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Exam 3 Flashcards

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1
Q

When does a chemical reaction occur

A

When atoms have enough energy to combine or change bonding partners

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2
Q

Metabolism

A

Sum of all chemical reactions in a biological system at a given time

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3
Q

Anabolic Reaction

A

Type of metabolism; complex molecules are made from simple molecules; energy is required

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4
Q

Catabolic Reaction

A

Type of metabolism; complex molecules are broken down to simpler ones; energy is released

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5
Q

Kinetic Energy

A

One of the two types of energy; the energy of movement (like temperature)

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6
Q

Potential Energy

A

One of the two types of energy; energy stores as chemical bonds, concentration gradient, or charge imbalance

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7
Q

First Law of Thermodynamics

A

Energy is neither created or destroyed; when energy is converted from one form to another, the total energy before and after is the same; total energy in the universe is constant

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8
Q

Second Law of Thermodynamics

A

When energy is converted from one form to another, some of that energy becomes unavailable to do work; no energy transformation is 100% effective since some is lost to disorder

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9
Q

Entropy (S)

A

A measure of the disorder/randomness in a system (takes energy to impose order on a system; unless energy is applied to system it will be disordered)

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10
Q

How do we find out whether there’s energy available for a reaction

A

By considering the unusable energy

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11
Q

Total Energy Equation

A

Total Energy = free energy + temp*entropy

H = G + TS

Enthalpy = Usable Energy + unusable energy

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12
Q

Gibbs Free Energy Change

A

Used to predict whether a reaction will occur spontaneously

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13
Q

Gibbs Free Energy Change Formula

A

change in G = change in H - T*Change in S

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14
Q

If change in G<0

A

Energy is released (reaction occurs spontaneously)

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15
Q

If change in G>0

A

Energy is required (reaction can’t occur on its own)

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16
Q

Exergonic Reactions

A

Release E (change in G<0)

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17
Q

Are catabolic reactions exergonic or endergonic

A

Exergonic

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18
Q

Polar Molecules

A

Shortest, strongest bonds

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19
Q

Nonpolar molecules

A

Longest, weakest bonds

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20
Q

In molecules, what is potential energy directly related to

A

The electron positioning in nuclei; Nonpolar molecules have more potential energy

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21
Q

Endergonic reactions

A

Consume energy (change in G>0)

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22
Q

Are anabolic reaction usually endergonic or exergonic

A

Endergonic

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23
Q

Chemical reaction proceed until they reach

A

Equilibrium (change in G = 0)

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24
Q

Enzymes

A

Catalysts that increase the rate of chemical reaction by reducing the activation energy; made of proteins

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25
Q

What does “~” symbolize

A

High energy bond

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26
Q

Is ATP formation endergonic or exergonic?

A

Endergonic

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27
Q

Why does the P~O bond that links phosphate groups in ATP store/release so much energy?

A
  1. There’s a lot of energy stored in P~O; it cost a lot of energy to create in the first place
  2. O~P stores more potential energy than the new bonds formed; the leftover energy must be released
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28
Q

What can happen to Pi after ATP hydrolysis

A
  • Incorporated into a product that will serve as a reactant/provide fuel for an endergonic reaction
  • Incorporated into a protein product, which changes its shape and activity
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29
Q

Is ATP hydrolysis reversible?

A

Yes

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30
Q

The more negative change in G is

A

The more fully it proceeds to completion

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31
Q

The closer change in G is to 0

A

The more fully reversible the reaction is

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32
Q

Why are some reactions with change in G less than 0 slow

A

They have a high activation energy

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33
Q

How do enzymes cause substrates to adopt transition states?

A
  • Orientation
  • Physical strain (makes easier to break)
  • Adding chemical groups (charge)
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34
Q

How do R groups of an enzymes composite amino acids directly participate in adding chemical groups

A
  • Acid base catalysis: Enzyme acts like an acid
  • Covalent catalysis
  • Metal ion catalysis: Metal ions lose or gain electrons without detaching from the enzymes
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35
Q

Enzymes are highly what to their substrates

A

Specific

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36
Q

What determines the specificity of an enzyme

A

Its 3D shape (structure = function)

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37
Q

Induced Fit

A

Some enzymes change shape when bound to their substrate, which alters the shape of the active site

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38
Q

Do enzyme chemical compositions change before and after catalysis?

