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Enzymes Flashcards

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Organic Chemistry 101 flashcards
1
Q

What are enzymes responsible for?

A

The assembly and disassembly of macromolecules and the processing of their intermediates

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2
Q

What is a polymer and give biological examples

A

A polymer is a long molecule consisting of many similar building blocks = Carbohydrates, proteins, and nucleic acids are polymers

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3
Q

What are monomers?

A

The repeating units that serve as building blocks

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4
Q

What are enzymes?

A

Enzymes are specialized macromolecules that speed up chemical reactions such as those that make or break down polymers

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5
Q

What is a dehydration reaction?

A

A dehydration reaction occurs when two monomers bond together through the loss of a water molecule (forms a longer polymer)

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6
Q

What is a hydrolysis reaction?

A

Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction, involves the breaking of a bond

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7
Q

Naming a biological polymer and give the components, examples and their functions

A

Nucleotide (monomer of a poly nucleotide)
Sugar, Phosphate Group and Nitrogenous Base
Examples : DNA - sugar = deoxyribose, nitrogenous base = C, G, A, T and double stranded
and RNA - sugar = ribose, nitrogenous base = C, G, A, U, single stranded
Functions :
DNA - Stores hereditary information
RNA - various functions in gene expression, including carrying instructions from DNA to ribosomes

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8
Q

How do macromolecules vary?

A

Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species

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9
Q

Naming a biological polymer and give the components, examples and their functions

A

Monosaccharide monomer
Examples : Monosaccharides, Disaccharides, Polysaccharides
Functions : Fuel, Carbon sources that can be converted to other molecules or combined into polymers
Strengthens plant cell walls, Stores glucose for energy, strengthens exoskeletons and fungal cell walls

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10
Q

Naming a biological polymer and give the components, examples and their functions

A

Amino acid monomer
Examples : Enzymes, Defensive proteins, storage proteins, hormones
Functions : Catalyse chemical reactions, Protect against diseases, Store amino acids, Function in cell movement

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11
Q

What properties of a molecule are key to its function?

A

A molecule’s size and shape are key to its function, it determines how biological molecules recognize and respond to one another with specificity.
Example : Enzymes
One nerve cell in the brain signals another by releasing molecules of a specific shape to go find matching receptor molecules on the surface of the receiving cell. The signal molecules pass across a tiny gap (otherwise known as the synapse) between the two nerve cells and attach to the receptors by forming weak bonds which then stimulate the receiving cell. This process is very much like the way a key fits into a lock, where the matching puzzle-piece shapes help in the forming of weak bonds.
Opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and they bind the same receptors in the brain

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12
Q

How is a molecules shape determined?

A

A molecule’s shape is determined by the positions of its atoms’ orbitals

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13
Q

What are the 6 different classes of enzymes?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases (‘‘synthases’’)
  5. Isomerases
  6. Ligases (‘‘synthetases’’
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14
Q

What are oxidoreductases?

A

An oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor.

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15
Q

Where is oxidoreductase found in the body?

A

Oxidoreductase enzymes play an important role in both aerobic and anaerobic metabolism. They can be found in glycolysis, TCA cycle, oxidative phosphorylation, and in amino acid metabolism

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16
Q

What are transferases?

A

An enxyme which transfers specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor)

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17
Q

Give an example of transferases in the body?

A

Some transferases also transfer phosphate groups between ATP and other compounds, sugar residues to form disaccharides such as hexokinase in glycolysis.

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18
Q

What are hydrolases?

A

A biochemical catalysts that utilize water to break a chemical bond. This results in a division of a larger molecule to smaller molecules.

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19
Q

Give an example of hydrolases in the body?

A

Some hydrolases function as digestive enzymes because they break the peptide bonds in proteins.

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20
Q

What are Lyases?

A

They catalyze the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure) and does not require any energy

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21
Q

Give an example of lyases in the body?

A

Pyruvate decarboxylase is a lyase that removes CO2 from pyruvate

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22
Q

What are Isomerases?

A

an enzyme which catalyses the conversion of a specified compound to an isomer (where a functional group is moved to another position within the same molecule)

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23
Q

Give an example of isomerases in the body?

