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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

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slide2

Metabolism

    • totality of an organism’s chemical reactions
    • arises from interactions between molecules within the cell
slide3

Catabolic pathways

    • release energy
    • break down complex molecules into simpler compounds
  • Anabolic pathways
    • consume energy
    • build complex molecules from simpler ones
thermodynamics
Thermodynamics
  • 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

First Law

Second Law

slide5

LE 8-3

CO2

Heat

Chemical

energy

H2O

First law of thermodynamics

Second law of thermodynamics

types of reactions
Types of Reactions
  • exergonic reaction
    • net release of free energy
    • is spontaneous
    • exothermic
  • endergonic reaction
    • absorbs free energy from its surroundings
    • is nonspontaneous
    • endothermic
slide7

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

ATP (adenosine triphosphate)

Adenine

Phosphate groups

Ribose

slide9
ATP

P

P

P

Adenosine triphosphate (ATP)

H2O

+

P

P

P

+

Energy

i

Adenosine diphosphate (ADP)

Inorganic phosphate

slide10

ATP hydrolysis

    • Exergonic
    • the energy can be used to drive an endergonic reaction
slide11

LE 8-11

P

i

P

Protein moved

Motor protein

Mechanical work: ATP phosphorylates motor proteins

Membrane

protein

ADP

ATP

+

P

i

P

P

i

Solute transported

Solute

Transport work: ATP phosphorylates transport proteins

P

NH2

NH3

P

+

+

Glu

i

Glu

Reactants: Glutamic acid

and ammonia

Product (glutamine)

made

Chemical work: ATP phosphorylates key reactants

regeneration of atp
Regeneration of ATP

ATP

Energy for cellular work

(endergonic, energy-

consuming processes)

Energy from catabolism

(energonic, energy-

yielding processes)

P

ADP

+

i

enzymes1
Enzymes
  • Catalytic proteins
  • Usually end in –ase
    • Ex. Sucrase
      • Hydrolyzes sucrose

Sucrose

C12H22O11

Glucose

C6H12O6

Fructose

C6H12O6

How Enzymes Work

substrate specificity of enzymes
Substrate Specificity of Enzymes
  • 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
slide16

Substrate

Active site

Enzyme-substrate

complex

Enzyme

slide17

The active site can lower an EA barrier by:

    • Orienting substrates correctly
    • Straining substrate bonds
    • Providing a favorable microenvironment
    • Covalently bonding to the substrate
slide18

Substrates enter active site; enzyme

changes shape so its active site

embraces the substrates (induced fit).

Substrates held in

active site by weak

interactions, such as

hydrogen bonds and

ionic bonds.

  • Active site (and R groups of
  • its 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

Enzyme-substrate

complex

Active

site is

available

for two new

substrate

molecules.

Enzyme

Products are

released.

Substrates are

converted into

products.

Products

factors affecting enzyme function
Factors Affecting Enzyme Function
  • 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
slide20

LE 8-18

Optimal temperature for

typical human enzyme

Optimal temperature for

enzyme of thermophilic

(heat-tolerant

bacteria)

Rate of reaction

40

0

20

60

80

100

Temperature (°C)

Optimal temperature for two enzymes

Optimal pH for pepsin

(stomach enzyme)

Optimal pH

for trypsin

(intestinal

enzyme)

Rate of reaction

2

3

6

7

9

10

0

1

4

5

8

pH

Optimal pH for two enzymes

slide21

LE 8-19

A substrate can

bind normally to the

active site of an

enzyme.

Substrate

Active site

Enzyme

  • 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

Normal binding

A competitive

inhibitor mimics the

substrate, competing

for the active site.

Competitive

inhibitor

Competitive inhibition

A noncompetitive

inhibitor binds to the

enzyme away from the

active site, altering the

conformation of the

enzyme so that its

active site no longer

functions.

Noncompetitive inhibitor

Noncompetitive inhibition

enzyme regulation
Enzyme Regulation
  • 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
allosteric activation and inhibition

Allosteric activator

stabilizes active form.

Allosteric Activation and Inhibition

Allosteric enzyme

with four subunits

Active site

(one of four)

  • 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

Regulatory

site (one

of four)

Activator

Active form

Stabilized active form

Oscillation

Allosteric inhibitor

stabilizes inactive form.

