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Biology 241 > Thermodynamics and Life > Flashcards

Thermodynamics and Life Flashcards

1
Q

What properties do life consist of?

A

Matter, Energy, Information

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2
Q

How does life interact with matter, energy and infomation?

A

Life transfers, transforms and allows for the flow of those properities.

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3
Q

What is potential energy?

A

Stored energy due to the position of an object in a force field. The potential of an object to do work or release energy.

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4
Q

What is kinetic energy?

A

The energy an object has due to its motion. The energy consumed from the potential energy in order to do work.

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5
Q

What is a chemotroph?

A

An organism that takes energy from chemical bonds in order to produce ATP or energy.

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6
Q

What is a phototroph?

A

An organism that absorbs energy from the Sun in order to produce ATP or energy.

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7
Q

What is a chemolithotroph?

A

An organism that uses inorganic chemical sources in order to produce ATP or energy.

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8
Q

What is a chemoorganotroph?

A

An organism that uses organic chemical sources in order to produce ATP or energy.

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9
Q

Is oxygen essential to life on Earth?

A

No, oxygen is actually a toxin that many organisms do not require in order to live. However, human beings or homo sapiens require it to live.

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10
Q

Is it possible for animals to be phototrophs?

A

Yes, it is possible for animals to become phototrophs. However, genetic engineering is the only method that can do so.

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11
Q

What do animals require in order to be phototrophs?

A

They require not only chlorophyll through genetic engineering but also photosystems or electron transport chains/systems.

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12
Q

Do “strong bonds” have high or low levels of energy?

A

Strong bonds have lower levels of energy as it allows the molecule to be stable.

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13
Q

What is enthalpy?

A

It is the sum of every kind of potential and kinetic energy within the system. It also refers to the change in heat content of a system.

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14
Q

What does exothermic mean?

A

Exothermic reactions or processes refer to instances in which energy is released from the system into the surroundings.

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15
Q

What does endothermic mean?

A

Endothermic reactions or processes refer to instances in which energy is added into a system from the surroundings.

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16
Q

What does the 1st law of thermodynamics state?

A

Energy is neither created or destroyed, however it can be transformed or changed from one form to another.

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17
Q

It is important to always consider what two elements when studying energetics?

A

The system and the surrounding.

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18
Q

What is an open system?

A

An open system allows for both matter and energy to flow into and out of the system.

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19
Q

What is a closed system?

A

A closed system does not allow matter to flow into or out of the system. However, a closed system still allows for the flow of energy.

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20
Q

What is an isolated system?

A

An isolated system does not allow for either the flow of energy or matter into or out of the system.

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21
Q

What is ATP?

A

Adenosine triphosphate is a molecule that contains energy within its chemical bonds. ATP is the universal “currency” of cellular energy.

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22
Q

What is an autotroph?

A

An organism that create their own carbon from inorganic sources such carbon dioxide.

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23
Q

What is a heterotroph?

A

An organism that obtains carbon from organic sources. They generally consume other organisms.

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24
Q

What does metabolism mean?

A

It is the entire set of chemical reations that convert molecules into other moecules and trasnfer energy in living organisms.

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25
Q

What is catabolism?

A

It is the set of chemical reactions that break down molecules into smaller molecules. It releases energy.

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26
Q

What is anabolism?

A

It is the set of chemical reactions that build larger molecules from smaller molecules. It requires energy.

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27
Q

Why do organic molecules contain large amounts of chemical energy?

A

Organic moleucles consist mainly of covalent bonds in which the shared electrons are far from the atoms thus storing a large amount of chemical potential energy.

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28
Q

What is ATP composed of?

A

ATP is made of the base adenine, a five carbon sugar, ribose, and three phosphate groups, triphosphate.

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29
Q

Why does ATP contain large amounts of chemical energy?

A

The phosphate groups are negatively charged and thus they repel each other. As a result, the chemical bond stores potential energy that is released when the bonds are broken.

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30
Q

What is entropy?

A

It is the measure of disorder within a system. It is also the measure of the dispersion of energy.

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31
Q

What does the second law of thermodynamics state?

A

The transformation of energy will increase the entropy or disorder of the universe. This is because the transformation of energy is never 100% efficient, therefore some energy to do work is always lost as an increase in disorder.

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32
Q

What does catabolism do to the level of entropy?