A

triosephosphate isomerase and phosphoglucose isomerase for converting glucose 6-phosphate to fructose 6-phosphate.

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24
Q

What are ligases?

A

can catalyze the joining of two large molecules by forming a new chemical bond by removal of the water component

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25
Q

Give an example of ligases in the body?

A

DNA ligase - that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.

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26
Q

What are chemical reactions?

A

Chemical reactions are the making and breaking of chemical bonds

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27
Q

What is metabolism?

A

Sum of all the chemical reactions in the body - An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics

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28
Q

What is energy?

A

Energy is the capacity to cause change and exists in various forms, some of which can perform work
Energy can be converted from one form to another

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29
Q

What is kinetic energy?

A

Kinetic energy is energy associated with motion

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30
Q

What is thermal energy?

A

Thermal energy is the kinetic energy associated with random movement of atoms or molecules. Heat is thermal energy in transfer between objects

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31
Q

What is potential energy?

A

Potential energy is energy that matter possesses because of its location or structure

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32
Q

What is chemical energy?

A

Chemical energy is potential energy available for release in a chemical reaction

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33
Q

Are organisms a closed, open or isolated system?

A

Organisms are open systems

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34
Q

What is free energy?

A

Free energy is a measure of a system’s instability, its tendency to change to a more stable state (energy in a system that is free to do work)

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35
Q

During a spontaneous change, what happens to free energy?

A

During a spontaneous change, free energy decreases and the stability of a system increases

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36
Q

When a process is spontaneous, when can it perform work?

A

A process is spontaneous and can perform work only when it is moving toward equilibrium

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37
Q

The higher the free energy (G), what is the stability and work capacity?

A

Less stable, greater work capacity

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38
Q

The lower the free energy (G), what is the stability and work capacity?

A

More stable, less work capacity

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39
Q

Are cells in equilibrium?

A

Cells are not in equilibrium; they are open systems experiencing a constant flow of materials, if it were they would die. A defining feature of life is that metabolism is never at equilibrium

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40
Q

What are catabolic pathways and give an example

A

Catabolic pathways release energy by breaking down complex molecules into simpler compounds. Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism

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41
Q

What are anabolic pathways and give an example

A

Anabolic pathways consume energy to build complex molecules from simpler ones. For example, the synthesis of protein from amino acids is an anabolic pathway

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42
Q

Reactions in a closed system - reaching equilibrium?

A

Reactions in a closed system eventually reach equilibrium and can then do no work

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43
Q

What is a living systems free energy?

A

Energy that can do work when temperature and pressure are uniform, as in a living cell

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44
Q

Biologists want to know which reactions occur spontaneously and which require input of energy, how do they do so?

A

They need to determine the energy and entropy changes that occur in chemical reactions

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45
Q

What does the free-energy change tell us about a reaction?

A

The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously, generates energy (exergonic) or is not spontaneous requires energy (endergonic)

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46
Q

What is an exergonic reaction?

A

reaction occurs spontaneously, generates energy (releases)

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47
Q

What is an endergonic reaction?

A

not spontaneous requires energy (absorbs free energy)

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48
Q

When is a reaction exergonic?

A

G < 0 , gibbs energy of reactants is higher than products

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49
Q

When is a reaction endergonic?

A

G > 0 gibbs energy of products is higher than reactants

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50
Q

How is the change in free energy (ΔG) during a process is related to the change in enthalpy—change in total energy (ΔH)—change in entropy (ΔS), and temperature in Kelvin units (T)?

A

ΔG = ΔH − TΔS
ΔG is negative for all spontaneous processes. Spontaneous processes can be harnessed to perform work
Processes with zero or positive ΔG are never spontaneous

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51
Q

What is activation energy?

A

The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA)
It is the energy needed to reach the transition state

52
Q

How is the activation energy supplied?

A

Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings

53
Q

How do enzymes speed up metabolic reactions?

A

Enzymes speed up metabolic reactions by lowering energy barriers (EA) (activation energy)
The lower the activation energy for a reaction, the faster the rate

54
Q

How does the active site of an enzyme lower the activation energy?

