Competency 3

“You must have knowledge of the chemical processes of living

things.”

Introduction to Metabolism

Catabolism, Anabolism, & the Laws of Thermodynamics

Metabolism

• Metabolism is the totality of an organism’s chemical processes, managing the cellular resources of material and energy

• Metabolic reactions are organized into pathways that are enzymatically controlled, so that no energy is wasted

• Metabolic reactions may be coupled to drive energy-requiring reactions in the cell

• In a living cell, break-down and build-up never reach equilibrium (otherwise the cell would be dead!!!)

• Usually, the products of most reactions will become reactants within the metabolic pathways for the next reaction

Build-up & Break-down

• Catabolic pathways release energy from complex molecules into simpler ones; free energy is lost & they are exergonic reactions

• Anabolic pathways consume energy to make complicated molecules (ex: stringing amino acids to make proteins) These increase order, & are endergonic reactions

Types of Energy

• Energy is the capacity to do work

• Kinetic energy is the process of doing work (energy of motion)– Thermal energy (heat) is expressed as

measure of the random movement of molecules

– Light energy from the sun is kinetic energy which powers photosynthesis

Potential Energy

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• Energy that matter posses because of location or arrangement– Chemical energy

stored in molecules because of bond arrangement

– Object high on a shelf due to gravity

Potential Energy & Free Energy

• Objects that have a high degree of order tend to have more potential energy because of their free energy available to do work

• Order is the antithesis of entropy- the quantitative measure of disorder that is proportional to randomness– Highly complex macromolecules (ex. Starches) have a lot of

free energy because if we break these down, we end up with less order, smaller substances with a higher kinetic energy, thus more random movements to create heat

Are autotrophs really producers?

• No! They are energy transformers!

• According to the First Law of Thermodynamics, energy can be transferred and transformed, but not created (or destroyed)

Open & closed systems

• The Second Law of Thermodynamics states that every energy transfer makes the universe more disordered

• A closed system is a collection of matter under study which is isolated from its surroundings

• Open systems react with their surroundings, so in living things, although it make seem that entropy may decrease (making the system more orderly) but the entropy of the system AND its surroundings must always increase– We extract chemical energy from molecules to build our cells, but

release to our surroundings low energy molecules & heat (King of Entropy)

Organisms live at the Expense of Free Energy (Just remember: nothing in

life is free..)• Energy can be transformed, but part is

dissipated as heat• Heat can only perform work if there is a

temperature gradient• The Quantity of energy in the universe

is constant, but the Quality is not• We express the amount of energy that

is available to do work as Free Energy

Free-Energy: Criterion for Spontaneity

• According to the Gibbs-Helmholtz equation:• ∆G = ∆H - T∆S;• G (Gibb’s free energy) is the portion available

to do work & is the difference between the total energy or enthalpy (H) & the energy NOT available for doing work (TS- which is a change in entropy times absolute temperature in Kelvin)

Significance of free energy

• A spontaneous reaction is one that will occur without additional energy (exergonic)

• Free energy decreases in a spontaneous process• Higher temperatures enhance entropy changes;

greater kinetic energy of molecules tend to disrupt order as collisions increase

• When a reaction reaches equilibrium, ∆G = 0 because there is no net change in the system

• When a reaction is forced away from equilibrium (requiring energy) the free energy increases & hence it is endergonic

Free Energy & Metabolism

• Exergonic reactions proceed with a net loss of free energy

• Products have less free energy than reactants• Reaction is energetically downhill• ∆G is negative

Endergonic reactions

• Products store more free energy than the reactants• They require an input of energy from their

surroundings to proceed; reaction is energetically uphill & non-spontaneous

• ∆G is positive

What goes up, must come down

• If chemical process is exergonic, its reverse in endergonic – Ex.- For each molecule of glucose oxidized in

exergonic process of cellular respiration, 2870 kJ are released (∆G = -2870 kJ/mol)

– To produce one mole of glucose, the endergonic process of photosynthesis requires an energy input of 2870 kJ (∆G = +2870 kJ/mol)

Energy in the Cell

ATP & Enzymes

ATP powers cellular work

• In cellular metabolism, endergonic reactions are driven by coupling them to reactions with a greater negative free energy (exergonic)