A

It increases the entrophy of the system because the smaller molecules, which are produced from the large molecule, is more free to move.

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33
Q

What does anabolism do to the level of entropy?

A

It decreases the entropy of the system because the large molecule, created from the smaller molecules, is not as free to move.

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34
Q

Why do anabolic reactions, which decrease the entropy of the system, NOT violate the second law of thermodynamics?

A

The second law of thermodynamics states that the entropy of the UNIVERSE is increased, thus anabolic reactions do not violate the law.

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35
Q

Do air conditioners violate the second law of thermodynamics?

A

No, air conditioners pump heat against their natural flow, from cold objects to hot objects. Therefore, the entropy of the universe still increases because energy is lost in order to reverse the flow of heat.

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36
Q

Are all bio-reactions endothermic or exothermic?

A

They can be either, some reactions are endothermic while others are exothermic. This is necessary in order to keep the energy of the system conserved.

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37
Q

Are all bio-reactions spontaneous or non-spontaneous?

A

They are ALL spontaneous or else we would die.

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38
Q

Is spontaneity determined by whether or not a reaction is endothermic or exothermic?

A

No, spontaneity is only determined by either the change in entropy or free energy change.

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39
Q

Does spontaneity relate to the rate of reaction?

A

No, spontaneity only means that the reaction occurs in forward motion in those conditions.

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40
Q

What does it mean for a reaction to be spontaneous?

A

It is able to macroscopically proceed forward in the real world.

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41
Q

If a reaction is spontaneous in one direction, is it also spontaneous in the order direction?

A

No, it is nonspontaneous in the other direction.

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42
Q

What are some conditions that determine whether or not a reaction is spontaneous?

A

Temperature, pressure, concentration of products and concentration of reactants.

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43
Q

Can a nonspontaneous reaction be changed into a spontaneous reaction?

A

Yes, by changing the conditions it is often possible to reverse the spontaneity of a reaction. In fact, some bio-reactions are only spontaneous at the intracellular level and nonspontaneous at standard conditions.

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44
Q

What determines spontaneity?

A

The change in entropy of a universe. (Stotal)

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45
Q

In order for a reaction to be spontaneous, what must be the Stotal be?

A

Greater than 0.

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46
Q

Do spontaneous reactions increase or decrease entropy?

A

They increase entropy.

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47
Q

How is Stotal calculated?

A

S + Ssurroundings

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48
Q

What are the units of entropy?

A

J / (mol*K) or Energy / (mol*temperature)

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49
Q

The 2nd Law of Thermodynamics states that entropy of an isolated system always…

A

Increases

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50
Q

How is Gibb’s free energy calculated? (With Total Entropy)

A

G = -T*Stotal

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51
Q

What must Gibb’s free energy change be in order for a reaction to be spontaneous?

A

Less than 0.

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52
Q

What are the units of Gibb’s free energy change?

A

J / mol, kJ / mol, cal / mol, energy / mol

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53
Q

What is free energy change?

A

The amount of energy that can be freed up to do work. It is a state function that describes the maximum amount of energy within a system that can actually do work, NOT ENERGY.

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54
Q

All cellular reactions have _______ free energy.

A

Negative

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55
Q

What is an exergonic reaction?

A

A reaction in which energy to do work (free energy) is released from the system to the surroundings. G < 0

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56
Q

What is an endergonic reaction?

A

A reaction in which energy to do work (free energy) is absorbed by the system from the surroundings. G > 0

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57
Q

All bio-cellular reactions are ___gonic.

A

Exergonic

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58
Q

How is GIbb’s free energy calculated? (Without total entropy)

A

G = H - T*Ssystem

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59
Q

Why is H in the GIbb’s free energy calculation that does NOT involve total entropy?

A

The heat leaving the system (enthalpy) is dispersed into the surroundings thus accounting for the Ssurroundings.

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60
Q

What is G0?

A

It is the standard free energy change or free energy change that occrurs in standard condition.

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61
Q

If G0 is greater than 0, is the reaction always nonspontaneous?

A

Not necessarily, at standard conditions the reaction is indeed nonspontaneous, however at other conditions the reaction could potentially be spontaneous.

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62
Q

Is G the same as G0?

A

No, G represents Gibb’s free energy change whereas G0 ONLY represents free energy change at standard conditions.

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63
Q

Is free energy conserved?