A

The active site can lower an EA barrier by

i. orienting substrates correctly
ii. straining substrate bonds providing a favorable microenvironment
iii. covalently bonding to the substrate

55
Q

Graph for free energy and progress

A

X axis - free energy

Y axis - progress

56
Q

Why must an exergonic reacton still require energy?

A

Energy is needed initially to break the bonds (EA) that acts as a barrier to ‘runaway reactions’.

57
Q

When a reaction is sped up, does gibbs energy change?

A

Enzymes do not affect the change in free energy (ΔG); instead, they hasten reactions that would occur eventually

58
Q

For a process to occur spontaneously, must the entropy of the universe increase or decrease?

A

For a process to occur spontaneously, it must increase the entropy of the universe

59
Q

Processes that decrease entropy are what?

A

Non-spontaneous

60
Q

What is the role of ATP?

A

ATP allows transfer of energy from catabolic to anabolic reactions

61
Q

What is ATP?

A

ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

62
Q

Where does the energy to phosphorylate ADP come from and where does the conversion take place?

A

catabolic reactions in the cell - The conversion takes place in the substance between the cell membrane and the nucleus, known as the cytoplasm, or in special energy-producing structures called mitochondria

63
Q

What is the ATP cycle?

A

The process of phosphorylating ADP to form ATP and removing a phosphate from ATP to form ADP in order to store and release energy respectively is known as the ATP cycle. It is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways

64
Q

What is ATP composed of?

A

ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

65
Q

The bonds between the phosphate groups of ATP’s tail can be broken by what?

A

Hydrolysis.

66
Q

When is energy released from ATP?

A

Energy is released from ATP when the terminal phosphate bond is broken
This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

67
Q

The cell does three main kinds of work, what are they?

A

i. Chemical work—pushing endergonic reactions
ii. Transport work—pumping substances against the direction of spontaneous movement
iii. Mechanical work—such as contraction of muscle cells

68
Q

How do cells do work?

A

Cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

69
Q

How does ATP drive endergonic reactions?

A

Phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
The recipient molecule is now called a phosphorylated intermediate

70
Q

What are coupled reactions?

A

Coupled reactions are two reactions with opposite signs of delta G. The idea is you have some reaction that is not favored energetically, so you pair it with a reaction that is. The favored reaction gives you the energy you need to complete the unfavored reaction.

71
Q

If endergonic reactions are not spontaneous, how does the cell complete these vital processes? Give an example

A

By coupled reactions
Glutamic acid + Ammonia to form Glutamine gives a positive gibbs energy. A reaction cannot be spontaneous (continue to happen) when the change in gibbs free energy is positive. For a spontaneous process to happen , the change in Gibbs free energy must be negative.
Therefore, the conversion reaction is coupled with ATP hydrolysis which changes free- energy to a negative value, and therefore the reaction can occur.

72
Q

The three types of cellular work (mechanical, transport, and chemical) are powered by what?

A

by the hydrolysis of ATP - leads to a change in protein shape and binding ability

73
Q

What is the enzyme substrate?

A

The reactant that an enzyme acts on is called the enzyme’s substrate

74
Q

What is an enzyme-substrate complex?

A

The enzyme binds to its substrate, forming an enzyme-substrate complex.
While bound, the activity of the enzyme converts substrate to product

75
Q

What is the active site of an enzyme?

A

The active site is the region on the enzyme where the substrate binds

76
Q

What is the induced fit of a substrate?

A

Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

77
Q

Describe what happens in an enzymatic reaction?

A

In an enzymatic reaction, the substrate binds to the active site of the enzyme.
Substrates are held in active site by weak interactions and forms an enzyme-substrate complex.
The active site is lowered as reaction is sped up, and substrates are converted to products.
Products are released and the active site returns to its original shape for new substrates.

78
Q

How come it only takes a small amount of enzymes to cause metabolic changes?

A

Very small amounts of enzyme can have huge metabolic effects because they are used repeatedly in catalytic cycles

79
Q

How can the rate of an enzyme-catalyzed reaction be sped up?

