabolic pathway (more on that later)

Overall, ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolism

Cells maintain high levels of ATP relative to ADP

maximizes energy available from hydrolysis of ATP

Cells maintain high levels of ATP relative to ADP

maximizes energy available from hydrolysis of ATP

ratio typically greater than 10 ATP: 1 ADP

Overall concentration of ATP still very low

supply typically only enough for a few seconds at best

instability prevents stockpiling

must be constantly produced

in a typical cell, the rate of use and production of ATP is about 10 million molecules per second

resting human has less than 1 g of ATP at any given time but uses about 45 kg per day

Why is ATP so darned important?

What is a phosphorylated intermediate?

How much ATP is in a cell at any given time?

Why must cells keep a high ATP/ADP ratio?

• What are redox reactions used for in cells?

• How (generally) can you tell which of two similar compounds is reduced and which is oxidized?

• Give some examples of compounds commonly used in redox reactions in cells.

Redox reactions are also used for energy transfer

Redox reactions are used to harvest energy from some chemicals.

The acceptors of that energy typically cannot be used directly as energy currency.

Electrons can also be used for energy transfer

Redox reactions: recall reduction, gain electrons; oxidation, lose electrons; both occur simultaneously in cells (generally no free electrons in cells)

Typically, the oxidized substance gives up energy with the electron, the reduced substance gains energy with the electron

08.04 Redox ReactionsSlide number: 6

Loss of electron (oxidation)

Gain of electron (reduction)

Low energyHigh energy

chain of redox reactions / electron transfers common

more on electron transport chains later

each electron transfer releases free energy

free energy can be used for other chemical reactions

each electron transfer releases free energy

free energy can be used for other chemical reactions

proton often removed as well

if so, equivalent of a hydrogen atom is transferred

Catabolism typically involves:

removal of hydrogen atoms from nutrients

(such as carbohydrates)

transfer of the protons and electrons to

intermediate electron acceptors

intermediate acceptor example: nicotinamide adenine dinucleotide (NAD+)

Use XH2 to represent a nutrient molecule:

XH2 + NAD+ X + NADH + H+

Use XH2 to represent a nutrient molecule:

XH2 + NAD+ X + NADH + H+

Often, the reduced form is just called NADH

Reduced state stores energy, which is partially released as free energy when NADH is oxidized

The free energy usually winds up being used to make ATP

Other commonly used acceptors are NADP+, FAD, and cytochromes

NADP+/NADPH – important in photosynthesis

FAD/FADH2 – flavin adenine dinucleotide

Cytochromes – small iron-containing proteins; iron serves as electron acceptor

• What are redox reactions used for in cells?

• How (generally) can you tell which of two similar compounds is reduced and which is oxidized?

• Give some examples of compounds commonly used in redox reactions in cells.

• What do enzymes do for cells, and how do they do it?

– Be sure to use the following terms:

• catalyst (or catalyze)

• activation energy

• enzyme-substrate complex

• active site

• induced fit

Enzymes

Manipulation of reactions is essential to and largely defining of life.

Enzymes

Organisms use enzymes to manipulate the speed of reactions.

Enzymes

Organisms use enzymes to manipulate the speed of reactions.

Understanding life requires understanding how enzymes work.

EnzymesEnzymes regulate chemical reactions in living organisms

An enzyme is an organic molecule (typically a protein) that acts as a catalyst

catalyst –increases the rate of a chemical reaction without being consumed in the reaction (the catalyst recycles back to its original state)

enzymes (catalysts) only alter reaction rate; thermodynamics still governs whether the reaction can occur

Fig. 8.9 (TEArt)

The substrate,sucrose, consistsof glucose andfructose bondedtogether.

The substratebinds to theenzyme, formingan enzyme-substratecomplex.

The binding ofthe substrateand enzymeplaces stress onthe glucose-fructose bond,and the bondbreaks.

Products arereleased, andthe enzyme isfree to bindothersubstrates.

Enzyme

Active site

Glucose Fructose

08.09 Enzyme Catalytic CycleSlide number: 2

1 The substrate, sucrose, consistsof glucose and fructose bonded together.

Enzyme

Active site

Enzyme

Active site

Enzyme

Active site

The substrate binds to the enzyme, forming an enzyme-substrate complex.

