Cell & Energetics

Metabolism◦ totality of an organism’s chemical reactions◦ arises from interactions between molecules

within the cell

Catabolic pathways ◦ release energy ◦ break down complex molecules into simpler compounds

Anabolic pathways ◦ consume energy ◦ build complex molecules from simpler ones

ThermodynamicsFirst Law Second Law

the energy of the universe is constant

Energy can be transferred and transformed

Energy cannot be created or destroyed

principle of conservation of energy

During every energy transfer or transformation, some energy is unusable, often lost as heat

LE 8-3

Chemical energy

Heat CO2

First law of thermodynamics Second law of thermodynamics

H2O

exergonic reaction ◦ net release of free energy◦ is spontaneous◦ exothermic

endergonic reaction◦ absorbs free energy from its surroundings◦ is nonspontaneous◦ endothermic

Types of Reactions

A cell does three main kinds of work:◦ Mechanical◦ Transport◦ Chemical

Cell energy management◦ energy coupling

the use of an exergonic process to drive an endergonic one

ATP (adenosine triphosphate)

LE 8-8

Phosphate groups

Ribose

Adenine

ATP

Adenosine triphosphate (ATP)

Energy

P P P

PPP i

Adenosine diphosphate (ADP)Inorganic phosphate

H2O

+ +

ATP hydrolysis◦ Exergonic◦ the energy can be used to drive an endergonic reaction

LE 8-11

NH2

Glu

P i

P i

P i

P i

Glu NH3

P

P

P

ATPADP

Motor protein

Mechanical work: ATP phosphorylates motor proteins

Protein moved

Membraneprotein

Solute

Transport work: ATP phosphorylates transport proteins

Solute transported

Chemical work: ATP phosphorylates key reactants

Reactants: Glutamic acidand ammonia

Product (glutamine)made

+ +

+

Regeneration of ATP

Pi

ADP

Energy for cellular work(endergonic, energy-consuming processes)

Energy from catabolism(energonic, energy-yielding processes)

ATP

+

Enzymes

Catalytic proteins Usually end in –ase

◦ Ex. Sucrase Hydrolyzes sucrose

Enzymes

SucroseC12H22O11

GlucoseC6H12O6

FructoseC6H12O6

How Enzymes Work

Substrate◦ The reactant that an enzyme acts on

Enzyme binds to its substrate◦ enzyme-substrate complex

Active site ◦ The region on the enzyme where the substrate binds

Substrate Specificity of Enzymes

Substrate

Active site

Enzyme Enzyme-substratecomplex

The active site can lower an EA barrier by:◦ Orienting substrates correctly◦ Straining substrate bonds◦ Providing a favorable microenvironment◦ Covalently bonding to the substrate

Enzyme-substratecomplex

Substrates

Enzyme

Products

Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).

Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.

Active site (and R groups ofits amino acids) can lower EA

and speed up a reaction by• acting as a template for substrate orientation,• stressing the substrates and stabilizing the transition state,• providing a favorable microenvironment,• participating directly in the catalytic reaction.

Substrates areconverted intoproducts.

Products arereleased.

Activesite is

availablefor two new

substratemolecules.

An enzyme’s activity can be affected by:◦ Environmental factors

Temperature pH

◦ Chemicals

Rate of reaction can also be affected by:◦ Amount of enzymes present◦ Concentration of substrate◦ Presence of cofactors/coenzymes◦ Presence of enzyme inhibitors

Factors Affecting Enzyme Function

LE 8-18

Optimal temperature fortypical human enzyme

Optimal temperature forenzyme of thermophilic (heat-tolerant bacteria)

Temperature (°C)

Optimal temperature for two enzymes

0 20 40 60 80 100

Rate

of

reacti

on

Optimal pH for pepsin(stomach enzyme)

Optimal pHfor trypsin(intestinalenzyme)

pH

Optimal pH for two enzymes

0

Rate

of

reacti

on

1 2 3 4 5 6 7 8 9 10

Enzyme Inhibitors◦ Competitive inhibitors

bind to the active site of an enzyme

competing with the substrate

◦ Noncompetitive inhibitors bind to another part of an

enzyme Cause the enzyme to

change shape make the active site less

effective

LE 8-19Substrate

Active site

Enzyme

Competitiveinhibitor

Normal binding

Competitive inhibition

Noncompetitive inhibitor

Noncompetitive inhibition

A substrate canbind normally to the

active site of anenzyme.

