Chapter 2 - Biochemistry and Cellular Respiration

Question 1

Enthalpy is defined by the following equation:

Answer 1

ΔH = ΔE - PΔV

H = enthalpy

E = bond energy of products or reactants in a system

P = pressure

V = volume

NOTE: H ≈ E, since the change in volume is negligible

Question 2

Standard free energy change denoted __1.__ , with all reactants and products present at __2.__ concentration

Standard free energy change determined at pH __3.__ is denoted __4.__ , which is related to the ____5.____ for a reaction by the following equation:

__________________6.___________________

Answer 2

1. ΔG^o
2. 1 M
3. 7
4. ΔG^o’
5. equilibrium constant (K ‘_eq)
6. ΔG^o’ = -RTln(K ‘_eq)

Question 3

It is K_eq that says something about the nature of ___1.___ and ___2.___ , since it describes their concentrations after ___3.___ has been reached. K_eq is the ratio at equilibrium.

K says nothing about the properties of the ___4.___ and ___5.___. K is calculated from whatever the initial ___6.___ happen to be. K is the ratio in any given set-up.

Answer 3

1. reactants
2. products
3. equilibrium
4. reactants
5. products
6. concentrations

Question 4

ΔG for a reaction in the body

ΔG = __1.__ + __2.__

The three factors that determine whether a reaction will occur spontaneously include:

_____3._____

_____4._____

_____5._____ (applies when you are in the lab)

Answer 4

1. ΔG^o’ ( = -RTln(K ‘_eq) )
2. RTln(K)
3. the intrinsic properties of the reactants and products (ΔG^o’)
4. the concentrations of reactants and products (RTlnK)
5. temperature

Question 5

Spontaneous means that a reaction may proceed without _____1._____ , but says nothing about the _____2.______

Answer 5

1. additional energy input
2. rate of reaction

Question 6

Two important characteristics of a catalyst is that it…

1. __________
2. __________

Answer 6

1. lowers the E_a of a reaction by stabilizing the transition state, making its existence less thermodynamically unfavorable
2. is NOT consumed in the reaction; it is regenerated with each reaction cycle

Question 7

In reaction coupling, one very favorable reaction is used to drive an unfavorable one.

This is possible because _____1._____

The ΔG^o’ for the hydrolysis of one phosphate group from ATP is __2.__

In the cell, ΔG is about __3.__ , so in the cell it is even ___4.___ favorable

Answer 7

1. free energy changes are additive
2. -7.3 kcal/mol
3. -12 kcal/mol
4. more

Question 8

Enzymes DO NOT alter _____1._____ because it only has a _____2._____

Answer 8

1. reaction equilibria (K_eq unaffected)
2. kinetic role

Question 9

How does ATP hydrolysis drive unfavorable reactions? (2 examples)

Answer 9

1. causing a conformational change in a protein; in this way ATP hydrolysis can be used to power energy-costly events like transmembrane transport
2. transfer of a phosphate group from ATP to a substrate

Question 10

Which configurations (D or L) are found in animals, for amino acids and sugars?

Answer 10

• L amino acids
• D sugars

Question 11

The most effective competitive inhibitors resemble the ____1.____ which the ____2.____ normally stabilizes

Structurally, competitive inhibitors must at least resemble the ____3.____

Answer 11

1. transition state
2. active site
3. substrate

Question 12

Describe what a recognition pocket is and how it applies to enzymes

Answer 12

• This is a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides
• NOTE: the enzyme always cuts polypeptides at the same site, just to one side of the recognition residue (ex. chymotrypsin always cuts on the carboxyl side of one of the large hydrophobic residues Tyr, Trp, Phe and Met)

Question 13

What are the 4 ways that enzymes are regulated?

Answer 13

1. covalent modification - phosphorylation
2. proteolytic cleavage - zymogens (inactive proteins) activated by cleavage (protease)
3. association w/other polypeptides - separate regulatory subunit (whose association with the enzyme is either inhibitory or stimulatory)
4. allosteric regulation - generally noncovalent and reversible (can increase or decrease catalysis upon binding)

Question 14

What is the difference between kinases and phosphorylases?

Answer 14

Phosphorylases phosphorylate proteins like kinases, but use free-floating inorganic phosphate (P_{<em>i </em>}) in the cell instead of ATP

Question 15

What are the three ways to oxidize?