A

No; but substrates do change as a result of the reaction

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39
Q

Ribozymes

A

Enzymes made of RNA

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40
Q

Oxidoreductases

A

One of the six categories of enzymes; moves electrons between molecules

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41
Q

Transferases

A

One of the six categories of enzymes; transfers functional groups between molecules

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42
Q

Hydrolases

A

One of the six categories of enzymes; Adds water to covalent bonds to break molecules

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43
Q

Lyases

A

One of the six categories of enzymes; catalyzes nonhydrolytic bond breakage, often forming a new bond in the process (ex: adenylyl cyclase aka ATP diphosphate-lyase; atp–>PPi)

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44
Q

What is another name for adenylyl cyclase?

A

ATP diphosphate-lyase (its a type of lyase enzyme)

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45
Q

Isomerases

A

One of the six categories of enzymes; moves functional groups from one place to another within the same molecule (same atoms, different bonds)

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46
Q

Ligases

A

One of the six categories of enzymes; ties two molecules together

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47
Q

Coenzymes

A

AKA cofactors; small c-containing molecules that are not permanently bound to an enzyme (helps enzymes function)

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48
Q

Prosthetic Groups

A

Non-amino acid groups bound to enzymes (helps enzymes function)

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49
Q

Inorganic Compounds

A

Ions permanently bound to an enzyme (helps enzyme function)

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50
Q

What affects reaction rate?

A

Substrate concentration (until maximum rate is reached)

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51
Q

How are chemical reactions in cells organized

A

In metabolic pathways that are interconnected

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52
Q

What helps organize and regulate metabolic pathways

A

Enzymes

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53
Q

Cyclooxygenase (COX2)

A

An enzyme that normally produces prostaglandin from the substrate arachidonic acid which leads to an inflammatory response (vasodilation)

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54
Q

Irreversible Inhibition

A

Inhibitor covalently binds to side chains in the active site, which permanently inactivates the enzyme (ex: aspirin permanently inhibits COX2)

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55
Q

Aspirin

A

Binds to cyclooxgenase and transfers and acetyl group, which binds to its active site; prostaglandins can no longer be produced

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56
Q

Cyclooxgenase cells produce (more/less) prostaglandin when aspirin is present

A

Less

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57
Q

Reversible Inhibition

A

Inhibitor bonds noncovalently to the active site of enzyme and prevents substrate from binding

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58
Q

Competitive Inhibition

A

Type of reversible inhibition; competes with the natural substrate for binding sites; binds before substrate

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59
Q

ESPS

A

Enzyme in weed killer RoundUp

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60
Q

Glyphosate

A

Competitive inhibitor of ESPS

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61
Q

Competitive inhibitors can be overcome by

A

Adding more substrates

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62
Q

Competitive Inhibitors have structures similar to

A

The enzyme’s substrate

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63
Q

Uncompetitive Inhibitors

A

Type of reversible inhibition; binds to the enzyme-substrate complex, preventing release of products; binds after the actual substrate binds to the enzyme

64
Q

Noncompetitive Inhibitors

A

Type of reversible inhibition; binds to an enzyme at a different site that isn’t the active site; the enzyme changes shape and alters the active site

65
Q

PKA being activated by high concentration of cAMP is an example of

A

Noncompetitive inhibition; catalytic subunits have the active site

66
Q

Allosteric Regulation

A

A non-substrate molecule binds enzyme at a site different from the active site, which changes enzyme shape

67
Q

Allosteric Inhibitor

A

A molecule that stabilizes the inactive conformation of an enzyme

68
Q

Allosteric Activator

A

A molecule that stabilizes the active conformation of an enzyme

69
Q

Regulatory Subunits

A

Regulatory sites where inhibitors and activators bind to on polypeptides during allosteric regulation (PKA is an allosteric enzyme that has multiple subunits; cAMP is an allosteric activator)

70
Q

Feedback Inhibition

A

Final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway (type of allosteric inhibition)

71
Q

Enzymes can be regulated by

A
  • Gene expression changes
  • Regulation of enzyme activity
  • Phosphorylation
  • Environmental Conditions (pH, temperature)
72
Q

Commitment Step

A

One of the first reactions in a metabolic pathway, other reactions then occur in sequence

73
Q

How are enzymes regulated by reversible phosphorylation?