Non-

functional

active site

Inhibitor

Stabilized inactive

form

Inactive form

Allosteric activators and inhibitors

cooperativity
Cooperativity
  • form of allosteric regulation
  • can amplify enzyme activity
  • binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits
slide25

LE 8-20b

Binding of one substrate molecule to

active site of one subunit locks all

subunits in active conformation.

Substrate

Inactive form

Stabilized active form

Cooperativity another type of allosteric activation

feedback inhibition
FeedbackInhibition

Initial substrate

(threonine)

Active site

available

Threonine

in active site

  • 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

Enzyme 1

(threonine

deaminase)

Isoleucine

used up by

cell

Intermediate A

Feedback

inhibition

Enzyme 2

Active site of

enzyme 1 can’t

bind

theonine

pathway off

Intermediate B

Enzyme 3

Intermediate C

Isoleucine

binds to

allosteric

site

Enzyme 4

Intermediate D

Enzyme 5

End product

(isoleucine)

slide28

LE 9-2

Light

energy

ECOSYSTEM

Photosynthesis

in chloroplasts

Organic

molecules

CO2 + H2O

+ O2

Cellular respiration

in mitochondria

ATP

powers most cellular work

Heat

energy

oxidation and reduction

becomes oxidized(loses electron)

Xe- + Y X + Ye-

becomes reduced(gains electron)

Oxidation and Reduction
  • 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)
slide30

becomes oxidized

C6H12O6 + 6O2 6CO2 + 6H2O + Energy

becomes reduced

  • Cellular respiration
    • fuel (such as glucose) is oxidized
    • oxygen is reduced
cellular respiration
Cellular Respiration
  • 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
slide32

LE 9-6_1

Glycolysis

Pyruvate

Glucose

Cytosol

Mitochondrion

ATP

Substrate-level

phosphorylation

slide33

LE 9-6_2

Glycolysis

Citric

acid

cycle

Pyruvate

Glucose

Cytosol

Mitochondrion

ATP

ATP

Substrate-level

phosphorylation

Substrate-level

phosphorylation

slide34

LE 9-6_3

Electrons carried

via NADH and

FADH2

Electrons

carried

via NADH

Oxidative

phosphorylation:

electron transport

and

chemiosmosis

Glycolysis

Citric

acid

cycle

Pyruvate

Glucose

Cytosol

Mitochondrion

ATP

ATP

ATP

Substrate-level

phosphorylation

Oxidative

phosphorylation

Substrate-level

phosphorylation

glycolysis
Glycolysis
  • “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
slide36

LE 9-8

Energy investment phase

Glucose

2 ATP

2 ADP + 2 P

used

Citric

acid

cycle

Glycolysis

Oxidative

phosphorylation

Energy payoff phase

formed

ATP

ATP

ATP

4 ADP + 4 P

4 ATP

2 NADH

+ 2 H+

2 NAD+ + 4 e– + 4 H+

2 Pyruvate + 2 H2O

Net

2 Pyruvate + 2 H2O

Glucose

4 ATP formed – 2 ATP used

2 ATP

2 NAD+ + 4 e– + 4 H+

2 NADH + 2 H+

slide37

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
electron transport chain
Electron Transport Chain
  • 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
slide39

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
slide40

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
fermentation
Fermentation
  • consists of glycolysis plus reactions that regenerate NAD+
    • Two common types:
      • alcohol fermentation
      • lactic acid fermentation
  • Fermentation
slide42

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
slide44

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)
slide45

LE 10-2

Plants

Unicellular protist

10 µm

Purple sulfur

bacteria

1.5 µm

Multicellular algae

Cyanobacteria

40 µm

slide46

Photosynthesis in plants

    • Primarily in leaves
    • Chlorophyll
      • green pigment
      • in chloroplasts
      • Absorbs light energy
    • Stomata
      • microscopic pores on leaf surface
        • CO2 enters
        • O2 exits
slide47

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
slide48

LE 10-3

Leaf cross section

Vein

Mesophyll

Stomata

O2

CO2

Mesophyll cell

Chloroplast

5 µm

Outer

membrane

Thylakoid

Intermembrane

space

Thylakoid

space

Stroma

Granum

Innermembrane

1 µm

photosynthesis1
Photosynthesis

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

slide50

LE 10-4

12 H2O

6 CO2

Reactants:

6 O2

6 H2O

C6H12O6

Products:

photosynthesis2
Photosynthesis
  • 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
slide52

LE 10-5_1

H2O

Light

LIGHT

REACTIONS

Chloroplast

slide53

LE 10-5_2

H2O

Light

LIGHT

REACTIONS

ATP

NADPH

Chloroplast

O2

slide54

LE 10-5_3

H2O

CO2

Light

NADP+

ADP

+

P

i

CALVIN

CYCLE

LIGHT

REACTIONS

ATP

NADPH

Chloroplast

[CH2O]

(sugar)

O2

slide55

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
slide56

Absorption Spectrum

Chlorophyll a

Chlorophyll b

Carotenoids

Absorption of light by

chloroplast pigments

400

700

500

600

Wavelength of light (nm)

Absorption spectra

slide57

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
slide58

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
slide59

LE 10-12

Thylakoid

Photosystem

STROMA

Photon

Light-harvesting

complexes

Reaction

center

Primary electron

acceptor

e–

Thylakoid membrane

Special

chlorophyll a

molecules

Pigment

molecules

Transfer

of energy

THYLAKOID SPACE

(INTERIOR OF THYLAKOID)

slide60

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
electron flow
Electron Flow
  • light reactions
    • Two routes for electron flow: cyclic and noncyclic
      • Noncyclic electron flow
        • the primary pathway,
        • involves bothphotosystems
        • produces ATP and NADPH
slide62

LE 10-13_5

H2O

CO2

Light

NADP+

ADP

CALVIN

CYCLE

LIGHT

REACTIONS

ATP

NADPH

Electron

Transport

chain

O2

[CH2O] (sugar)

Primary

acceptor

Primary

acceptor

Electron transport chain

Fd

e–

Pq

e–

e–

e–

NADP+

H2O

Cytochrome

complex

2 H+

+ 2 H+

NADP+

reductase

+

NADPH

O2

1/2

Pc

e–

+ H+

P700

Energy of electrons

e–

Light

P680

Light

ATP

Photosystem I

(PS I)

Photosystem II

(PS II)

slide63

LE 10-14

e–

ATP

e–

e–

NADPH

e–

e–

e–

Mill

makes

ATP

Photon

e–

Photon

Photosystem II

Photosystem I

electron flow1
Electron Flow
  • Cyclic electron flow
    • uses only photosystem I
    • produces only ATP
      • generates surplus ATP
        • satisfying the higher demand in the Calvin cycle
slide65

LE 10-15

Primary

acceptor

Primary

acceptor

Fd

Fd

NADP+

Pq

NADP+

reductase

Cytochrome

complex

NADPH

Pc

Photosystem I

ATP

Photosystem II

slide66

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

the calvin cycle
The 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
slide68

The Calvin cycle has three phases:

    • Carbon fixation (catalyzed by rubisco)
    • Reduction
    • Regeneration of the CO2 acceptor (RuBP)

Play

problems plants face
Problems Plants Face
  • Dehydration
    • Hot & Dry conditions
    • plants close stomata
    • conserves water
    • but limits photosynthesis
      • reduces access to CO2
      • O2 to build up
        • photorespiration
slide70

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
slide71

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
slide72

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
slide73

LE 10-20

Sugarcane

Pineapple

CAM

C4

CO2

CO2

Night

Mesophyll

cell

CO2 incorporated

into four-carbon

organic acids

(carbon fixation)

Organic acid

Organic acid

Bundle-

sheath

cell

Day

CO2

CO2

Organic acids

release CO2 to

Calvin cycle

CALVIN

CYCLE

CALVIN

CYCLE

Sugar

Sugar

Spatial separation of steps

Temporal separation of steps

photosynthesis review
Photosynthesis Review
  • 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
slide75

LE 10-21

Light reactions

Calvin cycle

H2O

CO2

Light

NADP+

ADP

+

P

i

RuBP

3-Phosphoglycerate

Photosystem II

Electron transport

chain

Photosystem I

ATP

G3P

Starch

(storage)

NADPH

Amino acids

Fatty acids

Chloroplast

O2

Sucrose (export)