A competitiveinhibitor mimics the

substrate, competingfor the active site.

A noncompetitiveinhibitor binds to the

enzyme away from theactive site, altering the

conformation of theenzyme so that its

active site no longerfunctions.

Genes◦ Specific genes coding for specific enzymes are

“turned on” or “turned off”

Allosteric regulation◦ protein’s function at one site is affected by binding of a

regulatory molecule at another site may either inhibit or stimulate an enzyme’s activity

Enzyme Regulation

allosterically regulated enzymes ◦ Usually polypeptide

subunits◦ has active and

inactive forms◦ binding of an activator

stabilizes the active form of the enzyme

◦ binding of an inhibitor stabilizes the inactive form of the enzyme

Allosteric Activation and Inhibition

Allosteric enzymewith four subunits

Regulatorysite (oneof four) Active form

Activator

Stabilized active form

Active site(one of four)

Allosteric activatorstabilizes active form.

Non-functionalactive site

Inactive formInhibitor

Stabilized inactive form

Allosteric inhibitorstabilizes inactive form.

Oscillation

Allosteric activators and inhibitors

• form of allosteric regulation • can amplify enzyme activity• binding by a substrate to one active site

stabilizes favorable conformational changes at all other subunits

Cooperativity

LE 8-20b

Substrate

Binding of one substrate molecule toactive site of one subunit locks allsubunits in active conformation.

Cooperativity another type of allosteric activation

Stabilized active formInactive form

the end product of a metabolic pathway shuts down the pathway◦ prevents a cell from

wasting chemical resources by synthesizing more product than is needed

FeedbackInhibition

Active siteavailable

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threoninedeaminase)

Enzyme 2

Intermediate A

Isoleucineused up bycell

Feedbackinhibition Active site of

enzyme 1 can’tbindtheoninepathway off

Isoleucinebinds toallostericsite

Enzyme 3

Intermediate B

Enzyme 4

Intermediate C

Enzyme 5

Intermediate D

End product(isoleucine)

Energy Release

LE 9-2

ECOSYSTEM

Lightenergy

Photosynthesisin chloroplasts

Cellular respirationin mitochondria

Organicmolecules

+ O2CO2 + H2O

ATP

powers most cellular work

Heatenergy

oxidation-reduction reactions◦ Aka. redox reactions◦ Chemical reactions that transfer electrons between

reactants • Oxidation• a substance loses electrons• is oxidized

Reduction substance gains electrons is reduced (the amount of positive charge is reduced)

Oxidation and Reduction

Xe- + Y X + Ye-

becomes oxidized(loses electron)

becomes reduced(gains electron)

Cellular respiration◦ fuel (such as glucose) is oxidized ◦ oxygen is reduced

C6H12O6 + 6O2 6CO2 + 6H2O + Energy

becomes oxidized

becomes reduced

3 stages:◦Glycolysis

breaks down glucose into two molecules of pyruvate

◦The citric acid cycle completes the breakdown of glucose

◦Oxidative phosphorylation accounts for most of the ATP synthesis it is powered by redox reactions