A

No, free energy is not even necessarily “real.” It is just a quantity or state function that describes the maximum amount of energy within the system that is actually able to do work.

64
Q

Is Gibb’s function energy?

A

No, it just describes the maximum amount of energy within a system that can do work.

65
Q

How do organisms make non spontaneous reactions occur?

A

They manipulated the concentrations of the products and reactants in order to allow certain reactions to occur.

66
Q

Why does water melt and evaporate spontaneously?

A

By changing states from a solid to a liquid or liquid to a gas, the entropy of the system is increased and thus is favourable.

67
Q

In order to have a greater entropy, is it more plausible to have two molecules or one molecule?

A

Two molecules have a greater entropy as there is more movement involved and thus disorder. Greater amounts of molecules will always have more entropy than fewer amounts.

68
Q

What is the first step in the metabolism of glucose?

A

glucose + ATP -> glucose 6-Pi + ADP (G = -35 kJ/mol) This is the phosphorylastion of glucose.

69
Q

What is the activation energy?

A

The amount of energy required to break chemical bonds and initiate the reaction. (Thus producing the products)

70
Q

What are the ways to symbolize activation energy?

A

Ea, G*, AE, E*

71
Q

Where is the transition state of a reaction found?

A

At the highest point on the free energy or energy to reaction progress graph. The point that illustrates the activation energy or G*.

72
Q

What are the ways to speed up chemical reactions?

A

Increase the concentration of the reactants, increase the temperature, or add a catalyst.

73
Q

What is a catalyst?

A

A substance that decreases the activation energy of a reaction in order to increase the rate of reaction. The substance however is NOT used up in the process.

74
Q

What is an enzyme?

A

They are protein-based bio-catalyst that are essential to the processes in life. Nearly all bio-reactions have their own enzyme.

75
Q

If G* is lowered, what happens to the rate of reaction?

A

It increases as less free energy is required for the reaction to occur.

76
Q

If G* is increased, what happens to the rate of reaction?

A

It decreases the rate of reaction as more free energy is required for the reaction to occur.

77
Q

How do enzymes catalyze reactions?

A

The enzyme binds to the substrates to create a enzyme-substrate complex which makes it easier to break and form bonds. It also positions the substrates together in order to initiate the reaction. As a result, the reaction is able to proceed much faster.

78
Q

Where does the substrate bind to?

A

The active site.

79
Q

What is the induced fit model?

A

It is the notion that enzymes change their shape in order to allow for the substrate to fit into the active site better.

80
Q

Can an enzymes work for any substrate?

A

No, enzymes are very specific to their allowed substrates. They either recognize the entire substance, or distinct features of it.

81
Q

What is the transition state?

A

It is the intermediate stage between the reactants and the products.

82
Q

Does the change in free energy of a reaction change when an enzyme is used?

A

No, the enzyme is used to lower the G* or activation energy required to allow the reaction to occur.

83
Q

Why are enyzmes so large when only a few amino acids actually contribute the its role?

A

These specific amino acids have to occupy certain spatial positions in order to align the substrates properly. Therefore, a large chain of amino acids is required to position and form the 3-D shape of the enzyme.

84
Q

What are inhibitors?

A

Substances that decrease the activity of enzymes.

85
Q

What are activators?

A

Substances that increase the activity of enzymes.

86
Q

How do inhibitors reduce the effectiveness of enzymes?

A

They either bind to the active site of the enzyme or alter the active site by binding to other parts of the enzyme.

87
Q

What are irreversible inhibitors?

A

Inhibitors that form covalent bonds with the enzymes and permanently inactive them.

88
Q

What are reversible inhibitors?

A

Inhibitors that only form weak bonds with the enzymes and thus are easily reversed.

89
Q

What are competitive inhibitors?

A

Inhibitors, that share a similar shape to the substrate, that bind to the active site of the enzyme and prevent the binding of hte substrate.

90
Q

What are non-competitive inhibitors?

A

Inhibitors that generally have a different shape than the substrates, however they bind to different parts of the enzyme in order to change the active site and lower the efficiency of the site. (And in some cases, deactivate the enzyme)

91
Q

Are enzymes only composed of protein?

A

No, they also generally contain metals or co-factors that help the enzyme to function.

92
Q

What is an enthalpy driven reaction?

A

A reaction that is made possible mainly from the change in enthalpy.

93
Q

What is an entropy driven reaction?

