BS-BIOCHEM
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- Gibbs Free Energy
-
<>G=<>H-T<>S
<>G increases with increasing <>H
<>G<0 is spontaneous, exergonic
<>G>0 is non-spontaneous, endergonic - Given that cellular reactions take place in the liquid phase, how is H related to E in a cell?
- H is about = to E because <>V=0
- Enthalpy
-
<>H=<>E-P<>V
<>H<0 exothermic
<>H>0 endothermic - Which equation relates <>G' (laboratory standard <>G) to the equilibrium constant?
- <>G'= -RT ln Keq
- What does the term "spontaneous" tell you about the rate of the reaction?
- Nothing whatsoever. Thermodynamics (spontaneity) is different from kinetics.
- The role of a catalyst
-
-Lowers the Ea of a reaction without changing the <>G (which has nothing to do w/what goes on in b/t)
-Lowers the Ea by stabilizing the transition state, making its existence less thermodynamically unfavorable
-NOT consumed in the rxn
ex: enzyme, its active site stabilizes the transition state of the reaction - Reaction Coupling
- 1 favorable reaction is used to drive an unfavorable one
- What type of structure does an enzyme have?
- Quaternary structure, globular- roughly spherical to form an active site in a cleft in the sphere
- Substrates
- The reactants in an enzyme-catalyzed reaction
- Enzyme Characteristics
-
Definition: proteins that accelerate the rxn rate by stabilizing the transition state, therefore lowering the Ea
-Enzymes do not alter reaction equilibria
-Do not inhibit reactions
-Have the ability to catalyze reactions in a stereospecific manner - Enzymes which catalyze reactions involving amino acids are specific for...
- D and L amino acids
- 5 Types of Enzyme Regulation
-
1) Covalent Modification: phosphorylate by kinases or dephosphorylate by kinases
2) Proteolytic Cleavage: protease cleaves off regulatory subunit of an inactive enzyme (zymogen) to yield an active enzyme
3) Allosteric Regulation: inhibitor or activator binds to enzyme at site other than active site
4) MOST ENERGY EFFICIENT: Transcriptional Regulation: transcription of enzyme regulated through the use of promoters (sequence of DNA) - Feedback Inhibition
-
aka negative feedback
-the inhibition of an early step in a series of events by the product of a later step in the series
-this has the effect of stopping the series of events when the products are plentiful and the series is unnecessary
-common in: body, enzyme reactions, hormone levels, blood pressure, body temperature, etc - Saturation Point in Enzymes
- When there is so much substrate that every active site is continuously occupie, and adding more substrate doesn't increase the reaction rate at all (enzyme is operating at Vmax)
- Reaction Rate
- The amount of product formed per unit time (V=mol/s). Depends on Substrate and Enzyme.
- Cooperativity
-
A type of substrate binding to a multi-active site enzyme, in which binding of one substrate molecule facilitates binding of subsequent substrate molecules
-one active site acts like the allosteric regulatory (amping something up or lowering it down) site for other active sites
ex: hemoglobin binding oxygen, CO2 can make O2 unbind from Hb
-graph= sigmoidal - What do Competitive Inhibitors structurally resemble?
-
The transition state at which the active site normally stabilizes.
-High levels of substrate can outcompete the inhibitor (so Vmax is not affected). - Km
-
affinity of substrate for enzyme
-low Km= high affinity for substrate to get into active site - Km and Vmax in competitive and non-competitive inhibition
-
Competitive: Km increases (lower affinity for substrate binding at active site), Vmax is unchanged
Noncompetitive: Km remains unchanged, Vmax decreases - Photosynthesis
- The process by which plants store energy from the sun in the bond energy of carbohydrates
- Photoautotrophs vs. Chemoheterotrophs
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Photoautotrophs- Use energy from light to make their own food
Chemoheterotrophs- Use energy of chemicals produced by other living things - 3 Meanings of Oxidize
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1) attach oxygen (or increase # bonds to oxygen)
2) remove hydrogen
3) remove electrons - 3 Meanings of Reduce
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1) remove oxygen (or decrease # bonds to oxygen)
2) add hydrogen
3) add electrons
-reducing something is like compressing a spring--you store PE - Catabolism
- The process of breaking down molecules
- Anabolism
- building up metabolism
- Oxidative Catabolism
-
The way to extract energy from glucose
1) Glycolysis
2) Pyruvate dehydrogenase complex
3) Krebs cycle
4) electron transport/oxidative phosphorylation - Cellular respiration could be considered a _______ reaction.
- A coupled reaction b/c the unfavorable synthesis of ATP is made possible by the favorable oxidation of glucose.