A

If an enzyme is inactivated when a protein kinase adds a phosphate group, it might be activated by a protein phosphatase

74
Q

How are enzymes regulated by pH

A

Every enzyme is most active at a particular pH, which influences ionization of functional group; the rates of most enzyme-catalyzed reactions depend on the pH of the solution they’re in

75
Q

How are enzymes regulated by temperature

A

Since noncovalent bonds break at high temperatures, which affects protein structure, temperature affects enzyme activity (there is an optimal temperature)

76
Q

ATP synthesis formula

A

ADP + Pi + free energy –> ATP + H20
Change in G = 7.3

77
Q

Is ATP synthesis endergonic or exergonic

A

Endergonic

78
Q

What releases enough energy to drive the formation of ATP?

A

The breakdown of glucose

79
Q

How do cells harvest energy from glucose

A

A series of metabolic pathways

80
Q

Breakdown of glucose formula

A

C6H12O6 + 6O2 –> 6CO2 + 6H2O + free energy
Change in G = -686

81
Q

What are the three catabolic processes that harvest energy from glucose

A
  • Glycolysis (always first)
  • Cellular Respiration
  • Fermentation
82
Q

Glycolysis

A

The first of three catabolic processes that harvest energy from glucose; a series of chemical rearrangements in which 1 molecule of glucose is converted into 2 molecules of pyruvate

83
Q

What are the end products of glycolysis

A

2 pyruvate, 2 ATP, 2 NADH

84
Q

True or false: Both prokaryotes and eukaryotes harvest energy from glucose

A

True

85
Q

Five Principles of Metabolic Pathways

A
  1. Complex transformation occur in a series of separate reactions
  2. Each reaction is catalyzed by a specific enzyme
  3. Many metabolic pathways are similar in all organisms
  4. In eukaryotes, metabolic pathways are compartmentalized in specific organelles
  5. Key enzymes can be inhibited or activated to alter the rate of the pathway
86
Q

What are the two types of reaction that occur repeatedly in many metabolic pathways

A

Oxidation-Reduction and Substrate-Level Phosphorylation

87
Q

Oxidation-Reduction Reaction

A

One substance transfers electrons and energy to another substance (exergonic)

88
Q

Oxidation

A

Loss of electrons

89
Q

Reduction

A

Gain of electrons

90
Q

What happens in redox reactions where it doesn’t involve a complete transfer of electrons

A

Electrons aren’t gained or lost, but an atom’s share of electrons is changed due to polar vs nonpolar bonds

91
Q

What is the transfer of electrons often associated with

A

Transfer of H+ ions (reduction is gain of H+, oxidation is loss of H+)

92
Q

Reducing Agent

A

The reactant that will become oxidized in a redox reaction

93
Q

Oxidizing Agent

A

The reactant that will become reduced in a redox reaction

94
Q

Are oxidation reactions endergonic or exergonic

A

Exergonic; the more reduced a molecule is, the more energy it has stored in its covalent bonds

95
Q

Are reduction reactions endergonic or exergonic

A

Endergonic

96
Q

NAD+/NADH

A

A coenzyme that is an electron carrier in redox reactions

97
Q

When do electrons have more potential energy

A

When paired with less electronegative atoms (ex: glucose has high potential energy because of many high energy C-C and C-H bonds vs low potential energy CO2 with low energy C-O bonds)

98
Q

What are the reducing/oxidizing agents in glucose metabolism?