Cellular Respiration

LE 9-6_1

Mitochondrion

Glycolysis

PyruvateGlucose

Cytosol

ATP

Substrate-levelphosphorylation

LE 9-6_2

Mitochondrion

Glycolysis

PyruvateGlucose

Cytosol

ATP

Substrate-levelphosphorylation

ATP

Substrate-levelphosphorylation

Citricacidcycle

LE 9-6_3

Mitochondrion

Glycolysis

PyruvateGlucose

Cytosol

ATP

Substrate-levelphosphorylation

ATP

Substrate-levelphosphorylation

Citricacidcycle

ATP

Oxidativephosphorylation

Oxidativephosphorylation:

electron transportand

chemiosmosis

Electronscarried

via NADH

Electrons carriedvia NADH and

FADH2

“splitting of sugar”◦ breaks down glucose◦ Produces two molecules of pyruvate◦ occurs in the cytoplasm ◦ 2 major phases:

Energy investment phase Energy payoff phase

Glycolysis

Glycolysis

LE 9-8

Energy investment phase

Glucose

2 ATP used2 ADP + 2 P

4 ADP + 4 P 4 ATP formed

2 NAD+ + 4 e– + 4 H+

Energy payoff phase

+ 2 H+2 NADH

2 Pyruvate + 2 H2O

2 Pyruvate + 2 H2O

2 ATP

2 NADH + 2 H+

Glucose

4 ATP formed – 2 ATP used

2 NAD+ + 4 e– + 4 H+

Net

Glycolysis Citricacidcycle

Oxidativephosphorylation

ATPATPATP

• citric acid cycle (Krebs Cycle)• 8 steps:• 1st step• The acetyl group of acetyl CoA joins the cycle by combining with

oxaloacetate, forming citrate• next seven steps • decompose the citrate back to oxaloacetate

• NADH and FADH2 produced by the cycle relay electrons extracted from food to the electron transport chain• which powers ATP synthesis via oxidative

phosphorylation

Located in the cristae of the mitochondrion Most of the chain’s components are proteins

◦ exist in multiprotein complexes Carriers alternate reduced and oxidized states Electrons drop in free energy as they go down the

chain ◦ Are finally passed to O2, forming water

generates no ATP

Function:◦ to break the large free-energy drop from food to O2 into

smaller steps that release energy in manageable amounts

Electron Transport Chain

Chemiosmosis ◦ the use of energy in a H+ gradient to drive cellular work

Example: Electron transfer in the electron transport chain causes proteins to

pump H+ from the mitochondrial matrix to the intermembrane space H+ then moves back across the membrane, passing through channels

in ATP synthase ATP synthase uses the exergonic flow of H+ to drive phosphorylation

of ATP

During cellular respiration, most energy flows in this sequence:◦ glucose NADH electron transport chain

proton-motive force ATP

About 40% of the energy in a glucose molecule is transferred to ATP during cellular respiration◦ making about 38 ATP

consists of glycolysis plus reactions that regenerate NAD+

◦ Two common types: alcohol fermentation lactic acid fermentation

Fermentation

Fermentation

alcohol fermentation◦ pyruvate is converted to ethanol in two steps

the first releasing CO2

◦ Ex. Yeast - brewing, winemaking, and baking

lactic acid fermentation◦ pyruvate is reduced to NADH◦ forming lactate as an end product◦ no release of CO2

◦ Ex. some fungi and bacteria is used to make cheese and yogurt

◦ Ex. Human muscle cells - generate ATP when O2 is scarce

Photosynthesis

Photosynthesis◦ Converts solar energy into chemical energy◦ Occurs in plants, algae, and some prokaryotes

Autotrophs◦ Sustain self without eating things derived from

other organisms

◦ Photoautotrophs Ex. Most plants Use solar energy to make organic molecules from

water and carbon dioxide (PHOTOSYNTHESIS)