• ATP (adenosine triphosphate) is a nucleotide with unstable phosphate bonds that the cell hydrolyzes for energy to drive endergonic reactions

• Unstable bonds in the phosphate groups (due to repelling charges) can be hydrolyzed in an exergonic reaction making ADP, a more stable molecule (like relaxing a spring)

ATP is the Source

• Enables mechanical work, such as the beating of cilia or muscle contraction

• Enables transport work, such as pumping• Enables chemical work such as polymerization

Energy coupling

• Exergonic hydrolysis of ATP is coupled with endergonic processes by transferring a phosphate group to another molecule

• Enzymatically controlled

Regeneration of ATP

• ATP is regenerated 10 million times per second/ per cell

• Reaction is endergonic

• Energy to drive the endergonic regeneration of ATP comes from cellular respiration (exergonic)

Enzymes

• Chemical reactions can occur spontaneously if it releases free energy, but it may be too slow to be effective

• Enzymes control reaction rates• They are biological catalysts & are usually

proteins; they don’t change the nature of reactions, only speed them up

• Are very selective; substrate-specific• Lower activation energy for a reaction

Activation Energy

• Amount of energy that reactant molecules must absorb to start a reaction

• Thermal energy is usually enough to break chemical bonds to form the transition state, but at cellular temp.s this is not enough!

Nutrients

• Nutrients are substances in food that are necessary for normal growth, maintenance & repair

• They may be classified as carbohydrates, proteins, or fats

Fats• Made of long carbon chains-

have many bonds which store LOTS of energy- 9 kilocalories per gram actually

• May be saturated (only single hydrogen bonds) or unsaturated (contain double bonds)

• Saturated fats are solids at room temp

• Unsaturated are liquid (oils)

Carbohydrates• Have the generic formula

CH2O• Can be classified two

ways:• Simple monosaccharide

or single sugars, such as sucrose

• Complex polysaccharides such as starch or cellulose, which is fiber for us

• Both provide FAST energy

Proteins

• Made up of smaller subunits called amino acids

• Enzymes, which are catalysts and speed up chemical reactions, are all proteins

• Enzymes chop up nutrients into small molecules that can be absorbed into the bloodstream

Cellular Respiration: Harvesting Chemical Energy

Breaking bonds is Spontaneous

• Order is Endergonic- like potential energy; in large molecules energy is stored in bonds

• Breaking these bonds to make smaller molecules is spontaneous; -ΔG; contributes to entropy of the universe

Order is intrinsically unstable

• Catabolism is the breaking down of large organic molecules to yield energy

• Most efficient catabolic pathway is cellular respiration

Understanding Redox Reactions

• “Oil Rig”• Something that is reduced gains electrons• Something that is oxidized looses electrons• The reducing agent is the electron donor• The oxidizing agent is the electron acceptor

Redox Reaction

• Oxygen is one of the most powerful oxidizing agents due to its electronegativity

• When oxygen pulls electrons toward it, or hydrogen electrons are transferred, energy is released.

Now, apply it to Glucose…

• C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy +

Heat• In this equation, glucose is oxidized…it

looses H electrons & makes carbon dioxide• Oxygen gas is reduced; being an electron

acceptor, it is an oxidizing agent• The transfer of the H’s to the O yields energy

How much energy, might you ask…

• Imagine if there were no energy barriers, and glucose just spontaneously combusted?

• Every time we would eat & breathe, we would release an enormous amt. of heat!

With no barriers…

• If hydrogens were just stripped & given directly to highly electronegative oxygen, all energy would be violently & immediately be emitted as heat & light (aka- Explosion)

Obviously, that’s not the case

• Explosions are not occurring in our body

• Glucose is broken down in a series of controlled steps

• Each step is catalyzed by a specific enzyme

• Energy is harnessed in an electron transport chain

The Bad way vs. The Good way

Basically…Electron flow goes

• Food enters the system- glucose• Enzymes known as dehydrogenases (and can you

guess what they do???) remove 2 hydrogens from the food & transfer them to a very important electron acceptor called NAD+ (oxidizing agent)

• NAD+ is a key intermediate during respiration• Dehydrogenases go by many different names- one

for each particular step of respiration

• NAD+ will take two electrons + one proton to become NADH

• H+ is released in solution• NAD is a coenzyme; it stands

for Nicotinamide Adenine Dinucleotide

• From here, the electrons will go to the electron transport chain & be pulled to oxygen which will be released as water

• Remember- substances such as FATS that are saturated with hydrogens make excellent fuels!

