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Biochem midterm 2 > Final > Flashcards

Final Flashcards

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1
Q

What is the first law of thermodynamics?

A

Energy cannot be created or destroyed, only transformed

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2
Q

What is the second law of thermodynamics?

A

All systems trend towards increasing entropy (increasingly disordered)

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3
Q

Define entropy?

A

entropy is a quantitative expression of the degree of randomness or disorder of the system.

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4
Q

When the delta S is negative what does it mean?

A

the disorder of the system has decreased

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5
Q

When the delta S is positive what does it mean?

A

the disorder of the system has increased.

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6
Q

Define enthalpy?

A

Enthalpy is the heat content of the system. it reflects the number and kinds of chemical bonds in the reactants and products.

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7
Q

When delta H is negative, what does it mean?

A

the chemical reaction produced heat and is exothermic

The heat content of the products is less than the reactants.

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8
Q

When delta H is positive, what does it mean?

A

the reaction system absorbs heat from its surroundings and is endothermic.

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9
Q

Define the Gibbs free energy? and give the equation

A

is equal to the amount of energy capable of doing work during a reaction at constant temperature and pressure.
deltaG= deltaH-T(deltaS)

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10
Q

When delta G is positive, what does it mean?

A

the product contains more free energy than the reactants. non-spontaneous endergonic.

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11
Q

When delta G is negative, what does it mean?

A

the products contain less free energy than the reactants. spontaneous exergonic

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12
Q

What is the chemical equilibrium?

A

the point in a reaction where the rates of the forward and reverse reactions proceed at an equal rate.

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13
Q

How do you calculate the keq?

A

concentration of products/concentration of reactants.

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14
Q

Give the equation for deltaG’

A

DeltaG’= -RT(lnK’eq)

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15
Q

Give the equation for delta G

A

DeltaG= deltaG’+ RT(lnKeq’)

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16
Q

When you have two delta G’ reactions and you want to know the deltaG’ of them both together, what do you do?

A

add both the delta G’ together.

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17
Q

The conversion of ATP to ADP +Pi is exergonic or endergonic?

A

exergonic

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18
Q

Why do the electrons of ATP have high potential energy?

A

Because the four negative charges in its three phosphate groups repel each other.

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19
Q

Why is the hydrolysis of ATP highly favourable under standard conditions?

A
  • better charge separation in products
  • more favourable resonance stabilization of products
  • Better solvation of products.
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20
Q

If you want to know the Keq’ of two reactions knowing their particular Keq’, what do you do?

A

multiply the two Keq’

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21
Q

What are the functions of hexokinases?

A
  • can regulate the rate at which glucose is used in glycolysis
  • can help regulate the amount of glucose-free in the body.
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22
Q

What are the two-steps groups involved in ATP-dependent reactions?

A
  1. a phosphoryl group is transferred from ATP to glutamate

2. The phosphoryl group is displaced by ammonia NH3 and release as Pi.

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23
Q

Where does the ATP come from?

A

Oxidation-reduction reactions

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24
Q

What happens when an atom is oxidized?

