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MCAT TPR Biology > Biochemistry and Cellular Respiration > Flashcards

Biochemistry and Cellular Respiration Flashcards

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1
Q

What are the two forms of energy in chemistry?

A
  1. Heat (movement of molecules)

2. Potential (energy stored in chemical bonds)

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2
Q

What is the most important potential energy storage molecule in all cells?

A

ATP

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3
Q

ATP stores energy in what bonds?

A

ester bonds between phosphate groups

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4
Q

The first law of thermodynamics states what?

A

energy of the universe is constant (law of conservation of energy)

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5
Q

When the energy of the system decreases, the energy of the surroundings ______.

A

increases

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6
Q

What does the 2nd law of thermodynamics state?

A

entropy of the universe increases

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7
Q

Spontaneous reactions tend to ______ the disorder of the universe.

A

increase

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8
Q

negative delta S means what?

A

system lost entropy, disorder decreased

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9
Q

positive delta S?

A

disorder increased

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10
Q

Gibbs free energy equation?

A

G = H - TS

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11
Q

Equation for delta H?

A

H = E - PV

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12
Q

How is enthalpy related to bond energy in the cell?

A

H = E, since change in volume is negligible

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13
Q

G increases with ______ H and ______ S.

A

increasing

decreasing

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14
Q

What is favorable, when G is negative or positive?

A

negative

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15
Q

Favorable G is spontaneous or nonspontaneous?

A

spontaneous (negative)

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16
Q

Exergonic reactions have a ______ delta G.

A

negative

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17
Q

Endergonic reactions have a ______ delta G.

A

positive

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18
Q

Exergonic meaning?

A

energy exits the system

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19
Q

Endergonic reactions only occur if energy is ______.

A

added

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20
Q

Reactions with a negative delta H are called?

A

Exothermic

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21
Q

Reactions with a positive delta H are called?

A

Endothermic

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22
Q

Most metabolic reactions are _____.

A

exothermic

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23
Q

signs of thermodynamic quantities are assigned from the point of view of the ______.

A

system

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24
Q

System always moves in the direction of the _____ free energy.

A

lowest

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25
Q

Spontaneous reactions move in the direction of the _____ free energy state.

A

lowest

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26
Q

If the products in a reaction have more entropy than the reactants, and the enthalpy of reactants and products are the same, does the reaction occur spontaneously?

A

yes
S>0
H=0
G=H-TS

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27
Q

In equation, G’ = -RTlnK, if k=1, what does G equal?

A

0

ln1=0

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28
Q

K equilibrium constant?

A

Products/reactants

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29
Q

G = G’ + RTlnK

A

equation to know

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30
Q

Can you calculate G with only G’?

A

no you need the concentrations of the materials

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31
Q

Difference between K and Keq?

A

K- ratio of products to reactants at any time

Keq- ratio of products to reactants at equilibrium

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32
Q

How can G be negative if G’ if positive?

A

if the ratio of products to reactants if small meaning there is more reactants and the reaction goes forward

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33
Q

Does Keq indicate rate of reaction?

A

No, only the concentrations at Eq

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34
Q

When Keq is large, which has lower free energy, P or R?

A

Large Keq means more products are present at Eq, since Eq tends toward the lowest free energy state, so the answer is products

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35
Q

When K is large, which has lower free energy?

A

None, K doesnt say anything about Eq

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36
Q

If delta G is 0, will the forward or backward reaction be favored?

A

Neither is favored

When delta G=0, K=Keq, so we are at equilibium

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37
Q

What two factors determine whether the reaction will occur spontaneously(-G) in the cell?

A
  1. Intrinsic properties of the reactants and products (G’)

2. Concentrations of reactants and products (RTlnK)

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38
Q

Does spontaneous mean the reaction goes fast?

A

It says nothing about rate, just that it may proceed without additional energy

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39
Q

Thermodynamics tells you what?

A
  • where a system starts and finishes but nothing about the path traveled to get there or the rate of reaction
  • measures the difference in free energy between reactants and products
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40
Q

What is the difference in G for a reaction burning sugar in a furnace as opposed to breaking down sugar in a human?