LE 10-2

Plants

Unicellular protist

Multicellular algae Cyanobacteria

Purple sulfurbacteria

10 µm

1.5 µm

40 µm

Photosynthesis in plants◦ Primarily in leaves◦ Chlorophyll

green pigment in chloroplasts Absorbs light energy

◦ Stomata microscopic pores on leaf surface

CO2 enters

O2 exits

Chloroplasts ◦ found mainly in cells of the mesophyll

interior tissue of the leaf typical mesophyll cell = 30-40 chloroplasts

◦ Thylakoids membranes containing chlorophyll Grana = stacks of thylakoid membranes Convert solar energy into ATP and NADPH (chemical

energy)

◦ Stroma dense fluid Surrounds thylakoid

LE 10-3

Leaf cross sectionVein

Mesophyll

Stomata CO2O2

Mesophyll cellChloroplast

5 µm

Outermembrane

Intermembranespace

Innermembrane

Thylakoidspace

Thylakoid

GranumStroma

1 µm

6 CO2 + 12 H2O + Light energy C6H12O6 + 6 O2 + 6 H2 O

Photosynthesis

LE 10-4

Reactants:

Products:

6 CO2 12 H2O

C6H12O6 6 H2O 6 O2

redox process ◦ water is oxidized ◦ carbon dioxide is reduced

light reactions (the photo part) ◦ In thylakoids ◦ split water ◦ release O2 ◦ produce ATP◦ form NADPH

Calvin cycle (the synthesis part)◦ In stroma ◦ forms sugar from CO2, using ATP and NADPH◦ begins with carbon fixation

incorporating CO2 into organic molecules

Photosynthesis

LE 10-5_1

H2O

LIGHTREACTIONS

Chloroplast

Light

LE 10-5_2

H2O

LIGHTREACTIONS

Chloroplast

Light

ATP

NADPH

O2

LE 10-5_3

H2O

LIGHTREACTIONS

Chloroplast

Light

ATP

NADPH

O2

NADP+

CO2

ADPP+ i

CALVINCYCLE

[CH2O](sugar)

Pigments ◦ substances that absorb visible light◦ pigments absorb specific wavelengths◦ Wavelengths that are not absorbed are reflected

or transmitted

Ex. chlorophyll ◦ reflects and transmits green light◦ Causes leaves to appear green

Absorption SpectrumChlorophyll a

Chlorophyll b

Carotenoids

Wavelength of light (nm)

Absorption spectra

Ab

sorp

tion

of

lig

ht

by

ch

loro

pla

st

pig

men

ts

400 500 600 700

Chlorophyll a ◦ main photosynthetic pigment

Accessory pigments◦ Ex. chlorophyll b

broaden the spectrum used for photosynthesis◦ Ex. carotenoids

absorb excessive light that would damage chlorophyll

photosystems ◦ consists of a reaction center surrounded by light-

harvesting complexes◦ light-harvesting complexes

pigment molecules bound to proteins funnel the energy of photons to the reaction center

• primary electron acceptor in reaction center accepts an excited electron from chlorophyll a 1st step of light reactions

Solar-powered transfer of an electron from a chlorophyll a molecule to the primary electron acceptor

LE 10-12

Thylakoid

Photon

Light-harvestingcomplexes

Photosystem

Reactioncenter

STROMA

Primary electronacceptor

e–

Transferof energy

Specialchlorophyll amolecules

Pigmentmolecules

THYLAKOID SPACE(INTERIOR OF THYLAKOID)

Th

yla

koid

mem

bra

ne

• 2 types of photosystems in thylakoid membrane• Photosystem II • functions first (the numbers reflect order of discovery) • best at absorbing a wavelength of 680 nm

• Photosystem I • best at absorbing a wavelength of 700 nm

• Photosystems II and I work together • use light energy • generate ATP and NADPH

light reactions ◦ Two routes for electron flow: cyclic and noncyclic

Noncyclic electron flow the primary pathway, involves both photosystems produces ATP and NADPH

Electron Flow

LE 10-13_5

LightP680

e–

Photosystem II(PS II)

Primaryacceptor

[CH2O] (sugar)

