Exam 1 Flashcards
Change in Enthalpy
🔺H=🔺G+T🔺S
🔺H must be <t>
</t>
Standard Gibbs Free Energy
Chemical : 🔺G0 @ T=25oC and pH=0
Biological : 🔺G0’ @ T=25oC and pH=7
Using Gibbs Free Energy
For reversible reaction: A+B yields Y+Z
🔺G=🔺G0’+RT ln[Y][Z]/[A][B]
@ Equilibrium 🔺G=0 and ratio=Keq
Therefore
🔺G0’= - RT ln Keq
Coupled Reactions
Use free energy released by an exergonic reaction to drive second energonic reaction.
Reduction of Pyruvate
Endergonic
Pyruvate + 2H++2e- —> Lactate
🔺G0’= 36 kJmol-1
Reduction of NADH/H+
Exergonic
NADH + H+—>NAD++2e- +2H+
🔺G0’ = -62 kJmol-1
Coupled Reaction
Exergonic
Pyruvate + NADH + H+—> NAD++ Lactate
🔺G0’ = -26 kJmol-1
Activation Energy
Ea
Amount of energy required to bring all molecules in a mole of reactant at a given temperature to a reactive state.
Increasing T decreases Ea by increasing kinetic energy of all molecules.
Adding enzyme reduces Ea and increasses reaction rates by 103 to 107 times.
Covalent Bonds
1) Van der Waals
2) Hydrogen
3) Ionic
4) Hydrophobic Bonds
1) Interaction between dipolar molecules
2) Sharing of electrons between dipolar molecules
3) Anion/Cation bonding
4) Non-polar water-averse regions or molecules.
Weak Bonds and Temperature
Affects and Consequences
Increasing Temperature
- weakens Hydrogen, Van der Waals, and Ionic bonds
- strengthens Hydrophobic bonds
Consequence: denaturing of 3D structures (DNA, proteins, membranes)
Can lead to clumping/strengthening of hydrophobic elements.
Water
Unique - Covalent and Polar
Hydrogen bonds inividually weak (1-5 kcal to break 1 mole)
Overall effects are strong - high melting/boiling points and high surface tension/cohesion.
Colligative Properties
Depend on concentration of solute(not size or type)
Increasing solute concentration of water increases boiling point, vapor/osmotic pressure, and reduces freezing point.
Rate of diffusion
Rate (dQs/dt) depends on solute size, electrical charge and solubility.
dQs/dt = P(C1-C2)
P=permeability constant (cm/s)
Partition coefficient (K)
K=[solute]lipid/[solute]water
pH
pH = -log[H+]
In pure water at 25oC, pH = 7
Strong Acids and Bases
vs
Weak Acids and Bases
Strong - readily release ions
Weak - are only partially ionized under biological conditions
Dissociation of Acids -
1) General Formula
2) pK
3) Consequences
1) HA <=> H+ + A-
2) pK = -log10Keq = pH at which [A-] = [HA]
3) pK (pH at equillibrium) is low, ex: <3 for HCl and Sulfuric Acid
Henderson-Hasselbach equation
pH = pK + log[A-] / [HA]
pH importance
Low pH means [H+] is high, amino and carboxyl protonated (valence electron is positive).
High pH means [H+] is low, amino and carboxyl groups ionized(valence electron is negative).
Buffers
1) What are they?
2) Adding Acid
3) Limits
4) Ideal conditions?
1) Usually weak acids
2) Liberated protons can bind with buffer and effect is reduced
3) Will only work over limited pH range
4) When pH=pK because half of buffer works against each direction of pH
Events of Enzyme Lowering Ea
3 Steps
1) Non-covalent bonding leads to formation of Enzyme-Substrate Complex
2) Non-covalent bonding leads to formation of Enzyme-Product Complex
3) Dissociation yields free Enzyme & Product
How Do Enzymes Work?
Substrate binds to active site and induces a change in the substrate of the structure:
Shifit in electron distributions, change in shape, pairs of destabilized reactants can be brought into proper conformity and proximity.
These changes reduce Ea
What Influenes rates of Enzymatic Reactions?
Increase in concentration of products creates competition.
Initial concentration of substrate since addition of substrate leads to max velocity at which nothing else happens.
Physiochemical environment such as temperature, pH and hydrostatic pressure.
1) Michaelis-Menten Kinetics
Hint : Involves V, S, and Km
2) Exception
1) V = Vmax x [S] / ([S] + Km)
where Vmax is the velocity at which enzyme saturation occurs.
2) Km = [S] required to reach 1/2 Vmax
3) enzymes with multiple binding sites cooperate because binded enzyme experiences change from substrate too, which promotes more binding.
1) Factors Determining Vmax
2) kcat
1) Number and catalytic effectiveness of enzyme molecules
2) Turnover number - Substrate molecules to product molecules per second, per saturated enzyme molecule
Biomolecules
Energy Carriers
Proteins
Carbohydrates
Lipids
Nucleic Acids
Biomolecule :
Energy Carriers
Adenotriphosphate (ATP) to ADP yields 🔺G0’ = -30.5 kJ/mol
Acetyl CoA produced within mitochondria can ber used to produced ATP, GTP and Heat
Acetyl CoA and Ketone Transport
When blood-glucose levels are low, insulin production inhibited.
When Insulin levels are low, increase in fat metabolism produces Acetyl CoA.
Liver cells convert Acetyl CoA —> ketones (ketogenesis)
In the CNS, neural cells convert ketones to Acetyl CoA
Biomolecules :
Proteins
Amino Acids bonded together with peptide bonds.