A

By increasing substrate concentration

80
Q

When does an enzyme become saturated?

A

When all enzyme molecules have their active sites engaged, the enzyme is saturated

81
Q

How can the reaction rate of an enzyme be sped up when saturated?

A

If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme

82
Q

What affects an enzyme’s activity?

A

General environ-mental factors
Temperature
pH
Interacting chemicals

83
Q

What are optimal conditions?

A

Optimal conditions favor the most active shape for the enzyme molecule and are often reflective of the conditions in which the organism live

84
Q

What is the optimal temperature of typical human enzymes?

A

37 degrees

85
Q

What is the optimal temperature of thermophilic bacteria?

A

75 degrees

86
Q

What is the optimal PH of

a) Pepsin (stomach enzyme)
b) Trypsin (intestinal enzyme)

A

a) 2

b) 8

87
Q

What are cofactors?

A

Cofactors are nonprotein enzyme helpers, they may be inorganic (such as a metal in ionic form) or organic

88
Q

What is a coenzyme?

A

An organic cofactor is called a coenzyme

89
Q

What acts as coenzymes?

A

Vitamins. Small quantities of these vitamins must be consumed in order for our enzymes to function correctly, to perform their important work of facilitating metabolism in the body.

90
Q

How do cofactors asist enzymes?

A

Many cofactors will sit in the enzyme active site and assist the binding of the substrate. Some chemical reactions within the cells of the body do require a cofactor or a coenzyme to work properly, while others do not

91
Q

What is an apoenzyme?

A

An inactive enzyme without the cofactor is called an apoenzyme

92
Q

What is a holoenzyme?

A

Complete enzyme with cofactor is called a holoenzyme

93
Q

Give examples of coenzymes

A

NAD+ and NADP+ are coenzymes that have a critical role in redox reactions

94
Q

An apoenzyme plus a cofactor (non-protein portion) activator gives you what?

A

A holoenzyme (complete active enzyme)

95
Q

What are competitive inhibitors?

A

They bind to the active site of an enzyme, competing with the substrate

96
Q

What are noncompetitive inhibitors?

A

They bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

97
Q

Give examples of inhibitors?

A

toxins, poisons, pesticides, and antibiotics

98
Q

How are enzymes regulated and why?

A

Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated - A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes

99
Q

What is allosteric regulation and how does it occur?

A

They may either inhibit or stimulate an enzyme’s activity
An allosteric site does not bind substrate, but instead binds another molecule that affects the enzyme’s regulation. When a molecule binds an allosteric site, it alters the enzyme’s shape, or conformation, which then changes how the enzyme functions

100
Q

Most allosterically regulated enzymes are made from what?

A

Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site

101
Q

The enzyme complex has active and inactive forms, the binding of an activator and binding of inhibtor effect?

A

The binding of an activator stabilizes the active form of the enzyme. The binding of an inhibitor stabilizes the inactive form of the enzyme

102
Q

What is feedback inhibition?

A

In feedback inhibition, the end product of a metabolic pathway shuts down the pathway
Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

103
Q

Give an example of feedback inhibition?

A

Feedback inhibition balances production of amino acids, the building blocks of proteins. For example, the enzyme threonine deaminase is inhibited by one of its products: the amino acid isoleucine.

104
Q

What is cooperativity?

A

It is a form of allosteric regulation that can amplify enzyme activity.
The binding of the first molecule of B to A changes the binding affinity of the second B molecule, making it more or less likely to bind.

105
Q

How is cooperativity allosteric?

A

Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site

106
Q

Give an example of allosteric cooperativity?

A

The binding of oxygen to hemoglobin. For example, when 2,3-BPG binds to an allosteric site on hemoglobin, the affinity for oxygen of all subunits decreases.

107
Q

In eukaryotic cells, some enzymes reside in specific organelles, give an example

A

Enzymes for cellular respiration are located in mitochondria

108
Q

What is the Michaelis-Menton?

A

enzyme kinetics
Vo = v max [S] / Km + [S]
Vo = initial velocity
Vmax is the maximum velocity or rate at which the enzyme catalyzed a reaction. It happens when all enzyme active sites are saturated with substrate.
Km is the concentration of the substrate where the velocity of the reaction is half maximal. Of enzyme concentration it is independent.

