UNIT FOURChapters 6, 7, and 8

ENERGY AND METABOLISMChapter 6

FIRST LAW OF THERMODYNAMICS

• Concerns the amount of energy in the universe

• States that energy can not be created or destroyed it can only change from one form to another

• The total amount of energy in the universe remains constant

SECOND LAW OF THERMODYNAMICS

• Concerns the transformation of potential energy into heat or random molecular motion during an energy transaction

• Disorder, or entropy, is constantly increasing

• In general reactions spontaneously proceed to turn more ordered, less stable form into a less ordered more stable form

FREE ENERGY

• Energy available to do work

• G = Gibbs free energy

• H = enthalpy, energy in the chemical bonds

• T = absolute temperature in Kelvin

• S = entropy, disorder of system

• G = H – TS

• ΔG = ΔH - TΔS

• Assumptions• Constant temperature• Constant pressure• Constant volume

PREDICTING REACTIONS

Endergonic

• ΔG is positive

• Input of energy

Exergonic

• ΔG is negative

• Energy is released

• Spontaneously proceeding reactions

ACTIVATION ENERGY

• Extra energy needed to destabilize chemical bonds

• Initiates the reaction

• Larger activation energy requirements tend to proceed more slowly

• Rate of reaction can be increased two ways• Increase the energy of the

reacting molecules• Lower activation energy

CATALYSTS

• Process of influencing chemical bonds is called catalysis

• Catalysts affect the transition state of chemicals making them more stable and thus lowering the activation energy

WHY RUN REACTIONS??

ATP CYCLEMost cells don’t stockpile ATP

Cells keep a few seconds worth of ATP on hand

Constantly producing more from ADP and inorganic phosphate

ENZYMES: BIOLOGICAL CATALYSTS

• The unique 3D shape of the enzyme is hugely important

• The enzyme creates a temporary association between the substrates

• Carbonic anhydrase example• CO2 + H2O H2CO3

• proceeds either direction, but huge activation energy• Under normal conditions perhaps 200 molecules per hour• When catalyzed 600,000 molecules can be produced per second

ENZYME ACTIVE SITES

• Active site is a pocket for the substrate

• Once the substrate bonds the whole structure is called the enzyme-substrate complex

• The amino acid side chains of the substrate and enzyme interact to weaken bonds and thus lower activation energy

• Substrate binding changes the enzyme shape—induced fit

MULTIENZYME COMPLEXES

• Pyruvate dehydrogenase has 60 sububnits

• Why have these?• Increase rate of reaction• Limits unwanted side reactions• All reactions can be controlled

NONPROTEIN ENZYMES: RIBOZYMES

• Thomas R. Cech, University of Colorado, 1981

• Discovered that certain reactions seemed to be catalyzed by RNA rather than enzymes

• Extraordinary specificity

• Intramolecular catalysis—run reactions on themselves

• Intermolecular catalysis—run reactions on other molecules

• Ribosomal RNA plays a role in ribosome function, the ribosome is a ribozyme

ENZYME SENSITIVITYConcentrations of enzyme and substrate

Temperature

pH

TURNING ENZYMES ON AND OFF

Activator

• A substrate that binds and increases activity

Inhibitor

• A substrate that binds and decreases activity

• Many times the end product of a pathway is the inhibitor

TYPES OF INHIBITORS

• Competitive—compete with the substrate for the active site

• Noncompetitive—bind the enzyme at a point other than the active site and cause a conformational shape change

• Many of the noncompetitive inhibitors bind at a place called the allosteric site, hence these are called allosteric inhibitors

ENZYME COFACTORS AND COENZYMES

• Typically metal ions that are found in the active site and directly participate in the catalysis• Zinc, Molybdenum, and Manganese

• If the cofactor is a nonprotein organic molecule it is a coenzyme• B6 and B12

WHAT’S THE POINT??