A

A reaction that is made possible mainly from the change in entropy.

94
Q

How do you maintain a high degree of order?

A

Either consistently use energy or create entropy (to the surroundings).

95
Q

Do all bio-reactions have enzymes?

A

Not all but nearly every reaction is catalyzed.

96
Q

If an organism has a larger genome does it have less or more bio reactions?

A

As the complexity of an organism increases, so does the amount of bio reactions.

97
Q

What are the two coupled reactions in the first step of glycolysis?

A

1 ) glucose + Pi -> glucose-6-Pi + H2O

2) ATP + H20 -> ADP + Pi

98
Q

What is a coupled reaction?

A

A single reaction that can be thought of as two events that occur at the same place, time and with the same enzyme.

99
Q

Why is the G for ATP hydrolysis so negative?

A

The enthalpy change within the system is extremely negative because large amounts of energy are released when ATP is converted to ADP.

100
Q

Which has stronger bonds? ATP and H20 or ADP and Pi?

A

ADP and Pi have stronger and more stable bonds.

101
Q

Why does ADP and Pi have less potential energy than ATP?

A

The electron to electron repulsion is reduced. There are more resonance (electron movement) and tautomeric (proton movement) structures. ADP and Pi are more ionized and they are more effectively solvated. (Less hydration energy)

102
Q

What are connected reactions?

A

Reactions in which the product of one reaction is also the substrate of the other reaction.

103
Q

What is the second step in the metabolism of glucose?

A

glucose-6-pi -> fructose-6-pi

104
Q

Why does the first reaction of glycolysis help make the second reaction have a more negative free energy change?

A

The first step increases the concentration of glucose-6-Pi which drives the second step towards the production of fructose-6-Pi.

105
Q

Why is it important that ATP requires an enzyme to hydrolize it?

A

If ATP did not require an enzyme to hydrolize it then it would not be a good molecule to store energy in it as it always loses the energy through hydrolysis.

106
Q

What is the enzyme for the first step of glycolysis?

A

Hexokinase

107
Q

Does ATP hydrolysis ACTUALLY happen in glycolysis?

A

No, an enzyme catalyzes the entire reaction.

108
Q

Are all enzymes protein based?

A

No, there are also other kinds of enzymes, but the majority are.

109
Q

How do you measure the velocity of an enzyme?

A

You can either measure the absorbance of the product (colour) or you can measure the disappearance of the substrate.

110
Q

How do you calculate the rate of an enzyme?

A

Use the absorbance to calculate the concentration of the products. Find the umoles of the product. Divide the umoles by time (min) to get the rate in umoles/min.

111
Q

How does [Enzyme] affect the rate of reaction?

A

As you increase the concentration of the enzyme, the rate of the reaction also increases linearly.

112
Q

What does the [Enzyme] vs. Velocity of Reaction graph look like?

A

A positively sloped linear graph.

113
Q

How does [Substrate] affect the rate of reaction?

A

As the concentration of the substrate, the rate of reaction increases, however it eventually plateaus at a maximum velocity, Vmax.

114
Q

What is Vmax?

A

The maximum velocity that a cellular reaction can occur at. It is affected by [Enzyme], [Substrate] and presence of an inhibitor.

115
Q

What is the concentration of substrate that is required for 1/2 Vmax called?

A

Km or Michaelis’ Constant

116
Q

What is the optimal velocity of reaction for cells?

A

At 1/2 of the Vmax. Thus, the cell generally monitors the substrate concentration to be around Km.

117
Q

Why can cells not operate at Vmax?

A

1/2 Vmax is the optimal speed because as reactions get faster than that, there tends to be more mistakes.

118
Q

How does an competitive inhibitors affect the velocity of the reaction?

A

The competitive inhibitor slows down the velocity of the reaction and shifts Km. However, eventually at extremely high substrate concentrations, the substrate will out-compete the inhibitor and still achieve the same Vmax.

119
Q

How do non-competitive inhibitors affect the velocity of the reaction?

A

They lower the velocity of the reaction and DOES NOT SHIFT Km, but even at high substrate concentrations, the substrate is NOT able to out-compete the inhibitor thus the Vmax is lower.

120
Q

Can a substrate out-compete irreversible inhibitors?

A

No, the enzyme is permantently deactivated and thus Vmax lowers until the enzyme eventually dies.