A

loses an electron

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25
what happens when an atom is reduced?
gains an electron
26
What is the impact of a reduced compound on free energy?
the more reduced a carbon atom is, the more free energy is released upon oxidation.
27
Which atoms are sharing the bonds with the highest level of energy?
C-H and C-C bonds are shared more equally and have higher potential energy
28
Which bonds are holding less energy?
C-O bonds are held more tightly and have low potential energy
29
What is the mechanism of an electron transport chain?
electron transported down a series of acceptors as long as they are attracted by a sufficiently electronegative element.
30
What is the reduction potential?
affinity for electrons--> higher E= higher affinity.
31
What is the equation of Gibbs free energy based on the reduction potential?
deltaG'=-nFdeltaE' n= number of electron transferred F= faraday constant
32
What is the equation to determine the reduction potential?
Delta E'= -(RT/nF) *(ln keq)
33
if you want to combine the reduction potential of 2 reactions what do you do?
delta E'= E'(acceptor)- E'(donor)
34
What are the three redox reactions in which glucose is oxidized?
1. Glycolysis 2. Tricarboxylic cycle 3. Electron transport and oxidative phosphorylation all part of cellular respiration
35
What are the two electron carriers involved in the oxidation of glucose?
NADH | FADH2
36
Give a general description of glycolysis
a six carbon glucose is broken down into two three-carbon pyruvate
37
Give a general description of the pyruvate processing?
each pyruvate is oxidized to form acetyl CoA
38
Give a general description of the citric acid cycle
Each acetyl CoA is oxidized to CO2.
39
Give a general description of the electron transport and oxidative phosphorylation
electrons move through a transport chain and their energy is used to set up a proton gradient, which is used to make ATP
40
What happens in cells when oxygen is absent as an electron acceptor?
fermentation and anaerobic respiration
41
What are the two fundamental requirements of cells?
Energy to generate ATP | A source of carbon to use as raw materials for synthetizing macromolecules
42
What are the four major pathway of glucose utilization?
Extracellular matrix and cell wall polysaccharides Glycogen, starch, sucrose Oxidation via pentose phosphate pathway --> ribose 5-phosphate Pyruvate
43
Generally describe the preparatory phase
One glucose molecule and two ATP are consumed | Two glycerahdehyde 3-phosphate are produced (both continue to the payoff phase
44
What is the product of the payoff phase?
4 ATP + 2 NADH
45
What are the two pathways for creating ATP?
Substrate-level phosphorylation, enzyme-catalyzed reaction. | oxidative phosphorylation, electron transport chain
46
How is glycolysis regulated?
Regulated by feedback inhibition. | high levels of ATP inhibit the third enzyme phosphofructokinase.
47
Where goes glycolysis occur in the cell?
the cytoplasm of the cell
48
Where does the citric acid cycle occur in the cell?
mitochondrial matrix
49
Where does oxidative phosphorylation occur in the cell?
inner membrane.
50
What are the cristae?
extensions of the inner membrane of the mitochondria. fill the interior of the mitochondria. the mitochondrial matrix is inside the inner membrane.
51
What are the three fates of pyruvate?
- -> lactate - -> ethanol + co2 - -> acetyl coa
52
What enzyme is catalyzing the pyruvate processing?
pyruvate dehydrogenase complex.
53
What are the 5 coenzymes required in pyruvate processing?
TPP, lipoyl lysine, FAD, NAD+ and CoA-SH
54
How is pyruvate processing regulated?
Feedback inhibition, when products of glycolysis or pyruvate are abundant: PDH is phosphorylated and inhibited through shape change.
55
What is the function of CoA?
only to accept and carry acetyl groups. Carrying the remaining carbons from glucose to the citric acid cycle to be further oxidized.
56
What are the two products of pyruvate processing?
1 NADH and 1 acetyl-CoA.
57
What do we call a process that involves both catabolism and anabolism? and give an example of such process
amphibolic | citric acid cycle.
58
What is the net result of the citric acid cycle?
2CO2, 3NADH, FADH2, GTP, CoA, 3H+
59
What is an anaplerotic reaction?
replenishment of the intermediates in order for the cycle and central metabolic pathway to continue.
60
Name the 4 anaplerotic reactions for the CAC cycle
pyruvate -->(pyruvate caboxylase) Oxaloacetate. liver kidney phosphoenolpyruvate--> (PEP carboxykinase) Oxaloacetate. heart, skeletal muscle Phosphoenolpyruvate --> (PEP carboxylase) Oxaloacetate. higher plants, yeast, bacteria Pyruvate --> (malic enzyme) Malate., eukaryote and bacteria
61
Which compounds are high-energy intermediates in glycolysis?
1,3 biphosphoglycerate, phosphoenolpyruvate. | the compounds that produce ATP when transformed.
62
What are the main reducing fuels for the cell?
carbohydrates, lipids and amino acids
63
Name the four protein complexes in the electron transport chain
complex 1: NADH dehydrogenase Complex 2: succinate dehydrogenase complex 3: ubiquinone-cytochrome C oxidoreductace complex 4: cytochrome C, cytochrome c oxidase, ubiquinone.
64
What happens with the reduction potential as the electron move in the transport chain?
reduction potential increases. larger and positive E' more likely to be reduced.
65
How does O2 enter the mitochondrial matrix?
diffusion through inner mitochondrial membrane
66
What is the net reaction of complex 1?
NADH + 5H+(matrix) +Q --> NAD+ + QH2 + 4H+ (inner membrane)
67
What is the function of complex 1?
2 NADH becomes NAD. (oxidation) | 2 H transferred to ubiquinone
68
What is the function of complex 2?
Oxidation of FADH --> FAD+ reduction of ubiquinone no pumping of H+
69
What is the function of complex 3?
oxidation of reduced ubiquinone QH2 1 electron transferred to cytochrome C 4H+ are ending up in the intercellular space.
70
What is the function of complex 4?
Oxidize the reduce Cyto C. | Oxygen is reduced to water.
71
What is the total net reaction of the electron transport chain?
2NADH + 22H+ + O2 --> 2NAD+ + 20H+ +2H2O
72
What provided the energy needed to phosphorylate ADP?
the flow of protons down the electrochemical gradient
73
What are the three ways in which the electrochemical proton gradient is formed?
1. actively transporting protons across the membrane with proton pumps. 2. chemically removing protons from the matrix 3. releasing protons into the intermembrane space
74
What are the two components of ATP synthase?
- an ATPase knob | - a membrane-bound proton transporting phase (rotor)
75
What is the impact of the rotor F0 on ATP formation?
the spinning changes the conformation of the F1 unit so that it phosphorylates ADP to form ATP
76
What is the total yield of ATP per glucose?
30-32
77
How can electron carriers be incorporated in the matrix knowing that it is impermeable to them?
Incorporating them into malate | transported through malate alpha-ketoglutarate integral membrane transporter.
78
What is the glycerol 3 phosphate shuttle?
electrons from the NADH produced during glycolysis instead enter the ECT directly. - electron from NADH transferred through glycerol-3-phosphate. - FAD --> FADH2 - electrons are then transferred to ubiquinone within the lipid bilayer. entering the ETC complex 3
79
What primarily regulates oxidative phosphorylation?
- NADH and ADP/Pi | substrate availability
80
What is the inhibitor of F1 and when is it active?
IF1 - prevents hydrolysis of ATP during low oxygen - active at lower pH
81
What does the inhibition of oxidative phosphorylation lead to?
accumulation of NADH in the cytosol | feedback inhibition up to phosphofructokinase.
82
How can you know that a product is reduced?
often gain a H+
83
How can you know that a product is oxidized?
often lose a H+
84
What is the function of tautomerization in the last step of glycolysis?
lowers the concentration of the products in order to push the reaction toward more ATP formation

Biochem midterm 2 (3 decks)

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