A

Glucose is the reducing agent, oxygen is the oxidizing agent

99
Q

The more reduced a molecule is

A

The more energy it has

100
Q

Substrate-Level Phosphorylation

A

Exergonic reaction that releases less energy than redox reactions, but still enough to convert ADP to ATP; a phosphate group on a substrate is phosphorylated to ADP

101
Q

What goes in/out of glycolysis

A

In: Glucose, 2ATP, 2NAD+
Out (net): 2 ATP, 2 NADH, 2 Pyruvate

102
Q

Where does the energy from the partial oxidation of glucose in glycolysis go

A

Energy from this exergonic reaction goes to substrate-level phosphorylation for creation of ATP and reduction of NAD+ to NADH

103
Q

Pyruvate Oxidation

A

Second step of cellular respiration after glycolysis; glucose is fully oxidized if oxygen is present (vs in glycolysis where glucose is partially oxidized)

104
Q

What goes in/out of pyruvate oxidaition

A

In: 2 pyruvate
Out: 2 NADH, 2CO2, 2 Acetyl CoA

105
Q

Site of pyruvate oxidation

A

Mitchondrial matrix

106
Q

What is pyruvate oxidation catalyzed by

A

The pyruvate dehydrogenase complex; three enzymes that catalyze the three intermediate steps in the process

107
Q

In pyruvate oxidation, what is pyruvate oxidized to?

A

CO2 and Acetate

108
Q

True or false: pyruvate oxidation is also regulated by feedback inhibition

A

True

109
Q

Starting point of the citric acid cycle

A

Acetyl CoA

110
Q

What goes in and out of the citric acid cycle

A

In: 2 acetyl CoA
Out: 6 NADH, 4 CO2, 2 FADH2, 2 ATP

111
Q

In the citric acid cycle, what does the acetyl group completely oxidize to

A

2 molecules of CO2

112
Q

What is the energy released in the citric acid cycle captured by

A

GDP, NAD+, and FAD

113
Q

What is regenerated in the last step of the citric acid cycle, showing that the citric acid cycle is a cycle

A

Oxaloacetate

114
Q

What is crucial in all pathways

A

Regeneration of substrates

115
Q

Step 8 of citric acid cycle

A

Example of redox reaction in the citric acid cycle; the oxidation of malate is exergonic and the energy released is trapped in the reduction of NAD+ to NADH

116
Q

What happens to the energy in GTP in the citric acid cycle

A

It is transferred to ATP; GTP can transfer its high-energy phosphate to form ATP

117
Q

Where does the energy from glucose oxidation go in the citric acid cycle?

A

The energy is harvest by phosphorylation of ATP (from GTP) and by reduction of NAD+ and FADH

118
Q

What does the activity of phosphofructokinase change in response to

A

Cellular energy demands (cellular concentration of ATP); this is an example of allosteric regulation and feedback inhibition

119
Q

Site of citric acid cycle

A

Mitochondrial matrix

120
Q

Between NADH, FADH2 and ATP, which molecule carries the most free energy?

A

NADH, then FADH2, then ATP

121
Q

What provides energy for electron transport chain?

A

The reduced electron donors NADH and FADH2

122
Q

What happens downstream of glycolysis in aerobic conditions (O2 available)

A

O2 is available as final electron acceptor; four metabolic pathways operate

123
Q

What happens downstream of glycolysis in anaerobic conditions (O2 not available)

A

The pyruvate produced by glycolysis is metabolized by fermentation

124
Q

Oxidative Phosphorylation

A

ATP is synthesized by reoxidation of electron carriers in the presence of O2; two components are electron transport and chemiosmosis

125
Q

What is the final electron acceptor in the in the electron transport chain

A

Oxygen

126
Q

Site of electron transport chain

A

Inner mitochondrial membrane

127
Q

Starting point of electron transport chain

A

NADH from glycolysis

128
Q

Do electrons lose or gain free energy stepwise as it travels through each complex in the electron transport chain

A

Loses; energy is released as electrons are passed between carriers

129
Q

What contains electron carriers and associated enzymes that carry out electron transfer

A

Four large protein complexes; complex I, II, III, and IV

130
Q

Complexes I, III, IV role

A

Active transport protons into the mitochondrial intermembrane space where they accumulate