- Cellular Respiration
-
-glucose is oxidized to release energy, very little ATP is directly generated
-NAD+ to NADH
-reduced energy in NADH creates a proton gradient that drives the production of ATP - Glucose Oxidation
- C6H12O6 + 6O2 --> 6CO2 + 6H20
- Glycolysis
-
-occurs in cytoplasm
-does not require O2
-NADH is produced in only one step: when an aldehyde is oxidized to a COOH (-ate)
Glucose (6 C's)+ 2ADP + 2Pi + 2NAD+ --> 2 Pyruvate (3 C's each) + 2 ATP + 2NADH + 2H20 + 2H+
-ATP --> ADP when P added to a substrate
-ADP--> ATP when P removed from substrate (except PO4-) - Locations of the Steps of Cellular Respiration
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1)Glycolysis: in cytoplasm
2) Pyruvate Dehydrogenase Complex: mitochondrial matrix
3) Krebs Cycle: mitochondrial matrix
4) Electron transport: inner mitochondrial membrane - Per pyruvate/per glucose molecule, how many NADH and ATP are yielded?
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Per pyruvate: 2 ATP and 1 NADH
Per glucose: 4 ATP and 2 NADH - Hexokinase
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Catalyzes the first step in glycolysis
-phosphorylation of G6P
-G6P feedback-inhibits hexokinase - Phosphofructokinase (PFK)
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-catalyzes the third step: transfer of a phosphate group from ATP to fructose-6-phosphate to form fructose-1,6 biphosphate (very favorable)
-COMMITTED STEP OF GLYCOLYSIS
-allosterically regulated by ATP (high amount of ATP means low PFK activity - Fermentation
-
-has evolved to regenerate NAD+ in anaerobic conditions, thereby allowing glycolysis to continue in the absence of O2
-uses pyruvate as the acceptor of the high energy electrons from NADH
ex's: 1) reduction of pyruvate to ethanol
2) reduction of pyruvate to lactate in human muscle cells - + CHANGE IN H AND + CHANGE IN S MEANS...
- SPONTANEOUS AT HIGH TEMP
- - DELTA H AND + DELTA S MEANS...
- SPONTANEOUS
- + DELTA H AND - DELTA S
- NON SPONTANEOUS (+ DELTA G)
- Pyruvate Dehydrogenase Complex
-
oxidatively decarboxylates pyruvate
-dehydrogenase converts pyruvate
(oxidizes it) to a 2-C molecule, CO2 given off, NADH made from NAD+
-pyruvate--> activated (bound to Coenzyme A) acetyl unit - AMP
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-adenosine MONOphosphate, helps regulate Pyruvate Dehydrogenase Complex by stimulating the PDC, increasing the rate of entry of pyruvate into the Krebs cycle
-a low-energy molecule produced by the hydrolysis of ATP during metabolism - Krebs Cycle
-
-aka citric acid cycle & tricarboxylic acid cycle: citrate= first intermediate, possesses 3 carboxylic acid functional groups (ready to be oxidatively decarboxylated)
2-C acetyl unit from acetyl-CoA combines with oxaloacetate & 2 CO2 are released
-6 NADH, 2 FADH2, & 2GTP are generated in the process
-Stage 1: 2 C's in acetate fragment of acetyl-CoA are condensed w/the 4 C compound oxaloacetate (recycled)
-Stage 2: citrate is further oxidized to release CO2 and to produce NADH from NAD+ w/each oxidative decarboxylation
-Stage 3: oxaloacetate is regenerated so cycle can continue. reducing power stored in 1 NADH and 1 FADH2, high-energy phosphate bond=GTP (transfers high-energy phosphate bond to ADP) - Would glycolysis increase or decrease were there to be a thiamine deficiency?
- Increase because glycolysis would become the only means for extracting energy from glucose
- Compartmentalization of Glucose Catabolism in Eukaryotes
-
site: mitochondria
Outer Membrane: smooth and contains large pores formed by porin proteins
Inner Membrane: Densely folded structures (cristae), impermeable
Matrix: innermost space of the mitochondrion
Intermembrane Space: continuous with the cytoplasm due to large pores in outer membrane - Where are the enzymes of Krebs cycle, Pyruvate Dehydrogenase Complex, Electron Transport Chain & ATP Synthase (involved in oxidative phosphorylation), and glycolysis located?
-
Krebs & PDC= matrix
ETC and ATP synthase= inner mitochondrial membrane
-electrons from 2 NADH from glycolysis in cytoplasm must be transported into mitochondria before they can be passed along the ETC - 2 GOALS OF ELECTRON TRANSPORT/OXIDATIVE PHOSPHORYLATION
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1) to reoxidize all the e- carriers reduced in glycolysis, PDC, and Krebs cycle
2) To store energy in the form of ATP in the process - Oxidative Phosphorylation in Prokaryotes
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All reduced e- carriers are in the cytoplasm (no mitochondria), don't have to waste energy to shuttle NADH into mitochondrial matrix during aerobic respiration
-use of cell membrane instead of inner mitochondrial membrane to establish proton gradient that is used to power ATP synthesis by membrane-bound ATP synthase - Oxidative Phosphorylation and Electron Transport
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Oxidative Phosphorylation: collective term for electron transport and ATP production/ the oxidation of the high-energy electron carriers NADH and FADH coupledto the phosphorylation of ADP to produce ATP
-the energy released through oxidation of NADH and FADH2 by the electron transport chain is used to pump protons out of the mitochondrial matrix (proton gradiernt is coupled w/ATP synthesis because use ATP synthase to synthesize ATP from ADP and PO4) - 5 Members of the Electron Transport Chain
-
-five e- carriers, named for redox roles
-each member reduces the next member down the line
-3= large, embedded in mitochondrial membrane, protein complexas w/ heme prosthetic groups; 2= small
-1st: NADH dehydrogenase (NADH--> NAD+)/ aka coenzyme Q reductase
-2nd: ubiquinone: small
-3rd: Cytochrome C reductase= large
-4th: cytochrome C=small
-5th: cytochrome C oxidase= passes its reducing power to O2, which is reduced to H20 (reason we breathe!) - Where are protons pumped during electron transport? Where does this create a lower pH?