Can have 4 structural levels, each shape related to function.
Biomolecules :
Carbohydrates
Monosaccharide: Glucose, Fructose and Galactose modify macromolecules
Disaccharides: Obtained by diet but need to be broken down to use
Polysaccharides: Glycogen and Startch serve in energy storage
Biomolecules :
Lipids
Diverse group that includes :
Fatty Acids (saturated or unsaturated)
Triglycerides (glycerol backbone with three fatty acids)
Phospholipids which are amphipathic
Steroids (lipid soluble so can diffuse through cell membrane)
Biomolecules :
Nucleic Acids
Nucleotide polymers made of sugar, phosphate, and a base
Dephosphorylation of Phosphocreatine
Creatine Phosphokinase(CPK) drives Phosphocreatine and ADP reaction to yield ATP, creatine and heat
🔺G0’ = -12.6 kJ/mol
Pros and Cons of CP hydrolysis
Pros : Max muscle power, no harmful by-products, no effect on pH, reaction is reversible.
Cons: Short duration (muscle stores rapidly exhausted), no beneficial by-product.
Anaerobic Glycolysis
Glucose + ATP
Glucose 6-phosphate + Glycogen
Fructose bisphosphate splits
Glyceraldehyde 3-phosphate AND Dihydroxyacetone phosphate (which forms a second G3p
Both G3ps combine with one NaD+ each to yield 2 NADH
(2) 1, 3 Biphosphogylcerates combine with one ADP each to yield 2 ATP
(2) 3-Phosphoglycerates —–>2-Phosphoglycerates yield H20
(2) Phosphoenolpyruvates combine with one ADP each to yield 2 ATP ENDING IN 2 PYRUVATES
Glycolysis Yields
1) ATP
2) 🔺G0’
3) Total Energy
4) Bonus
5) Problem
1) 2 ATP per Glucose (61.0 kJ/mol)
2) -73 kJ/mol
3) 134 kJ/mol
4) 2 moles of water per Glucose
5) 2 moles of NAD+ consumbed per Glucose
Anaerobic Solution for use of NAD+ in Glycolysis
and 🔺G0’
Pyruvate + NADH + H+<==>NAD+ + Lactate
🔺G0’ = -25.1 kJ/mol
Energetic Effect of Glycolysis
1) Glucose —> 2 Pyruvate
2) Glucose —> 2 Lactate
3) Glucosyl —2 Pyruvate
1) -134 kJ/mol
2) -184 kJ/mol
3) -152 kJ/mol
Pros and Cons of Anaerobic Glycolysis
Pros : Maximum muscle power possible, no Oxygen needed, 2 moles of water per glucose.
Cons : Short duration, low yield, Lactic acid, lowers pH, not reversible.
Oxidative phosphorylation
Four steps
1) Glycolysis but then the resulting 2 Pyruvate to Lactate
2) TCA cycle x two
3) Electron Transport System
4) Proton Motive Force
Tricarboxylic Acid Cycle
Acetyl CoA –> Citrate –> Isocitrate –>
2-Oxoglutarate (yielding NADH and CO2) –>
Succinyl CoA (yielding NADH and CO2) –>
Succinate (yielding GTP) —>
Fumarate (yielding FADH2) –>
Malate –>
Oxalaoacetate (yielding NADH) –>
Citrate
Electron Transport System
Complex 1 collects electrons from NADH
Complex 2 transfers electrons from succinate to FAD (ubiqunone) yielding Fumarate
Complex 3 transfers H+ out as electron passes through then onto cytochrome c
Complex 4 transfers H+ out and also creates H2O from O2
Complex 5 transfers a H+ in and creates an ATP from ADP
Proton Motive Force
Electrochemical gradient created by ETS allows H+ to return via Complex V (energy transformed into heat) and ATP created from ADP.
Oxidative phosphorylation theoretical yield
Glycolysis: 2 ATP + 2H2O + 2 NADH/H+
Pyruvate -> Acetyl CoA: 2 NADH/H+
TCA: 2 GTP + 2 FADH2 + 6 NADH/H+
10 NADH/H+ -> NAD+: 30 ATP + 10 H2O
2 FADH2 -> FAD: 4ATP + 2 H2O
Total: 36 ATP + 2 GTP & total Gibbs: -2854kJ/mol & 14 moles of H2O per glucose
Pros and Cons of Aerobic Glycolysis
Pros: High yield (2854 kJ/mol glucose), long duration, beneficial by-products.
Cons: Max muscle power not possible, requires O2, harmful by-products, lowers pH, overall not reversible.
Lipid Profile
Phosphoglycerides - phosphatidylcholine, phosphatidylserine, phosphatydlethanolamine.
Sphingolipids
Glycolipids
Cholesterol
Cholesterol
Strengthens interactions between polar heads and disrupts interactions between polar tails.
Reduces permeability, alters membrane fluidity
Membrane Heterogenity
Inner and outer layers different - outer PC and glycolipids, inner PE and PS
Lipid raftes - increased concentration of Cholesterol and glycolipids. Increases rigidity and thickness, reduce fluidity.
Passive Diffusion
Needs concentration gradient.
Does not need special transporters.
May enter if - can break H-bonds with water or can dissolve in lipid
Rate of Diffusion
J= D(C1-C2)/X
useful when interest in the effect of variation with respect to thickness
Facilitated Diffusion
Needs Electrochemical gradient AND specialized membrane proteins.
Used Channels, pores and carrier proteins.
Calculating Equilibrium - Nernst Equation
Ex = (RT/zF) ln ( {X} outside / {X} inside)
