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BIOL 2325 > quiz 3 > Flashcards

quiz 3 Flashcards

1
Q

What is thermodynamics

A

the study of energy and its transformations

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2
Q

what is the system and what is it called for things outside the system

A

system is the object under study and everything else is its surroundings

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3
Q

what are the three type of systems and describe them

A

isolated: system and surroundings does not exchange matter or energy
closed: only exchanges energy
open: exchanges energy and matter

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4
Q

name an example of an open system

A

Humans, organisms

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5
Q

What is the first law of thermodynamics

A

energy can be transformed from one form to another but it can’t be created nor destroyed

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6
Q

what is the second law of thermodynamics (2)

A

1) the total disorder (entropy) of a system and its surroundings always increase but the total energy of the universe does not change
2) Entropy of universe always increase

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7
Q

what is energy

A

the capacity to do work

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8
Q

what are the two states of energy and what is the difference

A

kinetic (energy of motion) and potential (stored energy)

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9
Q

name some forms of energy

A

chemical, thermal, electrical, radiant, mechanical

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10
Q

How (or to where) is energy transformed/transferred

A

energy is transferred between reactants and products, and between reactants or products and their surroundings.

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11
Q

What is the energy of reaction/ energy of formation

A

energy released or absorbed during chemical reaction

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12
Q

What is a spontaneous reaction

A

a chemical or physical reaction that will occur without an input of energy

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13
Q

what are two factors that determine whether a reaction is spontaneous or not

A

1) the change in energy content of a system

2) its change in entropy

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14
Q

Do reactions tend to be spontaneous when products have less potential energy than reactants or more PE?

A

reactions tend to be spontaneous when products have less potential energy than reactants

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15
Q

what is enthalpy and what is the variable assigned to it

A

Enthalpy is the potential energy in a system, (H)

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16
Q

When is a reaction exothermic

A

Reactions that release energy or when the products have less PE than reactants (Delta H is negative)

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17
Q

When is a reaction endothermic

A

Reactions that absorb energy or when products have more PE than reactants (Delta H is positive)

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18
Q

Reactions tend to be spontaneous if products are (more or less) ordered than the reactants

A

less ordered

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19
Q

Reactions tend to be spontaneous if products have (greater or lesser) entropy than the reactants

A

greater

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20
Q

What is gibbs free energy

A

the portion of a system’s energy that is available to do work

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21
Q

what is the equation of gibbs free energy

A 
Delta G= Delta H - T(delta S)
Delta G is change in free energy
Delta H is change in enthalpy
T is temp in kelvin
Delta S is change in entropy
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22
Q

For a reaction to be spontaneous, Delta G must be (positive or negative)

A

Delta G must be negative

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23
Q

Name an example where a negative Delta H dominates making the reaction spontatneous

A

Combustion of methane (large loss of potential energy meaning negative enthalpy

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24
Q

Name an example where delta S dominates making the reaction spontaneous

A

Melting of ice at room temp, decrease in order dominates

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25
Q

Fix this statement.

In many spontaneous biological reaction, reactants fully convert to products since the reaction has a negative delta G

A

In many spontaneous biological reaction, reactants may not fully convert to products even though the reactions have a negative delta G

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26
Q

What is the equilibrium point in a reaction

A

a state of balance between the opposing factors pushing the reaction in either directions

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27
Q

As a system moves toward equilibrium, what happens to free energy and delta G

A

free energy progressively lowers to its lowest point when system achieves equilibrium (delta G= 0)

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28
Q

Why is moving away from equilibrium not spontaneous

A

it requires free energy

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29
Q

When delta G is near 0, is the reaction reversible

A

yes

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30
Q

in a chemical equation, how are reversible reactions showed

A

double arrow

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31
Q

why do many reaction in living organism never reach equlibrium

A

because living systems are open and the supply of reactants is constant and products don’t accumulate

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32
Q

why is delta g of life always negative

A

organisms constantly take in energy rich molecules and use them to do work

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33
Q

when do organisms reach equilibrium (delta G = 0)

A

only when they die

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34
Q

What is an exergonic reaction (3)

A

Reaction that releases free energy
Delta G is negative because the products contain less free energy than reactants
spontaneous reaction

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35
Q

what is an endergonic reaction (3)

A

reactants must gain free energy from surroundings to form products
Delta G is positive because products contain more free energy than the reactants
non spontaneous reaction

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36
Q

Define metabolic pathway

A

a series of reactions in which the products of one reaction are used immediately as reactants in the next reaction