- protons are pumped out of matrix, into intermembrane space-- so, electron transport creates a large proton gradient with pH being HIGHER INSIDE the matrix than the rest of the cell
- The pumping of protons to form a pH gradient has a + or - delta G?
-
a large, positive delta G-- making UNDOING it favorable enough to drive ATP synthesis
-creation of the proton gradient is dependent upon the very negative delta G of e- transport - How many protons are required for ATP?
- 4 protons
- How many ATP are made every time an FADH2 is reoxidized to FAD?
- 1.5...FADH2 pumps 6 protons across inner mitochondrial membrane into intermembrane space/ 4 protons per ATP = 1.5 ATP
- How many ATP are generated from each molecule of NADH?
- 2.5....NADH pumps 10 protons across inner mitochondrial membrane into intermembrane space/ 4 protons per ATP= 2.5 ATP
- What are the molecules used/formed in Glycolysis?
-
-2 ATP (used)
4 ATP
2 NADH - What are the molecules formed/used in Pyruvate Dehydrogenase Complex?
- 2 NADH (formed)
- What are the molecules formed/used in the Krebs Cycle?
-
6 NADH
2 GTP
2 FADH2
(formed) - The # NADH in Glycolysis convert to different amonts of ATP in eukaryotes vs. prokaryotes. What are these ATP values? And why do they differ?
-
2 NADH * 1.5 ATP/NADH in eukaryotes =3 ATP in eukaryotes
2 NADH * 2.5 ATP/NADH in prokaryotes= 5 ATP in prokaryotes
Difference is on account of e-'s generated in glycolysis being transported into the mitochondria before entering ETC (and when does, fed directly to ubiquinone)-->1.5 ATP for cytosolic NADH instead of 2.5 for matrix NADH
-Bacteria don't need to transport across any membrane -->discrepancy b/t ATP from NADH in prokaryotes vs. eukaryotes - What is the total amount of ATP made in eukaryotes/prokaryotes?
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30 ATP eukaryotes
32 ATP prokaryotes - Aerobe vs. anaerobe in relation to ATP involvement
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-Aerobes: use e- transport to produce the proton gradient, which is used in turn to drive ATP synthesis
-Anaerobes: consume ATP to produce a proton gradient - What drives lactose import in both anaerobic and aerobic bacteria?
- a proton gradient
- Uncoupling?
- induced by substances which carry protons through the membrane, reducing the proton gradient w/o generating ATP
- Osmosis: Hypertonic, Hypotonic, Isotonic
-
Osmosis: the movement of water molecules from an area of high concentration of water to an area of low water concentration
-hypertonic solution: contain a high concentration of solute relative to another solution (e.g. the cell's cytoplasm). When a cell is placed in a hypertonic solution, the water diffuses out of the cell, causing the cell to shrivel
-hypotonic: contain a low concentration of solute relative to another solution (e.g. the cell's cytoplasm). When a cell is placed in a hypotonic solution, the water diffuses into the cell, causing the cell to swell and possibly explode
-isotonic: contain the same concentration of solute as an another solution (e.g. the cell's cytoplasm). When a cell is placed in an isotonic solution, the water diffuses into and out of the cell at the same rate. The fluid that surrounds the body cells is isotonic. - What is necessary for optical activity?
- Optical activity is the ability of a substance to rotate plane-polarized light. To be optically active, a substance MUST be CHIRAL, and 1 enantiomer must be present in excess of the other.
- What effect does lactic acid have on respiratory rate?
- Lactic acid will decrease the pH of plasma. CO2 dissolved in plasma also decreases the pH through conversion to carbonic acid. The respiratory rate is regulated to increase when the plasma becomes more acidic, getting rid of CO2 and making the plasma more alkaline again.
- What are facultative anaerobes?
- These are able to optionally respond a certain way to circumstances (i.e., fermentation instead of glycolysis) rather than by nature.
- ALCOHOL--> KETONE IS CONSIDERED A...
- DEHYDROGENATION
- Fatty acid oxidation, the citric acid cycle, and the decarboxylation of pyruvate to acetyl-CoA (transition between glycolysis and TCA) occur in which location?
- In the mitochondrial matrix
- Depriving a cell of oxygen would have what effect on the cycle of B-oxidation (fatty acid break down)?
- FADH2 and NADH would accumulate (wouldn't be oxidized) and the cycle would slow