MCAT Study Guide Biology Ch. 2 – Thermodynamics and Cellular Respiration 2017-08-15T06:45:06+00:00

I.          2.1 THERMODYNAMICS:  the study of the energies of chemical reactions (heat and potential energy)

A.     1st law:  the law of conservation of energy; energy in the universe is constant

1.     2nd law:  disorder (entropy) tends to increase

B.     Gibbs free energy:

1.     ΔG = ΔH – TΔS  (H = enthalpy, which is heat or thermodynamic potential)

a)   ΔG > 0 → needs heat, nonspontaneous

b)   ΔG < 0  → energy released, spontanous

2.     ΔH = ΔE – PΔV (E = bond energy)

C.    Standard Gibbs free energy:

1.     ΔGº → all at 1 M concentration

2.     ΔGº’ → 1 M concentration and @ pH 7

3.     ΔGº’ = -RtlnK’eq (R = gas constant, Keq = ratio of products to reactants at equilibrium)

a)     Keq =

[C]eq[D]eq/[A]eq[B]eq

4.     Remember:  spontaneity says nothing about the reaction rate!

II.          2.2 KINETICS AND ACTIVATION ENERGY

A.     Kinetics:  the study of reaction rates

B.     Activation energy (Ea):  energy required to produce a transient intermediate (denoted ‡)

1.     ↑ Ea = slower rxn rate

2.     The energy for bob to apply for a job is higher than Bob with or without a job

C.    Catalysts (enzymes) will lower Ea but will not affect ΔG!!

D.    Because enzymes lower Ea, they increase the rate at which favorable rxns occur!

1.     Ea is lower with catalyst than without, but notice ΔG does not change!

2.     ΔG represents net change of energy from reactants to products

 

E.     ATP as energy source:  useful for reactions with + ΔG

1.     Reaction coupling:  a favorable rxn is used to drive an unfavorable rxn by combining 2 together

2.     ATP hydrolysis drives unfavorable reactions

3.     Ex:

 

A + PO42- → APO42-                         ΔG = +2 kcal/mol

APO42-  + B → C + PO42-                ΔG = +5 kcalmol

total ΔG = +7 kcal/mol

ATP → ADP + PO42-                           ΔG = -12 kcal/mol

A + PO42-  → PO42-                          ΔG = +2 kcal/mol

APO42-  + B → C + PO42-                  ΔG = +5kcal/mol

total ΔG = -5 kcal/mol

4.     Note that reaction coupling will alter total free energy, making an unfavorable rxn proceed!

III.          2.3:  ENZYME STRUCTURE AND FUNCTION

A.     Enzymes:  may consist of a single polypeptide chain, or several subunits in quaternary structure (globular)

IV.          2.4:  REGULATION OF ENZYME ACTIVITY

A.     Covalent modification – a phosporyl group (normally from ATP) can be covalently added to enzymes to either activate or inactivate them

B.     Proteolytic cleavage – protease can activate inactive forms of enzymes (called zymogens)

C.    Associated with other polypeptides – some enzymes are regulated by another portion of themselves; either inhibitive or required to function

1.     Constitutive activity – continuous activity (when regulatory subunit is removed)

D.    Allosteric regulation – enzymes can have multiple active sites and are regulated by the activity of these other sites

1.     These allosteric sites are located far away from the active site

2.     Binding of the allosteric regulator to these allosteric sites is generally noncovalent and reversible

3.     When bound, these alter the conformation of the enzyme to increase or decrease catalysis

E.     Feedback inhibition  – enzymes are usually part of a pathway, with multiple reactions and enzymes needed to go from reactants to final products

1.     In a pathway where the following enzymes catalyze each reaction, too much of the end product “D” will shut off Enzyme E1

2.     This is negative feedback, or feedback inhibition

3.     There is also feedback stimulation (but this is less common)

F.     Feedforward stimulation is common, where A might stimulate E3

 

V.          2.5:  BASIC ENZYME KINETICS:  the study of the rate of formation of products from substrates in the presence of enzymes