121
Q

Can coupled reactions have more than two steps?

A

Yes, the minimum for a coupled reaction is 2 steps.

122
Q

What is a true coupled reaction?

A

A reaction that actually has intermediates rather than hypothetical intermediates.

123
Q

Does sequence matter in an amino acid chain?

A

YES, it is absolutely essential.

124
Q

How many natural amino acids are there?

A

20

125
Q

What is the structure of an amino acid?

A

There is an alpha carbon that is bonded to an amino group, carboxyl group, hydrogen atom and an r-group.

126
Q

What distinguishes the amino acids from each other?

A

The r-group is what makes them unique.

127
Q

What does it mean to be hydrophilic?

A

They are molecules that highly attracted to water.

128
Q

What does it mean to be hydrophobic?

A

They are molecules that strongly dislike/repel water.

129
Q

What is another name for r-groups?

A

Side chains

130
Q

What properties do the general hydrophobic side chains exhibit and where are they usually on the protein?

A

They either have no charge or contain aromatics. They are found on the inside of the protein’s folded structure.

131
Q

What properties do the general hydrophilic side chains exhibit and where are they usually on the protein?

A

They either have charges, carboxyl groups, amine groups, and are either bases or acids. They are found on the outside of the folded protein.

132
Q

What is the amino end?

A

The end of the amino acid with the amine group.

133
Q

What is the carboxyl end?

A

The end of the amino acid with the carboxyl group.

134
Q

How are peptide bonds formed?

A

Through dehydration synthesis where the OH group from the carboxyl and H from the amine groups are taken off as water in order for the bond to form.

135
Q

Are r-groups involved in peptide bonds?

A

No, they are key parts of the protein structure however.

136
Q

What are oligopeptides?

A

Amino acid chains that contain 10 or less amino acids.

137
Q

What are polypeptides?

A

Amino acid chains that contain more than 10 amino acids.

138
Q

How many amino acids are required for a polypeptide to be considered a protein?

A

16

139
Q

What is the primary structure of a protein?

A

The sequence of the amino acids.

140
Q

What is the secondary structure of a protein?

A

The shape that forms from the interaction of local amino acids. It can consist of helices, sheets, turns, and random meander regions.

141
Q

What are the two types of secondary structures?

A

Alpha helix and Beta sheet

142
Q

Can a protein have more than one secondary structure?

A

Yes, in fact many proteins have both a-helix and b-sheet structures.

143
Q

What is the tertiary structure of a protein?

A

The three-dimensional shape that forms from the folding of the protein.

144
Q

What is the quaternary structure of a protein?

A

It is the complex that arises from the interaction of protein subunits.

145
Q

What is a protein subunit?

A

One folded polypeptide chain with primary, secondary and tertiary structures.

146
Q

What are some of the forces that help a protein maintain its shape?

A

Non-covalent forces such as hydrogen bonds, Van der Waals’ forces, hydrophobic interactions and ionic interactions.

147
Q

Does heat increase the enzymes efficiency?

A

At moderate temperatures, every 10C doubles the rate of reaction, however if too much heat is added it denatures the protein.

148
Q

What is denaturation?

A

When a protein loses shape/structure (2, 3, 4) due to changes in condition, mainly heat.

149
Q

How are enzymes denatured?

A

High temperatures, abnormal pHs, non-polar solvents and vigourous stirring may all denature an enzyme.

150
Q

What is inactivation?

A

When an enzyme is no longer able to function due to denaturation.

151
Q

Can denaturation be reversed?

A

In some cases, however denaturation generally is permanent as it alters the secondary, tertiary and quaternary structures of the protein.

152
Q

How do peptide bonds compare to single bonds?

A

They are shorter and more rigid.

153
Q

What are chaperones?

A

Evolved proteins that help protect slow-solding or denatured proteins until they can properly form their 3-D structure.

154
Q

What is energetic coupling?

A

It is when the energy released from one reaction drives the next reaction.

155
Q

How does ATP energize molecules?

A

By transferring a phosphate group to the a molecule which primes it for subsequent reactions (adding potential energy).

156
Q

What is fragmentation of a protein by proteolysis?

A

It is the severing of the amino acid’s primary sequence.

157
Q

What is the difference between polypeptides and proteins?

A

A polypeptide is a linear chain of amino acids, a protein is composed of folded polypeptides.

Biology 241 (2 decks)

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