Answer 15

1. attach oxygen (or increase the # of bonds to O)
2. remove hydrogen
3. remove electrons

Question 16

What are the three ways to reduce?

Answer 16

1. remove oxygen (decrease the # of bonds to O)
2. add hydrogen
3. add electrons

Question 17

When one atom gets reduced, another one must be ___1.___ ; hence the term ___2.___

Answer 17

1. oxidized
2. redox pair

Question 18

The PDC is composed of three different enzymes. Why might a complex of three enzymes be more efficient than three independent enzymes?

Answer 18

Simply because intermediates are passed directly from active site to active site, without having to diffuse

Question 19

Which molecules are formed/used in glycolysis (assuming we start with one glucose)?

Answer 19

• 2 ATP used
  
  • hexokinase (1) and PFK (3)
• 4 ATP produced
  
  • phosphoglycerate kinase (7) and pyruvate kinase (10)
• 2 NADH produced
  
  • glyceraldehyde 3 phopsphate dehydrogenase (6)

Question 20

Which molecules are formed/used in PDC (assuming we start with one glucose)?

Answer 20

• 2 NADH
  
  • PDC performs an oxidative decarboxylation, in which a molecule is oxidized to release CO₂ and produce NADH
  • PDC also changes pyruvate into an activated acetyl unit (activated = acetyl is not floating around freely but rather is attached to a carrier named coenzyme A)

Question 21

Coenzyme is basically a long handle with a sulfur at the end, abbreviated CoA-SH. It is used in many reaction systems to pass ___1.___ around (e.g., ___2.___ and ___3.___ synthesis and degradation)

When loaded with an ___4.___ , CoA-SH is abbreviated ___5.___

The bond between sulfur and the ___6.___ group is ___7.___ energy, making it easy for acetyl-CoA to transfer the ___8.___ fragment into the ___9.___ cyle for further ___10.___

Answer 21

1. acetyl units
2. fatty acid
3. cholesterol
4. acetyl unit
5. acetyl-CoA
6. acetyl
7. high
8. acetyl
9. Krebs
10. oxidation

Question 22

A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a ___1.___ (examples include TPP [thiamine pyrophosphate] with the thiamine being vitamin __2.__ ; vitamins often serve as prosthetic groups)

Various organic and inorganic substances necessary to the function of an enzyme, but which never actually interact with the enzyme are ___3.___ (examples include Fe²⁺, Mg²⁺, Mn²⁺, Zn²⁺ )

Answer 22

1. prosthetic group
2. B₁
3. co-factors

Question 23

Which molecules are formed/used in the Krebs Cycle (assuming we start with one glucose)?

Answer 23

• 6 NADH
  
  • isocitrate dehydrogenase (3), α-ketoglutarate dehydrogenase complex (4), and malate dehydrogenase
• 2 FADH₂
  
  • succinate dehydrogenase
• 2 GTP
  
  • succinyl-CoA synthetase

Question 24

How many pumped protons does it take produce ATP? What is the breakdown?

For every NADH that is oxidized to NAD⁺ , the three large electron transport proteins pump about __1.__ protons across the inner mitochondrial membrane, into the intermembrane space

By bypassing the first proton pump, FADH₂ is only responsible for the pumping of __2.__ protons

Cytosolic NADH shuttles it’s electrons directly to ubiquinone ( just like FADH₂ ); total protons pumped = __3.__

Answer 24

• 4 protons to produce ATP
  
  • 3 to generate ATP
  • 1 to shuttle P_<em>i</em> into the matrix

1. 10 = 2.5 ATP
2. 6 = 1.5 ATP
3. 6 = 1.5 ATP (less than prokaryotes; explains why they generally produce 2 more ATP per cellular respiration since their NADH does not have be transported via the glycerol phosphate shuttle)

Question 25

Order of Electron Transport in the ETC

• ___1.___ dehydrogenase (aka ___2.___ reductase)
  
  • pumps __3.__ protons
• ___4.___ (aka Coenzyme __5.__ )
• Cytochrome __6.__ reductase
  
  • pumps __7.__ protons
• Cytochrome __8.__
• Cytochrome __9.__ oxidase
  
  • pumps __10.__ protons

Answer 25

1. NADH
2. Coenzyme Q
3. 4
4. Ubiquinone
5. Q
6. C
7. 4
8. C
9. C
10. 2