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37
Q

Name the 2 different metabolic pathways

A 
Catabolic pathway (or a single catabolic reaction) and anabolic pathway (anabolic reaction or biosynthetic reaction). 
Catabolic pathway is breakdown of complex molecules to simpler compounds (delta G is negative)
Anabolic pathway is build of complicated molecules from simpler ones (delta G is positive)
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38
Q

What is the chief energy currency of the cell

A

ATP (adenosine triphosphate)

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39
Q

What is ATP composed of

A

ribose, adenine, and 3 phosphate group

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40
Q

where is the energy stored in ATP

A

in the high energy bonds between the phosphates

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41
Q

What is the purpose of ATP( other than being the primary energy currency)

A

ATP is used to drive endergonic reactions

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42
Q

What is made after hydrolysis reaction with ATP

A

ADP and a inorganic phosphate (Pi)

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43
Q

What is the delta G of ATP hydrolysis

A

-7.3 kcal/mol

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44
Q

ADP can be hydrolyzed into what

A

AMP

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45
Q

what is energy coupling

A

ATP hydrolyzed where the terminal phosphate group is transferred to a reactant molecule involved in endergonic reaction

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46
Q

What is phosphorylation

A

addition of a phosphate group to a molecule

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47
Q

What is a requirement for phosphorylation

A

An enzyme is needed with a specific site that binds both ATP and the reactant molecule to bring the two together

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48
Q

Is ATP synthesis an endergonic or exergonic reaction

A

Endergonic reaction

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49
Q

Where do we find the energy for ATP synthesis

A

energy from exergonic breakdown of carbohydrates, proteins, and fats (food)

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50
Q

Approximately how many ATP molecule are hydrolyzed and resynthesized each second in a typical cell

A

10 million

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51
Q

What is the ATP/ADP cycle

A

continual hydrolysis and resynthesis of ATP

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52
Q

What are redox reactions

A

Where oxidation and reduction occurs in a reaction

Electrons pass from one atom to another carry energy with them

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53
Q

what is oxidation and what is reduction

A

Oxidation is when an atom or molecule loses an electron

Reduction occurs when an atom or molecule gains an electron

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54
Q

T/F

A spontaneous reaction has a activation energy of 0

A

false

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55
Q

What is the variable assigned to activation energy

A

Ea

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56
Q

What is activation energy

A

The amount of energy needed to make bonds unstable (destabilize chemical bonds) and ready to be broken (the transition state)

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57
Q

What is a catalyst

A

substance that lowers the activation energy thereby accelerating the rate of reaction

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58
Q

What are enzymes

A

catalyst that cannot violate the law of thermodynamic

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59
Q

Do enzymes alter delta G of the reaction

A

no

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60
Q

How does an enzyme work in enzymatic reactions

A

enzymes combines briefly with reacting molecules and is unchanged when the reaction is complete

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61
Q

what is the reactant that an enzyme acts on called?

A

substrate

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62
Q

what is enzyme specificity

A

Each type of enzyme catalyzes the reaction of a single type of substrate or group of closely related molecules

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63
Q

What is an active site

A

a small pocket or groove in the enzyme that the substrate interacts with

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64
Q

what is induced fit

A

when the substrate binds at the active site, both enzyme and substrate molecules are distorted, making the chemical bonds in substrate ready for reaction (as opposed to lock and key model)

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65
Q

Once an enzyme substrate complex is formed, catalysis occurs- the substrate is converted into (how many products?)

A

one or more

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66
Q

which macromolecule do enzymes belong in

A

protein

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67
Q

Are enzymes consumed in a reaction

A

no, they are not consumed and can be reused so only a small amount is needed

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68
Q

What allows enzyme to stabilize a temporary association between substrates

A

unique 3d shape of enzyme (active site)

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69
Q

Cells have (how many) enzymes (inside, outside, or both) the cell

A

thousands, inside and outside

70
Q

how do we know if something is an enzyme by its name and how do we know its respective substrate

A

the enzyme will end in -ase and refer to its substrate or type of reaction (maltase, amylase, proteinase, ribonuclease in ainfensens experiment, etc)

71
Q

What is a cofactor

A

a nonprotein group that binds to the enzyme for catalytic activity. Some are metallic ions (iron, copper, magneisum, zinc, manganese)

72
Q

what is a coenzyme

A

a cofactor that is a small organic molecule, which are often derived from vitamins

73
Q

what is an example of a coenzyme

A

NAD/NADP

74
Q

Name 3 major mechanisms that are part of enzymes that stabilize the transition state