Enzyme

Active site

The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks.

Enzyme

Active site

The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks.

Glucose Fructose

Products are released, and the enzyme is free to bind other substrates.

Enzymes work by lowering activation energy of a reaction

all reactions have a required energy of activation

energy required to break existing bonds and bring reactants together

must be supplied in some way before the reaction can proceed

Enzymes activation energy

catalysts greatly reduce the activation energy requirement, making it easier for a reaction to occur

Enzymes Enzymes lower activation energy by forming a complex with the

substrate(s)

the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzyme

substrate(s)

the site where the substrate(s) binds to the enzyme is called the active site

substrate(s)

the site where the substrate(s) binds to the enzyme is called the active site

when the enzyme-substrate complex forms, there are typically shape changes in the enzyme and substrate(s) – called induced fit

Enzymes ES complex typically very unstable

short-lived

breaks down into released product(s) and a free enzyme that is ready to be reused

short-lived

breaks down into released product(s) and a free enzyme that is ready to be reused

overall: enzyme + substrate(s) ES complex enzyme + product(s)

• What do enzymes do for cells, and how do they do it?

– Be sure to use the following terms:

• catalyst (or catalyze)

• activation energy

• enzyme-substrate complex

• active site

• induced fit

• What are the four main things that enzymes do to lower activation energy?

Enzymes reduction in activation energy is due primarily to four things:

an enzyme holds reactants (substrates) close together in the right orientation for the reaction, which reduces the reliance on random collisions

an enzyme may put a “strain” on existing bonds, making them easier to break

an enzyme provides a “microenvironment” that is more chemically suited to the reaction

sometimes the active site of the enzyme itself is directly involved in the reaction during the transition states

Enzymes enzyme + substrate(s) ES complex enzyme + product(s)

• What are the four main things that enzymes do to lower activation energy?

• How are enzymes named (what suffixes indicate an enzyme)?

Enzymes Enzyme names

many names give some indication of substrate

most enzyme names end in –ase (example: sucrase)

some end in –zyme (example: lysozyme)

some traditional names are less indicative of enzyme function (examples: pepsin, trypsin)

Enzymes

Enzymes are generally highly specific

overall shape as well as spatial arrangements in the active site limit what enzyme-substrate complexes can readily form

Enzymes

the amount of specificity depends on the particular enzyme

example of high specificity: sucrase splits sucrose, not other disaccharides

Enzymes

the amount of specificity depends on the particular enzyme

example of high specificity: sucrase splits sucrose, not other disaccharides

example of low specificity: lipase splits variety of fatty acids from glycerol

Enzymes

enzymes are classified by the kind of reaction they catalyze

The International Union of Biochemistry and Molecular Biology has developed a nomenclature for enzymes; the top-level classification is

Oxidoreductases: catalyze oxidation/reduction reactions Transferases: transfer a functional group (e.g. a methyl or phosphate

group) Hydrolases: catalyze the hydrolysis of various bonds Lyases: cleave various bonds by means other than hydrolysis and

oxidation Isomerases: catalyze isomerization changes within a single molecule Ligases: join two molecules with covalent bonds

The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/enzyme/

• How are enzymes named (what suffixes indicate an enzyme)?

• Explain the terms cofactor, apoenzyme, and coenzyme.

Enzymes Many enzymes require additional chemical

components (cofactors) to function

apoenzyme + cofactor active enzyme (bound together)

alone, an apoenzyme or a cofactor has little if any catalytic activity

cofactors may or may not be changed by the reaction

Enzymes cofactors can be organic or inorganic

organic examples (coenzymes):

ADP, NAD+, NADP+, FAD

typically changed by the catalyzed reaction

inorganic examples:

metal ions like Ca2+, Mg2+, Fe3+, etc.

typically not changed by the catalyzed reaction

inorganic examples:

metal ions like Ca2+, Mg2+, Fe3+, etc.

typically not changed by the catalyzed reaction

most vitamins are coenzymes or part of coenzymes, or are used for making coenzymes

Fig. 8.3 (TEArt)

Product

Energy-rich molecule

1. Enzymes that harvesthydrogen atoms have abinding site for NAD+

located near anotherbinding site. NAD+ andan energy-richmolecule bind tothe enzyme.