A.     Reaction rate (V):  total amount of product formed in mol/s

1.     Depends on the concentration of the substrate [S], and the enzyme

2.     if [S] is low, doubling it will double V (linear relationship) until all active sites of enzymes are occupied most of the time

3.     if the active sites of enzymes are occupied ALL of the time, adding more substrate does not increase reaction rate, and rate is denoted as Vmax

4.     Michaelis constant (Km):  the substrate concentration at which V is ½ of Vmax

5.     A low Km means high enzyme affinity

 

B.     Cooperativity:  Some enzymes have multiple binding sites, and the binding of 1 site allosterically increases the affinity of other subunits (think about hemoglobin)

1.     Tense:  the conformation of the above enzyme prior to binding, with low substrate affinity

2.     Relaxed:  the conformation of the above enzyme with increased affinity, after partial binding

a)     Region 1:  at low [S], the enzyme complex has low affinity for substrate (in tense state), adding more substrate doesn’t really increase the reaction rate until…

b)     Region 2:  the range of substrate concentrations where adding substrate greatly increases reaction rate because the enzyme is in a relaxed state

c)     Region 3: represents enzyme saturation

C.    Inhibition of enzyme activity

1.     Competitive inhibition

a)     Molecules that compete with the substrate for binding to the active site (Vmzx not affected; just increase concentration of substrate to increase competition)

b)     Km is affected; takes higher concentration to get to ½Vmax

2.     Noncompetitive inhibition

a)     Molecule binds at an allosteric site to “turn off” molecule; Vmax is affected, regardless of [S]

b)     Km is typically not affected

 

VI.          2.6 CELLULAR RESPIRATION

A.     Vocabulary

1.     Photosynthesis – the process by which plants store energy from the sun in bond energy of carbs

2.     Photoautotrophs – organisms that use the sun to produce their own food (plants)

3.     Chemoheterotrophs – organisms that use energy from other living organisms to make their own food

4.     Catabolism:  breaking down molecules (we get energy from glucose via oxidative catabolism:

a)     C6H12O6 + 6O2 → 6CO2 + 6H2O

B.     OXIDATION AND REDUCTION:

1.     Oxidation (3 meanings, opposite of reduction)

a)     Attach oxygen

b)     Remove hydrogen

c)     Remove electrons

2.     Reduction (3 meanings, opposite of oxidation)

a)     Remove oxygen

b)     Attach hydrogen

c)     Attach electrons

d)     *When molecules are reduced, they are “compressed”, have more stored energy, they want to be oxidized and release energy

3.     Oxidizing agents allow for the oxidation of other chemicals by getting reduced themselves

 

C.    4 STEPS OF CELLULAR RESPIRATION (also optional fermentation)

 

1.     GLYCOLYSIS:  splits 6C glucose into 2-3C pyruvates + 2ATP + 2NADH

a)     All cells do glycolysis

b)     Location: cytoplasm

c)     Oxygen independent!!

(1)   F6P → F 1,6-bP is practically irreversible

(2)   This is a key regulatory point of glycolysis

(3)   Known as a “committed step”; F1,6-bP can only go down glycolysis, where F6P can be used elsewhere

(4)   allosterically regulated by ATP

(5)   5th rxn:  NADH is produced when an aldehyde is oxidized to COOH

d)     NET RXN:  Glucose + 2ADP + 2Pi + 2NAD+ → 2PYR + 2ATP + 2NADH + 2H2O + 2H+

(1)   Glycolysis produces 2 NADH

 

2.     FERMENTATION

a)     Anaerobic conditions only

b)     Goal:  regenerate NAD+

c)     Location:  cytoplasm

d)     Eukaryotes:  lactic acid fermentation

e)     Prokaryotes:  alcoholic fermentation (ethanol)

f)       Excessive lactate is brought back to the liver where it is converted back to pyruvate

 

3.     PYRUVATE DEHYDROGENASE COMPLEX (PDC):  Pyruvic acid into Acetyl CoA

a)     Pyruvate gets oxidatively decarboxylated (oxidized to release CO2)

b)     Location:  mitochondrial matrix

c)     Goals:  3C → 2C, NADH

(1)   Once pyruvate is decarboxylated, the acetyl group is “activated” by attachment to coA.