A

1) bringing the reacting molecules together
2) exposing the reactant molecules to altered charge environment that promote catalysis
3) changing the shape of the substrate molecules

75
Q

name 4 factors affecting enzyme activity

A

1) Concentration of substrate and other molecules that bind to enzymes
2) control mechanisms that modify enzyme activity (inhibitors)
3) temperature
4) pH- ionic interactions hold enzymes together

76
Q

when enzyme concentration is kept constant, what happens to the rate of reaction as we increase substrate concentration

A

the rate of reaction will increase until it flattens out, this means the enzymes are saturated and the rate is solely dependent on the amount of enzyme molecules and how fast they work, no longer increase of substrate will increase rate

77
Q

what are enzyme inhibitors

A

nonsubstrate molecules that bind to an enzyme and decrease its activity

78
Q

what are competitive inhibitors

A

a inhibitor that competes with the substrate for the same active site

79
Q

what are noncompetitive inhibitors

A

a inhibitor that binds at a site other than active site, causing the enzymes shape to change so that substrates can’t bind to the active site

80
Q

what is allosteric regulation and allosteric site

A

reversible binding of a regulatory molecule to the allosteric site (location on enzyme other than active site). Enzymes will have 2 alternate conformations: high affinity state (active) and low affinity state (inactive)

81
Q

what is allosteric activation

A

an allosteric activator binds to an enzyme on the allosteric site and the enzyme goes from low affinity state to high affinity state

82
Q

what is allosteric inhibiton

A

allosteric inhibitor goes into allosteric site and enzyme goes from high affinity state to low affinity state

83
Q

what is negative feedback (feedback inhibition) and how is it related to allosteric inhibition

A

the product inhibits the process. The product is the allosteric inhibitor

84
Q

What is regulation by chemical modification of an enzyme

A

chemical linkages to ions, functional groups, or other molecules that induce changes in enzyme that increase or decrease its activity

85
Q

name an example of regulation by chemical modification of an enzyme

A

phosphorylation by protein kinases may activate or deactivate a protein

86
Q

what do kinases do

A

transfer phosphate group from ATP to another molecule (kinase like kinetic energy??)

87
Q

Typically, as temperature rises, how does the rate of reaction respond

A

rate of reaction typically increases

88
Q

why can too high a temperature lower rate of reaction for an enzymatic reaction

A

kinetic motion increases and eventually hydrogen bonds break and the enzymes denature

89
Q

What is optimum temperature

A

the ideal temperature for an enzyme where enzymatic activity is at its peak

90
Q

what is the optimal pH of most enzymes

A

neutral, 7

91
Q

what is the optimal pH of stomach enzymes (like pepsin)

A

acidic, 2

92
Q

what is the RNA world

A

earliest forms of life might have inhabited RNA world, with no DNA or proteins to play critical roles.
This is because ribozymes were informational molecules and had enzymatic function (could accelerate rate of certain biological reactions)

93
Q

Name some functions of ribozymes (2)

A

cutting and splicing reactions that remove surplus segments from RNA molecules
Catalyze linkage of amino acids in protein synthesis

94
Q

What are autotrophs

A

Organisms that harvest sunlight and convert radiant energy into chemical energy

95
Q

what are heterotrophs

A

organisms that live off the energy produced by autotrophs

extract energy from food via digestion and catabolism

96
Q

what is cellular respiration

A

collection of metabolic reactions that breaks down food molecules to produce energy in the form of ATP (think mitochondria)

97
Q

what is aerobic respiration and what organisms is it found in

A

form of cellular respiration in eukaryotes and many prokaryotes, oxygen is reactant in ATP producing process

98
Q

what is anaerobic respiration and what organisms is it found in

A

form of cellular respiration found in some prokaryotes, molecule other than oxygen (sulfate or nitrate) is used in ATP producing process

99
Q

what is the end goal of respiration

A

to produce ATP

100
Q

is cellular respiration one redox reaction or many

A

many redox reactions

101
Q

energy is released from oxidation in the form of what?

A

electrons

102
Q

electrons are shuttled by electron carriers, name a electron carrier and where does it deliver to

A

NAD+ to an electron transport chain

103
Q

at the electron transport chain, what happens

A

electron energy is converted to ATP

104
Q

what is the final electron acceptor in aerobic respiration, anaerobic, and fermentation

A

oxygen for aerobic
inorganic molecule for anaerobic
organic molecule for fermentation

105
Q

how do we obtain free energy for cellular work such as ATP synthesis in redox reactions

A

electrons release some of their energy as they pass from a donor molecule to an acceptor molecule

106
Q

in redox reactions, do molecules only accept electrons? name an example or counter example

A

no they don’t only accept electrons, they accept protons too. Oxygen accepts protons to make water

107
Q

what is the standard chemical equation for making ATP from glucose. Is this aerobic or anaerobic? What is the delta G

A

C6H12O6 + 6O2 + 32ADP + 32Pi –> 6H2O + 6CO2 + 32ATP
Aerobic
-686kcal/mol

108
Q

in aerobic respiration, can the large amount of energy be released at the same time?