• Metabolism is totally based on biochemical pathways, proteins, and enzyme function

• Anabolism—building

• Catabolism—breaking

FEEDBACK INHIBITIONEnd product many times binds the allosteric site

CELLULAR RESPIRATIONChapter 7

ENERGY HARVESTING

Heterotrophs

• Live on organic compounds

• “fed by others”

Autotrophs

• Produce organic compounds

• “self-feeders”

CELLS OXIDIZE ORGANIC COMPOUNDS

• The reactions we will examine are oxidation reactions

• Transfer of electrons

• Dehydrogenations reactions—loss of hydrogen protons

THREE POSSIBLE OUTCOMES

• Aerobic respiration—the final electron acceptor is oxygen

• Anaerobic respiration—the final electron acceptor is an inorganic molecule other than oxygen

• Fermentation—final electron acceptor is an organic molecule

“BURNING” CARBS

• C6H12O6 + 6O2 6CO2 + 6H2O + energy (heat and ATP)

• Change in energy is -686 kcal/mol at STP

• In a cell the change in energy can be -720 kcal/mol

HOW DO WE COMPLETE THE REACTION?

• Electron movement is critical

• If the electrons were given directly to O2 it would be a combustion reaction

• Why don’t we burst into flames?

INTERMEDIATE ELECTRON CARRIER

• NAD+ is a very important electron carrier

• Made of two nucleotides• Nicotinamide monophosphate,

active portion of molecule• Adenosine monophosphate, shape

recognition portion of molecule

STAGES OF METABOLISM

• Glycolysis

• Oxidation of pyruvate (sometimes called intermediary metabolism)

• Krebs cycle

• Electron transport chain

WHAT BINDS THE STAGES TOGETHER?ATP

It is the molecule that drives endergonic reactions

7kcal of energy in ATP, activation energy

AN OVERVIEW

GLYCOLYSISLiterally means “sugar splitting”

ATP needs be fed into the reaction to get it started—priming reactions

The glucose needs to be split—cleavage

NADH and ATP are formed—oxidation

GOTTA KEEP PROCESSES GOING

• Three things happened in glycolysis• Glucose is converted to 2 molecules of pyruvate• 2 molecules of ADP are converted to ATP using substrate level

phosphorylation• 2 molecules of NAD+ are reduced to NADH

• Problem!• Energy still locked in pyruvate molecules• Need NAD+ to continue glycolysis

RECYCLING NADH—NEED ANOTHER ELECTRON ACCEPTOR

Aerobic Respiration

• Oxygen will ultimately accept the electrons

• NADH can go back to NAD+

Fermentation

• Organic molecules can accept the electrons

• NADH can go back to NAD+

OXIDATION OF PYRUVATEDecarboxylation reaction

The carbon that is cleaved is converted to CO2

The remaining acetyl group attaches to coenzyme A

Acetyl Co-A is the new molecule

Pyruvate dehydrogenase—60 unit multienzyme

KREBS CYCLE

• The 2-carbon acetyl Co-A gets converted to 2 molecules of CO2

• Oxidation reactions

WHAT DO I DO WITH THE NADH AND FADH2?Electron transport chain and cash them in for ATP

CHEMIOSMOSIS

• The relative difference in electrical potential cause molecules to move from high concentration to low concentration

• ATP is made from ADP and Pi in the process

ATP SYNTHASERotary motor

F0 complex is membrane bound

F1 complex is the stalk, knob, and head

Movement cause changes in conformation, which causes enzymatic reaction

Result is oxidative phosphorylation

MOLECULAR ACCOUNTING

• How much ATP do we end up with?

• Each NADH is worth 2.5 ATP

• Each FADH2 is worth 1.5 ATP

• Retrace the steps, how much of everything was produced?

IS 30 OR 32 ATP GOOD?

• Each ATP is worth 7.3 kcal/mol

• One glucose is 686 kcal/mol

• (30 x 7.3)/686 = 32%

• Is that good?

WHAT INHIBITS AEROBIC RESPIRATION?

