Unit Four

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Unit Four

• Chapters 6, 7, and 8

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Energy and MetABOLISM

• Chapter 6

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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

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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

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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
• ?G ?H - T?S
• Assumptions
• Constant temperature
• Constant pressure
• Constant volume

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Predicting Reactions

• Endergonic

• Exergonic

• ?G is positive
• Input of energy

• ?G is negative
• Energy is released
• Spontaneously proceeding reactions

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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

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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

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Why run reactions??
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ATP cycle

• Most cells dont stockpile ATP
• Cells keep a few seconds worth of ATP on hand
• Constantly producing more from ADP and inorganic
  phosphate

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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

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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
  shapeinduced fit

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Multienzyme complexes

• Pyruvate dehydrogenase has 60 sububnits
• Why have these?
• Increase rate of reaction
• Limits unwanted side reactions
• All reactions can be controlled

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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 catalysisrun reactions on
  themselves
• Intermolecular catalysisrun reactions on other
  molecules
• Ribosomal RNA plays a role in ribosome function,
  the ribosome is a ribozyme

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Enzyme sensitivity

• Concentrations of enzyme and substrate
• Temperature
• pH

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Turning Enzymes On and Off

• Activator

• Inhibitor

• A substrate that binds and increases activity

• A substrate that binds and decreases activity
• Many times the end product of a pathway is the
  inhibitor

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Types of Inhibitors

• Competitivecompete with the substrate for the
  active site
• Noncompetitivebind 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

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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

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Whats the point??

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

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Feedback Inhibition

• End product many times binds the allosteric site

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Cellular Respiration

• Chapter 7

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Energy Harvesting

• Heterotrophs

• Autotrophs

• Live on organic compounds
• fed by others

• Produce organic compounds
• self-feeders

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Cells Oxidize Organic Compounds

• The reactions we will examine are oxidation
  reactions
• Transfer of electrons
• Dehydrogenations reactionsloss of hydrogen
  protons

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Three Possible outcomes

• Aerobic respirationthe final electron acceptor
  is oxygen
• Anaerobic respirationthe final electron acceptor
  is an inorganic molecule other than oxygen
• Fermentationfinal electron acceptor is an
  organic molecule

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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

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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 dont we burst into flames?

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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

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Stages of Metabolism

• Glycolysis
• Oxidation of pyruvate (sometimes called
  intermediary metabolism)
• Krebs cycle
• Electron transport chain

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What binds the stages together?

• ATP
• It is the molecule that drives endergonic
  reactions
• 7kcal of energy in ATP, activation energy

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An Overview
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Glycolysis

• Literally means sugar splitting
• ATP needs be fed into the reaction to get it
  startedpriming reactions
• The glucose needs to be splitcleavage
• NADH and ATP are formedoxidation

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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

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Recycling NADHneed another electron acceptor

• Aerobic Respiration

• Fermentation

• Oxygen will ultimately accept the electrons
• NADH can go back to NAD

• Organic molecules can accept the electrons
• NADH can go back to NAD

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Oxidation of pyruvate

• Decarboxylation 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 dehydrogenase60 unit multienzyme

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Krebs Cycle

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

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What do I do with the NADH and FADH2?

• Electron transport chain and cash them in for ATP

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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

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ATP synthase

• Rotary 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

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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?

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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?

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What inhibits Aerobic respiration?
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Oxidation without O2

• Methanogens

• Sulfur bacteria

• CO2 is the electron acceptor
• CO2 is reduced to CH4
• Found in soil
• Found in cows digestive system

• SO4 is the electron acceptor
• SO4 is reduced to H2S
• Hot springs and hydrothermal vents

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Fermentation

• Ethanol fermentation
• some bacteria and yeasts
• Lactic acid fermentation
• humans when exercising
• commercially to produce cheese and yogurt

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Protein and fat Catbolism
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Photosynthesis

• Chapter 8

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Two Types of Photosynthesis

• Anoxygenic

• Oxygenic

• Purple bacteria
• Green sulfur bacteria
• Green nonsulfur bacteria
• Heliobacteria

• Cyanobacteria
• Seven groups of algae
• Essentially all land plants

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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

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6CO2 12H20 light C6H12O6 6H2O
6O2
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Leaf Structure

• Mesophyll cells
• Stoma
• Chloroplast
• Thylakoids
• Grana
• Stroma

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Overview
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Pigments and light

• Any 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

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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

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Chlorophyll

• Chlorophyll 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

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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

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Photosystem structure

• Saturation

• Antenna Complex

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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

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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

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Bacteria and Single Photosystems

• Cyclic photophosphorylation
• Anoxygenic process
• Absorbed electrons are not at a high enough
  excitation level to produce NADPH

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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

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Enhancement effect

• The two photosystems work in series to enhance
  the output of each other

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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)

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Photorespiration

• Rubisco will pick up oxygen and send that into
  the Calvin cycle
• Why would this be a problem? What wouldnt you
  make?

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Fighting Photorespiration

• C3 plants fix carbon using the Calvin cycle
  directly
• C4 plants use and enzyme PEP carboxylase to make
  a four carbon compound malatephysical separation
• CAM plants open stomata at night, make
  oxaloacetate, store it, use the compounds during
  the day to run Calvin cycletemporal separation

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C4

• Physical separation yields higher levels of CO2
  entering the Calvin cycle
• Examples corn, crabgrass, sugarcane

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Cam plants

• Temporal separation yields higher levels of CO2
  entering the Calvin cycle
• Examples cactuses, pineapple, agave, many
  orchids