A

No difference because the difference in energy between products and reactants will the be the same in both cases.

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41
Q

The study of reaction rates is called ______.

A

chemical kinetics

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42
Q

Energy required to produce the transient intermediate is called ______.

A

Activation Energy

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43
Q

What determines the kinetics of a reaction?

A

activation energy barrier

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44
Q

How would the rate of a spontaneous reaction be affected if the activation energy were lowered?

A

rate would increase

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45
Q

What does a catalyst do?

A

lowers activation energy without changing delta G

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46
Q

How does a catalyst lower the Ea?

A

by stabilizing the transition state

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47
Q

T/F

A catalyst is used up in the reaction.

A

False

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48
Q

Example of Catalyst?

A

Enzymes

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49
Q

Will an enzyme affect the concentrations of the reagants at Eq?

A

No it will only affect the rate that Eq is reached

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50
Q

Example of Nonspontaneous (+G) reaction that occurs in the body?

A

Biosynthesis of macromolecules such as DNA or protein

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51
Q

How can thermodynamically unfavorable reactions in the cell be driven forward?

A

reaction coupling

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52
Q

What is the basic idea of reaction coupling? How is it possible?

A
  • one very favorable reaction is used to drive an unfavorable one
  • free energy changes are additive
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53
Q

What is a favorable reaction that the cell can use to drive unfavorable reactions?

A

ATP hydrolysis

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54
Q

How does ATP hydrolysis drive unfavorable reactions?

A
  • causing a conformational change in a protein (transmembrane transport)
  • transfer of a phosphate from ATP to a substrate
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55
Q

What is the difference between an enzyme in a test tube and the ones in our bodies?

A
  • the enzyme is a catalyst with a kinetic role only

- enzymes control outcomes by selectively promoting unfavorable reactions via reaction coupling

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56
Q

What must an enzyme do to its structure to act as a catalyst?

A

fold into a three dimensional structure

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57
Q

An enzyme may consist of a single polypeptide chain or several polypeptide subunits held together in a _____ structure.

A

Quaternary

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58
Q

Why is the folding of an enzyme important for function?

A

for the proper formation of the active site

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59
Q

What shape are enzymes more likely to have?

A

Globular to form an active site as a cleft in the sphere

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60
Q

The reactants in an enzyme catalyzed reaction are called ____.

A

substrates

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61
Q

The active site has amino acid residues that stabilize the ________.

A

transition state of a reaction

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62
Q

If a transition state intermediate possesses a transient negative charge, what amino acid residues might be found at the active site to stabilize the transition state?

A
  • a positive charge would stabilize the negative charge.
  • His, Arg, Lys
  • Hydrogen of NH2 group in glutamine or aspargnine
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63
Q

Is it possible that amino acids located far apart from each other in the primary protein sequence may play a role in the formation of the same active site?

A

Yes, they may be far away in the sequence but may end up close to each other in the final folded protein.

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64
Q

What happens if a positive enzyme that stabilizes the transition state is replaced with a negative enzyme?

A

Effectiveness would decrease or be destroyed altogether because the transition state would not be stabilized lowering the rate

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65
Q

Stereospecificity?

A

ability to distinguish between stereoisomers

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66
Q

Is the active site for enzymes highly specific for substrate?

A

yes

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67
Q

What configuration of amino acids are found in animals?

A

L amino acids and D sugars

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68
Q

Protease?

A

protein cleaving enzyme

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69
Q

Examples of proteases?

A

Trypsin, chymotrypsin, elastase

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70
Q

How do proteases work?

A

Have an active site with a serine residue whose OH group can act as a nucleophil, attacking the carbonyl carbon of an amino acid residue in a polypeptide chain

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71
Q

Recognition Pocket?

A

pocket in an enzymes structure which attracts certain residues on substrate polypeptides

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72
Q

Enzymes that act on hydrophobic substrates have ______ amino acids in their active sites while hydrophilic/polar amino acids will comprise the active site of enzymes with ______ substrates.

A

hydrophobic

hydrophilic

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73
Q

4 ways that enzyme activity is regulated?

A
  1. Covalent Modification
  2. Proteolytic Cleavage
  3. Association with other polypeptides
  4. Allosteric Regulation
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74
Q

What is the most common example of covalent modification?