A

no, it must be released in small steps

109
Q

Are the electron carriers soluble or insoluble? Are they membrane bounded or not?

A

soluble and membrane bound

110
Q

Are all carriers easily oxidized and reduced

A

yes

111
Q

what do electron carriers carry

A

electrons, some can carry electrons and protons

112
Q

what is the function of dehydrogenase enzyme

A

facilitate transfer of electrons from a fuel molecule to a molecule that acts as an electron carrier

113
Q

what is the most common electron carrier

A

coenzyme nicotinamide adenine dinucleotide (NAD+)

114
Q

in cellular respiration, what does the Dehydrogenase do to the NAD+

A

dehydrogenase transfers 2 electrons and 1 proton to NAD+ (oxidized form) to result into complete reduction to NADH (reduced form)

115
Q

what does NAD+ and NADH have in common in structure? how are they different?

A

Both have adenine, 2 ribose and 2 phosphate groups, and nicotinamide. NAD+ has just 1 hydrogen bonded to the top carbon while NADH has 2 hydrogens connected to the top carbon

116
Q

name the polymers of glucose that we need to know

A

glycogen, cellulose, and starch (and chitin if you want)

117
Q

what are the 4 stages of oxidation of glucose in order and where in the cell does each occur

A

glycolysis (cytosol), pyruvate oxidation (mitochondrial matrix), krebs cycle (mitochondrial matrix), electron transport chain and Chemiosmosis (ATP production)(inner mitochondrial membrane)

118
Q

in glycolysis enzymes break a (how many) carbon molecule of (what carbohydrate) into (what and how many)

A

enzymes break a 6 carbon glucose molecule into 2 3-carbon pyruvate molecules

119
Q

what is substrate level phosphorylation

A

enzyme catalyzed reaction that transfers phosphate group from substrate to ADP

120
Q

in pyruvate oxidation, enzymes convert what into what for the citric acid cycle

A

3-carbon pyruvate into a 2 carbon acetyl group

121
Q

in the electron transport chain, electrons are delivered to what molecule and what is chemiosmosis established and what is it used for

A

electrons are delivered to oxygen by a sequence of electron carriers in the ETC
free energy released by electron flow generates an H+ gradient by chemiosmosis and ATP synthase uses the H+ gradient as the energy source to make ATP

122
Q

whats the equation for Calories in terms of proteins fats and carbs?

A

9(fat)+4(carbs)+4(proteins) all in grams

123
Q

What is the difference between substrate level phosphorylation and oxidative phosphorylation

A

substrate level phosphorylation is transferring a phosphate group from the molecule directly to ADP
oxidative phosphorylation is ATP synthase using energy from proton gradient

124
Q

What is the chemical equation for glycolysis

A

Glucose + 2ADP + 2Pi + 2NAD+ + 4e- + 4H+ –> 2 pyruvate + 2ATP + 2 NADH + 2H+ + 2H2O

125
Q

How much TOTAL ATP is made in glycolysis? How about NET ATP? How much NADH is made?

A

4 total, 2 net, 2NADH

126
Q

what kind of transport moves pyruvate into the mitochondrial matrix

A

secondary active transport

127
Q

pyruvate oxidation occurs where in eukaryotes and where in prokaryotes

A

mitochondria in eukaryotes and cytosol in prokaryotes

128
Q

what is the equation for pyruvate oxidation for 1 glucose molecule (so start with 2 pyruvates)

A

2 pyruvate + 2CoA + 2NAD+ —> 2acetyl-CoA + 2NADH + 2H+ +2CO2

129
Q

what are other names of the citric acid cycle (2)

A

Krebs cycle, tricarboxylic acid cycle

130
Q

what are the products of Krebs cycle for 1 glucose molecule

A

6NADH, 4CO2, 2FADH2, 2ATP, 6H+, 2CoA

131
Q

what is needed for the first step of Krebs cycle

A

oxaloacetate, acetyl CoA and citrate synthase

132
Q

What has glucose been oxidized to up till the end of Krebs cycle

A

6CO2, 4ATP, 10NADH, 2FADH2

133
Q

What are some allosteric inhibitors for phosphofructokinase? (3), What activates it?