NADPH

ATP

ADPCALVINCYCLE

LIGHTREACTIONS

NADP+

Light

H2O CO2En

erg

y o

f ele

ctr

on

s

O2

e–

e–

+2 H+

H2O

O21/2

Pq

Cytochromecomplex

Electron transport chain

Pc

ATP

P700

e–

Primaryacceptor

Photosystem I(PS I)

e–e–

Electron

Transportchain

NADP+

reductase

Fd

NADP+

NADPH

+ H+

+ 2 H+

Light

LE 10-14

ATP

Photosystem II

e–

e–

e–e–

Millmakes

ATP

e–

e–

e–

Ph

oto

n

Photosystem I

Ph

oto

n

NADPH

• Cyclic electron flow • uses only photosystem I • produces only ATP

generates surplus ATP satisfying the higher demand in the Calvin cycle

Electron Flow

LE 10-15

Photosystem I

Photosystem II ATP

Pc

Fd

Cytochromecomplex

Pq

Primaryacceptor

Fd

NADP+

reductase

NADP+

NADPH

Primaryacceptor

Water is split by photosystem II on the side of the membrane facing the thylakoid space

The diffusion of H+ from the thylakoid space back to the stroma powers ATP synthase

ATP and NADPH are produced on the side facing the stroma, where the Calvin cycle takes place

Animation: Calvin Cycle

regenerates its starting material after molecules enter and leave the cycle

builds sugar from smaller molecules by using ATP and the reducing power of electrons carried by NADPH

Carbon enters the cycle as CO2 and leaves as a sugar named glyceraldehyde-3-phospate (G3P)◦ For net synthesis of one G3P, the cycle must take

place three times, fixing three molecules of CO2

The Calvin Cycle

The Calvin cycle has three phases:◦ Carbon fixation (catalyzed by rubisco)◦ Reduction◦ Regeneration of the CO2 acceptor (RuBP)

Play

Dehydration ◦ Hot & Dry conditions◦ plants close stomata◦ conserves water◦ but limits photosynthesis

reduces access to CO2

O2 to build up photorespiration

Problems Plants Face

• C3 plants• Most plants• initial fixation of CO2, via rubisco, forms a three-

carbon compound

• Photorespiration• rubisco adds O2 to the Calvin cycle instead of CO2

consumes O2 and organic fuel and releases CO2 without producing ATP or sugar

is a problem for many plants on a hot, dry days it can drain as much as 50% of the

carbon fixed by the Calvin cycle

C4 plants ◦ minimize the cost of photorespiration by

incorporating CO2 into four-carbon compounds in mesophyll cells Compounds are exported to bundle-sheath cells they release CO2 that is then used in the Calvin cycle

CAM plants ◦ open their stomata at night

incorporate CO2 into organic acids

◦ Stomata close during the day CO2 released from organic acids and is used in the

Calvin cycle

LE 10-20

Bundle-sheathcell

Mesophyllcell Organic acid

C4

CO2

CO2

CALVINCYCLE

Sugarcane Pineapple

Organic acidsrelease CO2 toCalvin cycle

CO2 incorporatedinto four-carbonorganic acids(carbon fixation)

Organic acid

CAMCO2

CO2

CALVINCYCLE

Sugar

Spatial separation of steps Temporal separation of steps

Sugar

Day

Night

energy ◦ enters chloroplasts as sunlight ◦ gets stored as chemical energy in organic

compounds sugar

◦ made in the chloroplasts ◦ supplies chemical energy ◦ creates carbon skeletons to synthesize the

organic molecules of cells oxygen in our atmosphere

Photosynthesis Review

LE 10-21

Light

CO2H2O

Light reactions Calvin cycle

NADP+

RuBP

G3PATP

Photosystem IIElectron transport

chainPhotosystem I

O2

Chloroplast

NADPH

ADP+ P i

3-Phosphoglycerate

Starch(storage)

Amino acidsFatty acids

Sucrose (export)