A

addition of a phosphoryl group from a molecule of ATP by a protein kinase to the OH of Ser, Threonine, or Tyr residues

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75
Q

What do protein phosphoylases use instead of ATP?

A

free floating inorganic phosphate (Pi)

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76
Q

What can reverse protein phosphorylation?

A

phosphatases

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77
Q

What is proteolytic cleavage?

A

enzymes in inactive forms are activated by cleavage by a protease

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78
Q

Allosteric Regulation?

A

modification of the active site through interaction of molecules with other specific sites on the enzyme called allosteric sites

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79
Q

The binding of the allosteric regulator to the allosteric site is generally ____ and ______.

A

noncovalent

reversible

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80
Q

Explain negative feedback or feedback inhibition.

A

An end product shuts off an enzyme early in the pathway

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81
Q

What is feedforward stimulation?

A

enzyme stimulated by its substrate or by a molecule in the synthesis of the substrate

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82
Q

What is enzyme kinetics?

A

study of the rate of formation of products from substrates in the presence of an enzyme

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83
Q

The reaction rate in enzyme kinetics is dependent on what?

A
  • the concentration of the subtrates

- enzyme

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84
Q

The rate, V, is ______ proportional to the amount of substrate added.

A

directly

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85
Q

What is the Vmax?

A

the reaction rate of an enzyme is saturated meaning that adding more substrate does not increase reaction rate

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86
Q

What is Vmax(1/2)?

A

linear portion of the curve where V is proportional to S

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87
Q

What is Km?

A

the substrate concentration at which the reaction velocity is half its maximum

88
Q

What does a low Km mean?

A

not very much substrate is required to get the reaction rate to half the maximum rate and thus has a high affinity for this particular substrate

89
Q

Tense? Relaxed?

A
  • turned off

- turned on

90
Q

Cooperativity?

A

binding of one substrate molecule to the enzyme complex enhances the binding of more substrate molecules to the same complex.

91
Q

How many active sites do cooperative molecules have?

A

more than one in a quaternary structure

92
Q

What type of curve results from cooperative binding?

A

sigmoidal

93
Q

The leveling off of the cooperativity curve represents what?

A

saturation, Vmax

94
Q

Name one protein that is cooperative and is not catalytic?

A

Hemoglobin has 4 binding sites

95
Q

Competitive Inhibitors?

A

compete with substrate for binding at active site

96
Q

Structurally competitive inhibitors resemble what?

A

substrate but the most effective resemble the transition state which the active site normally stabilizes

97
Q

What can overcome competitive inhibitors?

A

adding more substrate, if the concentration is high enough the substrate will outcompete the inhibitor

98
Q

Is Vmax affected in competitive inhibition?

A

no but it requires more substrate

99
Q

What happens to Km in competitive inhibition?

A

Km is increased

100
Q

Where do noncompetitive inhibitors bind?

A

at the allosteric site

101
Q

What happens to Vmax and (1/2) Vmax in noncompetitive inhibition?

A

decreases

102
Q

What happens to Km in noncompetitive inhibition?

A

stays the same

103
Q

Photosynthesis?

A

process by which plants store energy from the sun in the bond energy of carbs

104
Q

Photoautotrophs?

A

use energy from light to make their own food

105
Q

Chemoheterotrophs?

A

use energy of chemicals produced by other living things

106
Q

Three meanings of oxidize?

A
  1. attach Oxygen
  2. remove Hydrogen
  3. remove electrons
107
Q

Three meanings of Reduce?

A
  1. remove Oxygen
  2. add Hydrogen
  3. add electrons
108
Q

CH3CH3 to CH2CH2 oxidation of reduction?

A

oxidation

109
Q

Fe3+ to Fe2+ oxidation or reduction?

A

reduction

110
Q

O2 to H2O oxidation or reduction?

A

reduction

111
Q

Redox pair?

A

when one atom gets reduced, another must be oxidized

112
Q

catabolism?

A

breaking down molecules

113
Q

anabolism?

A

building up metabolism

114
Q

How do we extract energy from glucose?