OXIDATION WITHOUT O2

Methanogens

• CO2 is the electron acceptor

• CO2 is reduced to CH4

• Found in soil

• Found in cows digestive system

Sulfur bacteria

• SO4 is the electron acceptor

• SO4 is reduced to H2S

• Hot springs and hydrothermal vents

FERMENTATIONEthanol fermentation

some bacteria and yeasts

Lactic acid fermentation

humans when exercising

commercially to produce cheese and yogurt

PROTEIN AND FAT CATBOLISM

PHOTOSYNTHESISChapter 8

TWO TYPES OF PHOTOSYNTHESIS

Anoxygenic

• Purple bacteria

• Green sulfur bacteria

• Green nonsulfur bacteria

• Heliobacteria

Oxygenic

• Cyanobacteria

• Seven groups of algae

• Essentially all land plants

THREE STAGES OF PHOTOSYNTHESIS

• Capture sunlight

• Use the sunlight to make ATP and NADPH

• Use the ATP and NADPH to synthesize organic molecules from CO2

6CO2 + 12H20 + LIGHT C6H12O6 + 6H2O + 6O2

LEAF STRUCTUREMesophyll cells

Stoma

Chloroplast

Thylakoids

Grana

Stroma

OVERVIEW

PIGMENTS AND LIGHTAny molecule that absorbs light in the visible range is a pigment

Light can act as a wave or a photon, a discrete packet of energy

Short wavelength light is high energy

Long wavelength light is low energy

PHOTOELECTRIC EFFECT

• A beam of light is able to remove electrons from molecules creating a current

• Chloroplasts are photoelectric devices

• Different molecules have different absorption spectra

CHLOROPHYLLChlorophyll a is the main light conversion pigment in cyanobacteria and green plants

Chlorophyll b is an accessory pigment that helps chlorophyll a absorb more light

Porphyrin ring, alternating double and single bonds, magnesium in the middle

PHOTOSYSTEMS

• Experiments on photosynthesis show that output increases linearly at low light intensities

• At high light intensity saturation is reached

• Investigators used single-celled algae Chlorella

• One molecule of O2 per 2500 chlorophyll molecules

• Chlorophyll works in clusters called photosystems

PHOTOSYSTEM STRUCTURE

Saturation Antenna Complex

REACTION CENTER

• Transmembrane protein-pigment complex

• Passes an electron to a neighbor

• Chlorophyll transfers electron to quinone, the primary acceptor

• Electron replaced with low energy electron from splitting of water

LIGHT DEPENDENT REACTIONS

• Primary photoevent• Photon is captured by pigment• Electron in the pigment is excited

• Charge separation• Excitation energy transferred to

reaction center• Electron moves to acceptor

molecule• Electron transport initiated

• Electron transport• Electrons move through proteins

embedded in thylakoid membrane• Protons move across the

membrane to create a gradient• NADPH produced

• Chemiosmosis• Protons flow through ATP synthase

BACTERIA AND SINGLE PHOTOSYSTEMS

• Cyclic photophosphorylation

• Anoxygenic process

• Absorbed electrons are not at a high enough excitation level to produce NADPH

COUPLED, NONCYCLIC PHOTOSYSTEMS

• Photosystem I passes electrons to NADP+ to make NADPH

• Photosystem II can oxidize water to restore electrons to the whole process

• Known as noncyclic photophosphorylation

ENHANCEMENT EFFECTThe two photosystems work in series to enhance the output of each other

CARBON FIXATION: THE CALVIN CYCLE

• Energy to drive the cycle comes from the ATP made in the light dependent reactions

• Protons and electrons needed to build chemical bonds comes from BADPH produced in light dependent reactions

• Enzyme-catalyzed cycle similar to Krebs, but building molecules instead of breaking them down

• C3 photosynthesis because the first intermediate compound has 3 carbons

• CO2 attached to ribulose 1,5-bisphosphate (RuBP) by rubulose bisphophate carboxylase/oxygenase (rubisco)

PHOTORESPIRATION

• Rubisco will pick up oxygen and send that into the Calvin cycle

• Why would this be a problem? What wouldn’t you make?

FIGHTING PHOTORESPIRATION

• C3 plants fix carbon using the Calvin cycle directly

• C4 plants use and enzyme PEP carboxylase to make a four carbon compound malate—physical separation

• CAM plants open stomata at night, make oxaloacetate, store it, use the compounds during the day to run Calvin cycle—temporal separation

C4Physical separation yields higher levels of CO2 entering the Calvin cycle

Examples: corn, crabgrass, sugarcane

CAM PLANTSTemporal separation yields higher levels of CO2 entering the Calvin cycle

Examples: cactuses, pineapple, agave, many orchids