Glycolysis

• Splitting of sugar• Minor source of ATP-

accomplished by substrate level phosphorylation (2)

• Yields 2 NADH per glucose molecule

• Does NOT requireO2; does NOT produce CO2- Anaerobic!

Energy investment phase

• Glucose is phosphorylated twice making the molecule more chemically reactive- takes an investment of 2 ATP’s with help of enzymes

Energy payoff

• Six-carbon sugar is cleaved making 2-three-carbon sugars, which are actually isomers of each other

• Glyceraldehyde phosphate is favored & is removed as fast as it is made, so equilibrium leans in its favor

• Glyceraldehyde phosphate is oxidized (each one) to loose one hydrogen each

• These Hydrogens are donated to NAD+ to give 2 NADH; at the same time, a P is added to each Glyceraldehyde phosphate

• By substrate phosphorylation, each molecule will loose a P to makes 2 ATP’s

• Enolase removes H2O to make PEP (Phosphoenolpyruvate) a highly unstable molecule, which then makes two more ATP’s + pyruvate

The Krebs Cycle• Pyruvates enter mitochondrial matrix through a

transport protein• The carboxyl group is removed from each as CO2

• 2-carbon fragments then become acetates & extracted electrons go to NAD+ to make NADH

• Coenzyme A binds to the acetate, making an unstable acetyl CoA

• Acetyl CoA enters Krebs cycle to be fully oxidized

• First, oxaloacetate binds to 2-carbon fragment removing CoA

• Two carbons from the newly formed citrate will leave as CO2; at same time of release, 2 NAD+

become NADH• CoA enters cycle again- by substrate

phosphorylation an ATP is made• H2O is added to cycle to regenerate

oxaloacetate & one more NAD+ is reduced

• At the end of the Krebs cycle, oxaloacetate is restored to start cycle again

• We have produced 3 NADH for EACH molecule of pyruvate (6 per glucose molecule)

• 2 ATP were made by substrate level phosphorylation

• 2 FADH2 were made (flavin adenosine dinucleotide- same as NADH but lower level on electron transport chain)

• We’ve produced 6 CO2 for each glucose- hence, respiration!

Electron Transport Chain• Structure fits function: Mitochondrial cristae provide space for many copies of the chain; as we know a typical muscle cell regenerates ATP at a rate of appx. 10 million molecules per second; oxidative phosph. accounts for 90% of ATP generated

• NADH donates electron to flavoprotein (first acceptor in chain)

• Next passes to another protein, then to ubiquinone, the only non-protein carrier on chain (lipid)

• The remaining electron carriers are cytochromes which pass electrons downhill to highly electronegative Oxygen

• For every 2 NADH molecules, one O2 molecule is reduced to 2H2O

Generating ATP• ATP synthase- protein complex found in inner mitochondrial

membrane that acts as an enzyme to actually generate ATP• Oxidative Phosphorylation happens by chemiosmosis, where H+

gradient (proton-motive force) couples redox reactions of electron transport chain

• Each NADH that contributes a pair of electrons to the chain makes appx. 3 ATP

Efficiency of respiration

• Complete oxidation of a mole of glucose gives 686 kcal; 36 ATP produced in all

• Phosphorylation of ADP to ATP stores 7.3 kcal per mole ATP

• Efficiency is about 38%; rest is spent on heat to maintain body temperature, cooling mechanisms, or just dissipated

• ATP yield is contingent upon adequate supply of oxygen

In the end

Photosynthesis & Autotrophs

The making of organic food molecules from inorganic

materials

The Beauty of Nature

• Plants are the base of the ecological food web for biosphere

• Autotrophs have the ability to sustain themselves using their chloroplasts

• Heterotrophs rely on cellular respiration; they obtain their nutrients elsewhere