A

oxidative catabolism

115
Q

what are the 4 steps of oxidative catabolism?

A
  1. Glycolysis
  2. Pyruvate dehydrogenase complex
  3. Krebs cycle
  4. electron transport/oxidative phosphorylation
116
Q

Stoiciometry of glucose oxidation?

A

C6H12O6 + 6O2 = 6CO2 + 6H2O

117
Q

What are the two members of the redox pair in glucose oxidation?

A

C6H12O6 is oxidized to CO2

O2 is reduced to H2O

118
Q

What type of reaction is cellular respiration?

A

big coupled reaction

119
Q

Short summary of Glycolysis?

A

glucose is partially oxidized while it is split in half into two identical pyruvic acid molecules.

120
Q

How many carbon molecules does pyruvic acid have?

A

three because glucose is split in half

121
Q

What is produced from glycolysis?

A

2 ATP

2 NADH

122
Q

Where does glycolysis occur?

A

in the cytoplasm absent of oxygen

123
Q

Short summary of PDC?

A

pyruvate produced in glycolysis is decarboxylated to form an acetyl group. the acetyl group is then attached to coenzyme A that transfers the acetyl group into the Krebs cycle

124
Q

What is produced from PDC?

A

2 NADH per glucose, one per pyruvate

125
Q

Krebs cycle is also known as what?

A

tricarboxylic acid cycle

citric acid cycle

126
Q

Short summary of the Krebs cycle?

A

the acetyl group from the PDC is added to oxaloacetate to form citric acid which is then decarboxylated and isomerized to regenerate the original oxaloacetate

127
Q

What is produced from the Krebs cycle?

A

2 ATP
6 NADH
2 FADH2

128
Q

T/F

PDC and Krebs cycle use oxygen directly.

A

False

129
Q

Oxygen is necessary for which stage of cellular respiration?

A

oxidative phosphorylation

130
Q

Where do the PDC and Krebs cycle take place?

A

matrix of mitochondria

131
Q

All cells from all domains have the ability to perform _____.

A

Glycolysis

132
Q

What is needed to start the pathway of Glycolysis?

A

ATP

133
Q

Hexokinase?

A

catalyzes the first step of glycolysis, the phosphorylation of glucose to G6P.

134
Q

What inhibits hexokinase?

A

G6P feedback

135
Q

What catalyzes the third step of glycolysis?

A

Phosphofructokinase (PFK)

136
Q

Is the reaction catalyzed by PFK favorable or unfavorable?

A

favorable so its irreversible

137
Q

What is the key biochemical valve controlling the flow of substrate to product in glycolysis?

A

PFK

138
Q

What is committed step in glycolysis?

A

converting F6P to F1,6bP

139
Q

Very favorable reactions are generally subject to _____ regulation.

A

allosteric

140
Q

PFK is allosterically regulated by ____.

A

ATP

141
Q

What effect would high concentration of ATP have on PFK activity?

A

it would slow glycolysis because ATP binds to the allosteric site of PFK to inhibit it

142
Q

Lowering the amount of ATP will _____ reaction rate in glycolysis.

A

increase

143
Q

Two molecules of ____ are reduced in glycolysis per glucose catabolized, forming 2 NADH.

A

NAD+

144
Q

NADH is an ______ carrier.

A

electron

145
Q

What is NADH responsible for?

A

shuttling energy in the form of reducing power

146
Q

Aerobic? Anaerobic?

A
  • with oxygen

- without oxygen

147
Q

What is the problem with oxidative metabolism under anaerobic conditions?

A

no oxygen so electron transport cannot function and a limited supply of NAD+ becomes entirely to NADH

148
Q

Would a limited supply of NAD+ stimulate or inhibit glycolysis?

A

inhibit because NAD+ is needed as a substrate to produce NADH.

149
Q

What is the purpose of fermentation?

A

to regenerate NAD+ in anaerobic conditions, allowing glycolysis to continue without oxygen

150
Q

What does fermentation use pyruvate for?

A

acceptor of the high energy electrons from NADH

151
Q

Two examples of fermentation?

A
  1. reduction of pyruvate to ethanol (yeast makes beer)

2. reduction of pyruvate to lactate in human muscle cells

152
Q

What happens to the lactate in human muscle cells after a period of strenuous exercise?