A

Excess ATP, Citrate, and NADH inhibit it. AMP activates it

134
Q

What inhibits pyruvate kinase? (2), what activates it?

A

high levels of ATP and Acetyl CoA inhibits it. high levels of Fructose 1,6- bisphosphate activates it

135
Q

What inhibits pyruvate dehrdrogenase

A

high levels of NADH

136
Q

what inhibits citrate synthase (2)

A

high levels of ATP and citrate

137
Q

what inhibits hexokinase

A

glucose 6 phosphate

138
Q

what does ETC and ETS stand for

A

electron transport chain and electron transfer system

139
Q

ETC is where?

A

embedded in the inner mitochondrial membrane

140
Q

Which protein complex do electrons from NADH enter into? How about FADH2?

A

complex 1 for NADH and complex 2 to FADH2

141
Q

where is the higher concentration and where is the lower concentration of protons

A

high H+ in intermembrane compartment and low H+ in matrix

142
Q

what are the two small mobile electron carriers in the etc

A

cytochrome c and ubiquinone (coenzyme Q)

143
Q

what are cytochromes

A

proteins with a heme prosthetic group that contains an iron atom to accept and donate electrons

144
Q

are electron carriers organized from high to low free energy or low to high free energy

A

high to low free energy

145
Q

what is the last terminal electron acceptor and what is it reduced to

A

O2 accepts 4 protons to turn into 2H2O

146
Q

which protein complexes actively move protons

A

complexes 1 3 and 4

147
Q

what kind of gradient is the proton gradient

A

electrical and chemical gradient

148
Q

What is chemiosmosis/chemiosmotic hypothesis

A

that the proton gradient powers ATP synthesis by ATP synthase

149
Q

Is the basal unit towards the intermembrane compartment or the matrix

A

towards the compartment, where protons can enter

150
Q

What connects headpiece and basal unit

A

the stalk, a peripheral stator bridges the basal unit and headpiece

151
Q

which part rotates in ATP synthase and in which direction

A

the basal unit rotates counterclockwise

152
Q

What is the theoretical energy yield for bacteria and eukaryotes

A

38 ATP for bacteria and 36 ATP for eukaryotes

153
Q

what is the theoretical yield of energy per NADH and FADH2

A

3 ATP for NADH and 2 ATP for FADH2

154
Q

why does FADH2 make less ATP than NADH

A

FADH2 starts in complex 2

155
Q

why does eukaryotes produce 2 less ATP than bacteria

A

Eukarya use 2 ATP to move the NADH in glycolysis in the cytosol to the matrix while prokaryotes everything happens in the cytosol

156
Q

what is the actual yield of energy in bacteria and eukaryotes

A

32 ATP for prokaryotes and 30 ATP for eukaryotes per glucose

157
Q

What is the actual yield of NADH and FADH2

A

2.5 ATP’s for NADH and 1.5 ATP for FADH2

158
Q

what causes the reduce yield of actual energy yield vs theoretical yield (2)

A

Leaky inner membrane where Protons move through other channels other than the ATP synthase
use of proton gradient for other purposes other than ATP synthesis

159
Q

Describe Racker and Stoeckenius experiment

A

they made a synthetic phospholipid membrane vesicles with a portion made of bacteriorhodopsin, a light activated proton pump, and ATP synthase. The ATP synthase was oriented so the headpiece was on the outside of the vesicle and added ADP and Pi to the medium.
Results show that the light made a proton gradient and that gradient drove ATP synthase to make ATP.

160
Q

how many protons and electrons are removed in a molecule when making NADH from NAD+

A

2 electrons and 2 protons

161
Q

what did srikanth talk about siamese cats

A

near the nose and ears and paws , the enzyme that makes the dark pigment has optimal activity at lower temperatures, hence the different colors

162
Q

what is phosphatase

A

enzyme that dephosphorylates

163
Q

name an example of a reversible compeitive inhibitor

A

aspirin

164
Q

aspiring inhibits what enzyme

A

cyclo-oxygenase

165
Q

name an example of a irreversible compeitive inhibitor

A

pencillin

166
Q

name an example of non compeitive inhibitor

A

cyanide

167
Q

is dna negatively charged, why or why not

A

yes because of the phosphate group

168
Q

name an example of a cell that is in g0

A

neurons

169
Q

what is another name for anabolic pathway

A

biosynthetic reaction

170
Q

do catalyst and enzymes increase rate of rxn

A

yes

BIOL 2325 (9 decks)

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