(2)   The S-C bond is high energy, making it easy to transfer the acetyl group to the Krebs cycle.

(3)   Prosthetic group:  non protein molecule covalently bonded to an active site of an enzyme

(4)   TPP (thiamine pyrophosphate) is a prosthetic group of the PDC and Krebs

(5)   Cofactors:  various substances necessary to the function of the enzyme, but never interact with the enzyme (?)

 

4.     KREBS/TCA/CITRIC ACID CYCLE: 

a)     Acetyl CoA gets oxidized, lots of NADH and FADH2 are produced

b)     Location:  mitochondrial matrix

(1)   OVERVIEW OF KREBS

(2)   STAGE 1 KREBS

(a)   4-C OAA (oxaloacetate) combines with the acetyl group of Acetyl-CoA to form 6-C citric acid

(3)   Stages 2 and 3:

(4)   Stage 2:

(a)   Citrate (isocitrate) is further oxidized to release CO2 and produce NADH from NAD+; the product is alpha ketoglutarate (5C)

(b)   Alpha ketoglutarate is oxidatively decarboxylated to produce succinyl CoA, releasing another CO2 and NADH

(5)   Stage 3: OAA is regenerated; don’t worry about the individual steps

5.     ELECTRON TRANSPORT CHAIN

a)     Location: along inner mitochondrial membrane (eukaryotes) or cell membrane (prokaryotes)

b)     NADH and FADH2 are oxidized (e removed), and the energy released is used to pump protons out of the mitochondrial matrix (I think the e passing through drive this pump)

c)     Proton gradient drives ADP → ATP

d)     ATP synthase allows H+ back into mitochondrial matrix, and it captures their energy to make ATP

 

D.    ENERGETICS OF GLUCOSE CATABOLISM 

1.     Each NADH that is oxidized to NAD+ results in 10 H+ pumped across inner mitochondrial membrane

2.     Each FADH2 → FAH results in 6 Hpumped across the IM membrane

3.     Each ATP made by ATP synthase requires 4 H+ to pass through

4.     FFADH2 → FAD = 1.5 ATP

5.     NADH → NAD+ = 2.5 ATP

a)     However, because these molecules need to be transported to the mitochondria (which requires energy) by the GLYCEROL PHOSPHATE SHUTTLE, there is a slight discrepancy in energy produced

Process Molecules formed/used ATP equiv Net ATP
Glycolysis -2 ATP -2 ATP
4 ATP 4 ATP
2 NADH ≈ 3 ATP* 5 ATP
PDC 2 NADH ≈ 5 ATP 5 ATP
Krebs 6 NADH ≈ 15 ATP
2 FADH2 3 ATP
2 GTP 2 ATP 20 ATP
ETC (10 NADH, 2 FADH2) Already counted
TOTAL 30 ATP

b)     *these NADH need to be shuttled from cytoplasm to the mitochondria

 

E.     OTHER METABOLIC PATHWAYS OF THE CELL

1.     Glycogenolysis:  breakdown of glycogen, responds only to glucagon

2.     Gluconeogenesis:  conversion of non-carbohydrate precursor molecules into oxalate then glucose; occurs only when there are no dietary or liver stores of glucose (precursors include carbon skeleton of AAs, lactate, pyruvate)

3.     β-oxidation:  fatty acids are browke down this way in hepatocytes

a)     2 C are removed at a time, which are then converted into acetyl-CoA and then enter the Krebs

b)     The glycerol backbone gets converted to glucose and enters cellular respiration

4.     AA catabolism:  AAs are broken down, often converted to urea for excretion; the remaining carbon skeleton (α-keto acid) can be broken down into H2O and CO2 or converted to glucose or acetyl-CoA

MCAT Study Guide Biology - Kim Matsumoto


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