Natural Dynamics

• Nature has balance in that the products of photosynthesis are the reactants of cellular respiration

• In a simplistic sense, Photosynthesis:– CO2 + H2O (light) C6H12O6 + O2

– Cellular respiration:

• C6H12O6 + O2 CO2 + H2O

Producers vs. Consumers

• Also known as autotrophs, they produce organic molecules from inorganic

• Plants rely on CO2, H2O, & minerals as nutrients

• Require light as an energy source (photoautotrophic)

• Examples are plants, algae, some prokaryotes

• AKA heterotrophs• Must acquire organic

molecules from compounds produced by other organisms

• They are unable to synthesize organic molecules from raw inorganic materials

• Include herbivores, carnivores & decomposers

Special cases

• Photoautotrophs sustain themselves with energy from sunlight

• Chemoautotrophs get their energy from the oxidation of inorganic materials in their environment, such as H2S or NH3

• Examples include Sulfur bacteria or Giant tube worms

Let There Be Light!

• AKA electromagnetic energy or radiation• Entire range of radiation is called electromagnetic spectrum;

travels in waves• Wavelength varies across the spectrum; the shorter the

wavelength (higher frequency) more energy it contains

Light & plants

• Visible light is most important to us; it is the light we see (UV light is dangerous to us) & is most readily absorbed by plants

• Ranges from about 380 to 750 nm

• Pigments are light absorbing substances

Plant pigments

• Plants contain several types of light absorbing pigments, including chlorophyll, carotenoids & xanthophylls

• All absorb mostly blue & red light, therefore the plant reflects green

Parts of the Plant

• All green parts of a plant contain chloroplasts• Photosynthesis occurs mostly in the leaves• Chlorophyll is green pigment located in

chloroplasts• Chloroplasts are found mainly in the

mesophyll of the leaf (interior tissue), each cell containing 30-40 chloroplasts

Chloroplasts

• CO2 enters leaf via stomata (pores)

• H2O delivered by means of veins or vascular bundles (export sugar to roots too)

• Thylakoid sacs are layered as grana; chlorophyll is found in thylakoid membranes

• Stroma is dense fluid of c’plast; membranes separate stroma from thylakoid space

Photosynthesis as a Redox process

• Recall that respiration is an exergonic process; energy is released from the oxidation of sugar

• Electron’s associated with sugar’s hydrogens lose potential energy as carriers transport them to oxygen, forming water

• Electronegative oxygen pulls electrons down the transport chain, & potential energy released is used by mitochondria to produce ATP

• Photosynthesis is endergonic; energy is required to reduce carbon dioxide

Overview of Photosynthesis

• Occurs in 2 stages: Light & Dark reactions (aka Calvin Cycle)

• Light reactions convert solar energy to chemical bond energy in NADPH & ATP

• Calvin cycle involves carbon-fixation

Light Reactions

• Occur in thylakoid membranes of chloroplasts• Reduce NADP+ to NADPH• Light absorbed by c’phyll provides the energy to

reduce NADP+ to NADPH, which temporarily stores energized electrons from water

• NADP+, a coenzyme similar to NAD+ in respiration, is reduced by adding a pair of electrons plus a hydrogen nucleus, or H+

• Gives off O2 as a by-product from split of water• Generates ATP through photophosphorylation

Products of the Light Reaction

• 1 NADP+ becomes 1 NADPH

• 1 ADP becomes 1 ATP

• 2 H2O become 4 H+ + O2 gas

Pigment Absorption

• A pigment that absorbs all wavelengths of light appears black

• Absorption spectrum for a pigment in solution can be determined by using a spectrophotometer (shows % transmittance)

• Chlorophyll a is light absorbing pigment that participates directly in light reactions

• Accessory pigments absorb light at different wavelengths & transfer energy to c’phyll a

Photoexcitation!