131
Q

What provides energy for ATP synthase

A

The diffusion of H+ with its concentration and charge gradient by protein complexes I, III, and IV; when H+ diffuses through the channel, the potential energy (called protein-motive force) is converted to kinetic energy, causing the central polypeptide of ATP synthase to rotate

132
Q

Chemiosmosis

A

Diffusion of protons back across the membrane; it releases energy and is coupled to ATP synthesis

133
Q

ATP Synthase

A

The channel protein that captures energy that is released from chemiosmosis as ATP; it is the same in all species; ATP synthase can also act as ATPase, hydrolyzing ATP

134
Q

Parts of ATP synthase

A

ATP synthase is a molecular motor with two parts:
- F0 Unit: A transmembrane H+ channel
- F1 Unit: Projects into the matrix; rotates to expose active sites for ATP synthesis

135
Q

Chemiosmotic Theory

A

The electron transport chain creates a proton gradient and ATP synthase uses the gradient to synthesize ATP

136
Q

Why is ATP synthesis favored

A

ATP leaves the matrix as soon as its made, keeping ATP concentration in the matrix low

137
Q

How is ATP harvested from glucose without O2

A

Some ATP can be harvested from glucose via glycolysis and fermentation; fermentation allows cells to make ATP only using glycolysis

138
Q

Lactic Acid Fermentation

A

Pyruvate from glycolysis is reduced to lactate and NADH is oxidized to NAD+
Formula:
C6H12O6+2ADP+2Pi–>2 lactate+2ATP

139
Q

Alcoholic Fermentation

A

Occurs in other types of eukaryotic cells (yeast and some plants cells)
Formula:
C6H12O6+2ADP+2Pi–>2 ethanol+2CO2+2ATP

140
Q

Site of fermentation

A

Cytoplasm

141
Q

What happens in both types of fermentation

A

NAD+ is regenerated to keep glycolysis going, and 2 ATP per glucose are produced by substrate-level phosphorylation

142
Q

Does cellular respiration or fermentation yield more energy

A

Cellular respiration

143
Q

Glycolysis and fermentation formula summary

A

C6H12O6–> 2 lactate (or 2 ethanol+2CO2)+2ATP

144
Q

Glycolysis and cellular respiration summary

A

C6H12O6+6O2–>6 CO2+6H2O+32ATP

145
Q

What can carbon skeletons be used for

A

They can be broken down to release energy or used to build more complex molecules, depending on the cell’s needs

146
Q

Catabolic interconversion

A

How polysaccharides, lipids, and proteins can be broken down to provide energy

147
Q

What are polysaccharides like glycogen and starch hydrolyzed to (catabolic interconversion)

A

Glucose, which enters glycolysis

148
Q

What are lipids broken down to (catabolic interconversion)

A

Glycerol (glycolysis) and fatty acids (citric acid cycle)
- Glycerol–>DHAP–>Glycolysis
- Fatty acids–>Acetyl CoA–> CAC

149
Q

B-oxidation

A

Way in which fatty acids are slowly converted to acteyl CoA, which enters CAC

150
Q

What are proteins hydrolyzed to (catabolic interconversion)

A

Amino acids, which can enter glycolysis or citric acid cycle

151
Q

Anabolic interconversion

A

Way in which intermediates from metabolic pathways may be used to build polysaccharides, lipids, and proteins

152
Q

True or false: citric acid cycle intermediates can also be used to synthesize nucleic acid components

A

True

153
Q

Fatty acid biosynthesis

A

Acetyl-CoA is used to form long-chain fatty acids like palmitate

154
Q

Gluconeogensis

A

Glucose is produced from glycerol, pyruvate, lactate, or amino acids (same pathways in reverse)

155
Q

True or false: Cellular respiration interacts with other catabolic and anabolic pathways

A

True

156
Q

How do cells maintain a steady state between catabolism and anabolism

A
  • Having less substrate available (use intermediates in other pathways)
  • Making more/less enzyme present (transcription/translation)
  • Turning enzyme activity on/off (covalent modifications, allosteric inhibition)

Bio 1 (8 decks)

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