Transcript Unit Four

UNIT FOUR
Chapters 6, 7, and 8
ENERGY AND METABOLISM
Chapter 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 = H – TS
• G = Gibbs free energy
• ΔG = ΔH - TΔS
• H = enthalpy, energy in the
chemical bonds
• Assumptions
• T = absolute temperature in Kelvin
• S = entropy, disorder of system
• Constant temperature
• Constant pressure
• Constant volume
PREDICTING REACTIONS
Endergonic
Exergonic
• ΔG is positive
• ΔG is negative
• Input of energy
• 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 CYCLE
Most 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
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•
•
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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 SENSITIVITY
Concentrations 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
INHIBITION
End product many times binds the
allosteric site
CELLULAR RESPIRATION
Chapter 7
ENERGY HARVESTING
Heterotrophs
Autotrophs
• Live on organic compounds
• Produce organic compounds
• “fed by others”
• “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
GLYCOLYSIS
Literally 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
Fermentation
• Oxygen will ultimately accept the
electrons
• Organic molecules can accept the
electrons
• NADH can go back to NAD+
• NADH can go back to NAD+
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 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 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
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
Sulfur bacteria
• CO2 is the electron acceptor
• SO4 is the electron acceptor
• CO2 is reduced to CH4
• SO4 is reduced to H2S
• Found in soil
• Hot springs and hydrothermal vents
• Found in cows digestive system
FERMENTATION
Ethanol fermentation
some bacteria and yeasts
Lactic acid fermentation
humans when exercising
commercially to produce cheese and yogurt
PROTEIN AND FAT CATBOLISM
PHOTOSYNTHESIS
Chapter 8
TWO TYPES OF PHOTOSYNTHESIS
Anoxygenic
Oxygenic
• Purple bacteria
• Cyanobacteria
• Green sulfur bacteria
• Seven groups of algae
• Green nonsulfur bacteria
• Essentially all land plants
• Heliobacteria
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 STRUCTURE
Mesophyll cells
Stoma
Chloroplast
Thylakoids
Grana
Stroma
OVERVIEW
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
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
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
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
EFFECT
The 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
C4
Physical separation yields higher levels
of CO2 entering the Calvin cycle
Examples: corn, crabgrass, sugarcane
CAM PLANTS
Temporal separation yields higher levels
of CO2 entering the Calvin cycle
Examples: cactuses, pineapple, agave,
many orchids