• Light is all it takes to get these babies excited!• Absorbed photons boost one of pigment molecule’s

electrons in its lowest energy state (ground state) to an orbital of higher potential energy (excited state)

• Pigments have unique absorption spectra because pigments can only absorb photons corresponding to specific wavelengths

• Excited state is unstable, so electrons quickly fall back to ground state orbital, releasing excess energy in the process

Primary Electron Receptor

• Traps excited state electrons released from the reaction center chlorophyll

• Transfer of excited state electrons to primary electron acceptor starts light reactions

• Energy stored in the trapped electrons powers the synthesis of ATP & NADPH in subsequent steps

Electron transport continued

• Photosynthetic membranes use H2O to replace electrons in chlorophyll; 2 H2O molecules split to make 4 H+ ions and O2 gas (released into the air)

• An excess of H+ builds up inside the photosynthetic membrane, making a voltage potential (more positive on the inside)

• Voltage potential couples reaction of making ADP into ATP

Non cyclic electron flow

• Light excites electrons from P700, rxn center in Photosystem I

• Ultimately stored in NADPH which will be electron donor in Calvin cycle

• Primary electron acceptor passes excited state electrons to ferredoxin (Fd), an iron-containing protein

• NADP+ reductase catalyzes the redox rxn that transfers these electrons from ferredoxin to NADP+, producing reduced coenzyme NADPH

• Oxidized P700 c’phyll becomes oxidizing agent as its electron “holes” must be filled

Restoring electrons

• P680 becomes a strong oxidizing agent due to missing electrons

• A water-splitting enzyme extracts electrons from water

• Oxygen atoms combine to form O2, which is released as a gas

Chemiosmosis

• As excited electrons give up energy along the transport chain to P700, coupling of exergonic flow of electrons to endergonic rxns phosphorylate ADP to ATP

• ATP synthase enzyme in thylakoid membrane uses the proton-motive force to make ATP (called photophosphorylation since it requires light energy)

Cyclic electron flow

• Uses photosystsem I but not II• Generates ATP without producing

NADPH or oxygen gas• Excited electrons leave c’phyll a at the

reaction center, & return to the reaction center

• Ferredoxin immediately passes the electrons to transport chain to P700

Calvin Cycle Overview

• Occur in the stroma of the chloroplast

• First incorporate atmospheric CO2 into existing organic molecules by a process called carbon fixation, then reduce fixed carbon to carbohydrate

• Reduction of CO2 to sugar requires products of the light reactions (but not light itself)– NADPH provides the reducing power– ATP provides the chemical energy

Differences in Mitochondria & Chloroplasts

• Mitochondria transfer chemical energy from food molecules to ATP; high energy electrons extracted by oxidation of food

• Chloroplasts transform light energy into chemical; photosystems capture light energy to drive electron transport chain

• ATP synthase in intermembrane space of mitochondrial matrix; found in stroma side of thylakoid compartment

The Calvin Cycle

• Products of light reactions used to power Calvin cycle to reduce carbon dioxide to sugar

• Phase 1: Carbon fixation• Phase 2: Reduction of 3-

phosphoglycerate to glyceraldehyde phosphate

• Phase 3: Regeneration of starting material, RuBP

Photorespiration

• An evolutiobary relic?• Reduces yield of photosynthesis• Consumes oxygen, evolves carbon dioxide,

produces no ATP• Fostered by hot, dry, bright days since plants

close their stomata to prevent water loss• Occurs when oxygen concentration is greater

inside the leaf (rubisco accepts oxygen & transfers it to RuBP)

C4 Plants

• Calvin Cycle occurs in most plants & produces 3-phopsphoglycerate, a 3-carbon compound as the first stable intermediate

• Those plants are called C3 plants (3-C)• Most important for agriculture are rice, wheat, &

soybeans• C4 plants preface the Calvin cycle with a 4-C

compound; adaptative pathway because it enhances carbon fixation under conditions that favor photorespiration

• Used by several thousand species of plants, including sugarcane & corn

CAM Plants

• Found in succulent plants• Stomata open at night & close during day (opposite

of most plants)• Conserves water during the day, but prevents CO2

from entering leaves• When stomata open at night, CO2 is taken up &

incorporated into a variety of organic acids; called Crassulacean Acid Metabolism

• Acids are stored in vacuoles of mesophyll cells until morning, when light reactions supply ATP & NADPH for Calvin cycle