A

Cori Cycle- lactate is exported from muscle to liver. Liver converts it back to pyruvate when oxygen is available while making NADH from NAD+. It utilizes NADH to make ATP in oxidative phosphorylation

153
Q

Oxidative decarboxylation?

A

happens in PDC and Krebs, molecule is oxidized to release CO2 to produce NADH

154
Q

In oxidative decarboxylation, pyruvate is changed from a 3-carbon molecule to a ______, while _____ is given off and ______ is produced.

A

2 carbon molecule
CO2
NADH

155
Q

In PDC, an acetyl unit is activated and is attached to ______.

A

Coenzyme A

156
Q

What is produced by the hydrolysis of ATP during metabolism?

A

AMP

157
Q

What is the role of acetyl-CoA?

A

it is high energy, transfers acetyl fragment into Krebs cycle

158
Q

What effect would a high level of AMP have on the activity of pyruvate dehydrogenase?

A

stimulates PDC, increasing the rate of entry into the Krebs cycle

159
Q

PDC is composed of three enzymes, why is this more efficient than three independent enzymes?

A

intermediates are passed from active site to active site without having to diffuse

160
Q

Prosthetic group?

A

nonprotein molecule covalently bound to an enzyme as part of the active site

161
Q

What prosthetic group does PDC contain?

A

thiamine pyrophosphate (TPP)

162
Q

What is thiamine in TPP?

A

vitamin B1

163
Q

Vitamins are often _______.

A

prosthetic groups

164
Q

NAD+ is a ______.

A

cofactor

165
Q

cofactor?

A

various substances that are necessary to the function of an enzyme but never actually interact with the enzyme

166
Q

What would a thiamine deficiency do?

A

shutdown the PDC and Krebs cycle because it is required as a TPP prosthetic group, ATP production would fall. Glycolysis would increase to make up for lower levels of ATP

167
Q

What starts the Krebs cycle?

A

2 carbon acetyl unit from acetyl CoA

168
Q

what is released when the 2 carbon acetyl unit is combined with oxaloacetate?

A

CO2

169
Q

What is the first intermediate produced in the Krebs cycle?

A

citrate

170
Q

What does citrate possess?

A

three carboxylic acid functional groups

171
Q

What is a molecule with three carboxylic acid groups ready for?

A

oxidative decarboxylation

172
Q

What is stage 1 of the Krebs cycle?

A

the two carbons in the acetate fragment of acetyl CoA are condensed with the 4 carbon compound oxaloacetate to make citrate

173
Q

How many chiral carbons are present in citrate?

A

none, the C’s dont have 4 unique substituents

174
Q

If pyruvate is radiolabeled on its number one carbon, where will it end in the Krebs Cycle?

A

CO2

175
Q

What is stage 2 of the Krebs cycle?

A

citrate is further oxidized to release CO2 and to produce NADH from NAD+ with each oxidative carboxylation

176
Q

How many carbons from the CoA component of acetyl CoA enter the Krebs?

A

none, CoA assists in catalysis so it is not consumed but regenerated as CoA-SH

177
Q

What is stage 3 of the Krebs?

A

OAA is regenerated so the cycle can continue

178
Q

Up til the Krebs in glucose metabolism, most of the energy produced is from ______.

A

high energy electron carriers, not ATP

179
Q

What is the difference between the inner and outer layers of the mitochondrion?

A

inner layer- impermeable and folded into cristae

outer- contains large pores

180
Q

Cristae extend into the ______, which is the innermost space of the mitochondria.

A

matrix

181
Q

where are the enzymes of the Krebs and PDC located?

A

matrix

182
Q

Where are the enzymes for the electron transport chain and ATP synthase involved in oxidative phosphorylation found?

A

inner mitochondrial membrane

183
Q

What are the two goals of electron transport/ oxidative phosphorylation?

A
  1. reoxidize all the electron carriers reduced in glycolysis, PDC, and Krebs
  2. store energy in the form of ATP
184
Q

What needs to be transported into the mitochondria for oxidative phosphorylation to begin? What is already there?