3. NADH thendiffuses away andis available toother molecules.

2. In an oxidation-reduction reaction,a hydrogen atomis transferred toNAD+, formingNADH.

Enzyme

NAD+NAD+

Fig. 8.A

• Explain the terms cofactor, apoenzyme, and coenzyme.

• Discuss the effects of temperature and pH on enzyme activity.

Enzymes are most active under optimal conditions

each enzyme has an optimal temperature

most effective as a catalyst at the optimal temperature

rate of drop-off in effectiveness away from optimal temperature depends on the enzyme

high temperatures tend to denature enzymes

human enzymes have temperature optima near human body temperature (37°C)

each enzyme has an optimal pH

again, most effective at the optimum; drop-off varies

extremes of pH tend to denature enzymes

a particular organism shows more variety in enzyme pH optima than in temperature optima, but most of its enzymes will still be optimal at the pH normally found in the cytosol of its cells

• Discuss the effects of temperature and pH on enzyme activity.

• What is a metabolic pathway?

Enzymes Metabolic pathways use organized “teams” of

enzymes

the products of one reaction often serve as substrates for the next reaction

enzymes

removing products (by having them participate the “next reaction”) improves reaction rate (avoids equilibrium)

enzymes

removing products (by having them participate the “next reaction”) improves reaction rate (avoids equilibrium)

multiple metabolic pathways exit in cells, overlapping in some areas and diverging in others

Fig. 8.15

• What is a metabolic pathway?

• How do cells regulate enzyme activity?

– Include the terms:• inhibitors• activators• allosteric site• feedback inhibition

• Also, differentiate between:– irreversible and reversible inhibition– competitive and noncompetitive inhibition

Enzymes

Cells can regulate enzyme activity to control reactions

increase substrate amount increase reaction rate (up to saturation of available enzyme molecules)

Enzymes

increase enzyme amount increase reaction rate (as long as substrate amount > enzyme amount)

Enzymes

increase enzyme amount increase reaction rate (as long as substrate amount > enzyme amount)

compartmentation of the enzyme, substrate, and products can help control reaction rate

Enzyme concentration

Substrate concentration

When substrate concentration >> enzyme concentration….

inhibitors and activators of enzymes

activators allow or enhance catalytic activity

inhibitors reduce or eliminate catalytic activity

sometime, this uses an allosteric site – a receptor site on an enzyme where an inhibitor or activator can bind

a common example of allosteric control is feedback inhibition

the last product in a metabolic pathway binds to an allosteric site of an enzyme in an early step of the pathway (often the first)

this product inhibits activity of the enzyme

Enzyme #1(Threoninedeaminase)

Enzyme #2

Enzyme #3

Enzyme #4

Enzyme #5

Threonine

Isoleucine

-Keto-b-methylvalerate

,b-Dihydroxy-b-methylvalerate

-Aceto--hydroxybutyrate

-Ketobutyrate

Feedback inhibition

(Isoleucine inhibitsenzyme #1)

Fig. 9.20

irreversible inhibition – enzyme is permanently inactivated or destroyed; includes many drugs and toxins

reversible inhibition – if inhibitor is removed, the enzyme activity can be recovered

reversible inhibition – if inhibitor is removed, the enzyme activity can be recovered competitive inhibition –

inhibitor is similar in structure to a substrate; competes with substrate for binding to the active site

reversible inhibition – if inhibitor is removed, the enzyme activity can be recovered competitive inhibition –

inhibitor is similar in structure to a substrate; competes with substrate for binding to the active site

noncompetitive inhibition – binds at allosteric site, alters enzyme shape to make active site unavailable

• How do cells regulate enzyme activity?

– Include the terms:• inhibitors• activators• allosteric site• feedback inhibition

• Also, differentiate between:– irreversible and reversible inhibition– competitive and noncompetitive inhibition

chapter 8: energy and metabolism why do organisms need energy? how do organisms manage their energy...

thermodynamics energy

energy matter

cells energy

energy atp

energy conversions

energy needs

potential energy work

redox reactions energy

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