109
Q

Km And Vmax can be determined from a Michaelis Menton plot, how?

A

X axis - Reaction rate
Y axis - Concentration of substrate [S]
Vmax = Highest part (goes straight)
Km = 1/2 vmax

110
Q

What can the changes in genes lead to?

A

Changes (mutations) in genes lead to changes in amino acid composition of an enzyme
Altered amino acids, particularly at the active site, can result in novel enzyme activity or altered substrate specificity
Under environmental conditions where the new function is beneficial, natural selection would favor the mutated allele
For example, repeated mutation and selection on the β-galactosidase enzyme in E. coli resulted in a change of sugar substrate under lab conditions

111
Q

In what kind of reactions are NADPH and NADH involved in

A

NADPH – anabolic

NADH – catabolic

112
Q

What are three ways a reaction can be sped up?

A
  1. increasing temperature
  2. increasing pressure
  3. lowering activation energy with an enzyme
113
Q

Do enzyme catalyze exergonic or endogonic reactions?

A

Exergonic

114
Q

Where is the cofactor located?

A

they are part of the active site (bind to active site)

115
Q

Give example of metal cofactor

A

minerals

116
Q

How does enzyme concentration affect enzyme activity?

A

because there are more enzymes to react with the substrate, the enzyme activity will be higher (assuming excess substrate)

117
Q

What does Km depend on?

A

The shape of enzyme and substrate

118
Q 
What can cause a reaction to occur spontaneously?
a) ​–∆G
​b) –∆S
​c) +∆H
​d) ∆T
A

a) ​–∆G

119
Q

The form of energy that is most often least useful to life is energy in

a) concentration gradients.
b) electrical gradients.
c) differences between distinct forms of molecules.
d) the form of heat.
e) electromagnetic radiation.

A

d) the form of heat.

120
Q

A friend tells you that his hamster has reached equilibrium. You

a) send a sympathy card since the hamster is dead.
b) congratulate your friend on teaching the hamster a trick.
c) say that the hamster must produce lots of ATP.

A

a) send a sympathy card since the hamster is dead.

121
Q

The oxidation of glucose to CO2 and H2O is highly exergonic: ∆G = –636 kcal/mole. This is spontaneous, but why is it very slow?

a) Few glucose and oxygen molecules have the activation energy at room temperature.
b) There is too much CO2 in the air.
c) CO2 has higher energy than glucose.
d) The formation of six CO2 molecules from one glucose molecule decreases entropy.
e) The water molecules quench the reaction.

A

a) Few glucose and oxygen molecules have the activation energy at room temperature.

122
Q

For the reaction shown, which statement is true? [exothermic]

a) The greater the activation energy barrier, the slower the reaction rate.
b) The less energy released when products form, the slower the reaction rate.
c) The more types of reactants involved in the reaction, the faster the reaction.
d) The higher the net ∆G of the reaction, the faster the reaction rate.
e) The more bonds altered by the reaction, the faster the reaction rate.

A

a) The greater the activation energy barrier, the slower the reaction rate.

123
Q

What factors affect the reaction rate?

A
  • surface area of a solid reactant.
  • concentration or pressure of a reactant.
  • temperature.
  • nature of the reactants.
  • presence/absence of a catalyst.
124
Q

Some enzymes can couple the hydrolysis of ATP to ion transport by having

a) energy from ATP hydrolysis alter the free energy changes of another reaction.
b) cofactors that act to transfer energy and matter from one reaction to another.
c) phosphate groups from the ATP temporarily donated to the ions.
d) the coupled processes both be exergonic.
e) changes during ATP hydrolysis alter the enzyme’s shape, forcing ionic transport to occur.

A

e) changes during ATP hydrolysis alter the enzyme’s shape, forcing ionic transport to occur.

125
Q

If you’re not getting enough vitamins in your food, what are you missing?

a) allosteric regulators
b) cofactors
c) coenzymes
d) minerals
e) none of the above

A

b) cofactors

From Molecules to Cells (9 decks)

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