A
  • NADH from glycolysis

- other NADH, FADH2

185
Q

What is different in prokaryotes with cellular respiration?

A

everything is located in the cytoplasm because there are no organelles so they do not have to shuttle into the mitchondrial matrix like in eukaryotes

186
Q

How do prokaryotes carry out oxidative phosphorylation?

A

establish a proton gradient, so they need a membrane impermeable to protons

187
Q

What membrane is used for oxidative phosphorylation in Eukaryotes? Bacteria?

A
  • inner mitochondrial membrane

- cell membrane

188
Q

Oxidative Phosphorylation?

A

oxidation of high energy electrons carriers NADH and FADH2 coupled with phosphorylation of ADP to produce ATP

189
Q

What is the energy released through oxidation of NADH and FADH2 used for in the electron transport chain?

A

pump protons out of the mitochondrial matrix

190
Q

What is the proton gradient used as a source for?

A

energy used to drive phosphorylation of ADP to ATP

191
Q

How many electron carriers does the electron transport chain have?

A

5

192
Q

What is the first large carrier in the electron transport chain?

A

NADH dehydrogenase (coenzyme Q reductase)

193
Q

What does NADH dehydrogenase pass its electrons to?

A

ubiquinone(coenzyme Q)- small carrier

194
Q

What does ubiquinone pass its electrons to?

A

cytochrome C reductase- large membrane bound complex

195
Q

What is the next carrier in the chain of ETC after cytochrome C reductase?

A

cytochrome C- small hydrophilic

196
Q

What is the last member of the ETC? Where does it pass its electrons?

A
  • cytochrome C oxidase

- passes its reducing power to O2, reducing it to H2O

197
Q

What is the pH in the matrix as opposed to the rest of the cell?

A

much higher because H+ is pumped out of the matrix

high pH= low H+

198
Q

ATP production is dependent on a ________.

A

proton gradient

199
Q

The passage of protons from the intermembrane space through the ________ causes it synthesize ATP from ADP + Pi.

A

ATP synthase

200
Q

If the proton gradient is destroyed, what is inhibited first?

A

muscular contraction because ATP would run out

201
Q

What has a positive delta G under normal aerobic conditions in the cell?

A

pumping protons to form a pH gradient

202
Q

How much ATP is generated per NADH? FADH2? GTP?

A

2.5
1.5
1

203
Q

Total ATP generated in cellular respiration from a single molecule of glucose?

A

30 Eukaryotes

32 Prokaryotes

204
Q

What is glycogenolysis?

A

glycogen breakdown

205
Q

Glycogenolysis occurs in response to ______.

A

glucagon when blood sugar levels are low, it releases glucose into the blood

206
Q

How are fatty acids broken down in hepatocyte mitochondria?

A

Beta oxidation

207
Q

4 other processes that convert on the Krebs?

A

Glycogenolysis
Glucogenesis
Beta oxidation
Amino Acid Catabolism

208
Q

In Eukaryotes, the ultimate yield of ATP from NADH is lower when NADH is produced by _______.

A

Glycolysis

209
Q

What category of enzymes irreversibly modifies their substrate?

A

proteases

210
Q

In cellular respiration in bacteria, which area has the lowest pH?

A

extracellular space because protons are pumped out of the cytoplasm to the outside of the cell

211
Q

Reaction rate changes ____ as substrate concentration is increased when it was originally at low concentration.

A

linearly

212
Q

T/F

The effect of estrogen on luteinizing hormone one day before ovulation is an example of feedback inhibition.

A

False

as ovulation approaches, high levels of estrogen stimulate the release of lutenizing hormone

213
Q

If the affinity of hemoglobin for oxygen is decreased, the oxygen dissociation curve shifts to the _____.

A

right

214
Q

Oxygen binding to the active site of one subunit of the hemoglobin tetramer causes the other subunits to have increased affinity for oxygen. this is an example of ______.

A

cooperativity

215
Q

Protein phosphatases regulate the activity of metabolic pathways by ______.

A

covalent modification

216
Q

A competitive inhibitor binds to the ____ site and has ____ effect on Vmax.

A

active

no

MCAT TPR Biology (7 decks)

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