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Bioenegetics Flashcards

Bioenergetics

1
Q

what is bioenergetics

A

the study of the transformation of energy in living organisms

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2
Q

what is bioenergetics based on

A 
thermodynamics
energy capture
energy conversion
energy storage 
biochemistry
enzyme kinetics
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3
Q

what is the first law of thermodynamics

A

energy cannot be created or destroyed - only converted - principle of conservation of energy

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4
Q

what is the second law of thermodynamics

A

energy transfer increases the entropy of the universe

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5
Q

where does photosynthesis occur

A

chloroplast

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6
Q

where does cellular respiration occur

A

mitochondria

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7
Q

what is Gibbs free energy

A

the portion of energy in a system used to perform work

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8
Q

under what conditions will a reaction proceed in terms of free energy

A

a reaction will occur spontaneously if it decreases G - that is, delta G is negative

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9
Q

what is an exergonic reaction

A

spontaneous - one that involves energy release - proceeds with a net release of free energy (G decreases) - deltaG is -ve - the greater the decrease in energy the greater the amount of work that can be done

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10
Q

what is an endergonic reaction

A

one that requires energy - absorbs free energy - G increases -deltaG is +ve - nonspontaneous - the magnitude of deltaG is the energy required to drive the reaction

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11
Q

where is the chemical energy stored in ATP

A

in the last phosphate group

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12
Q

in what two ways can ATP be formed

A
  1. substrate level phosphorylation (transfer of phosphate group)
  2. oxidative phosphorylation (proton gradient, ATP synthase)
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13
Q

relocating electrons from sugars (weakly electronegative) to oxygen (strongly electronegative)results in an energy intake/release

A

release

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14
Q

what is chemiosmosis

A

movement of ions across a semipermeable membrane, down their electrochemical gradient e.g. the generation of ATP by the movement of H across a membrane

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15
Q

electron transport chain is accompanied by a directional movement of what across the membrane

A

hydrogen ions

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16
Q

reactions that make and use H gradient are separate and require what characteristic of the membrane

A

it needs to be intact

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17
Q

name the 4 main parts of ATP synthase

A

rotor
stator
rod
knob

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18
Q

what is the function of the rotor of ATP synthase

A

it spins clockwise when H ions flow past it

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19
Q

what is the function of the stator of ATP synthase

A

holds rotor and knob in position

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20
Q

what is the function of the rod of ATP synthase

A

turns the rotor and activates the knob

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21
Q

what is the function of the knob of ATP synthase

A

catalytic sites join phosphate to ADP making ATP

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22
Q

the energy released in an exergonic reaction can be used for what

A

to trigger endergonic reaction

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23
Q

NAD+ captures electrons from redox reactions and delivers them to what

A

the electron transport chain

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24
Q

what does the electron transport chain establish across the inner membrane of chloroplasts and mitochondria

A

a proton gradient

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25
Q

what happens when protons flow back through ATP synthase

A

ATP is produced

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26
Q

The trans-membrane H+ gradient acts as what between redox potential and ATP synthesis

A

a ‘high-energy’ intermediate

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27
Q

when proteins are needed sugars can be broken down into what to enable this

A

amino acids

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28
Q

which process drives cellular economy by extracting energy stored in sugars and other fuels

A

cellular respiration

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29
Q

what kind of activities do cells use the energy gained by cellular respiration for

A

e. g. transport of solutes between the cellular interior and the extracellular environment
e. g. changing cell shape

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30
Q

how the single celled marine organisms called dinoflagellates become illuminated

A

they convert the energy stored in certain organic molecules into light. This process is called bioluminescence

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31
Q

what is metabolism

A

the totality of an organisms metabolic reactions

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32
Q

each step of a metabolic pathway is catalysed by what

A

a specific enzyme

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33
Q

what does metabolism control

A

material and energy resources of the cell

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34
Q

describe a catabolic reaction

A

a reaction during which larger more complex molecules are broken down into smaller more simpler ones (exergonic reaction) e.g. cellular respiration (sugar/other fuels broken down in the presence of oxygen to form carbon dioxide and water)
The energy that was stored in the organic molecules is released and becomes available to do the work of the cell

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35
Q

can metabolic pathways have more than one starting molecule or product

A

yes there can be multiple starting molecules and/or products involved in a metabolic reaction

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36
Q

describe anabolic pathways

A

the reaction of smaller less complex molecules to form larger more complex molecules. These reactions consume energy (endergonic reaction) and are sometimes called biosynthetic pathways

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37
Q

give an example of an anabolic reaction

A

e. g. amino acid synthesis

e. g. protein synthesis

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38
Q

explain how catabolic and anabolic reactions support each other

A

the energy released from catabolic reactions can be stored and used to drive the energy consuming anabolic reactions

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39
Q

what is bioenergetics

A

the study of how energy flows through living organisms

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40
Q

what is kinetic energy

A

the energy associated with the relative motion of objects

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41
Q

what is thermal energy

A

kinetic energy associated with the random movement of molecules or atoms

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42
Q

what is heat

A

thermal energy in transfer from one object to another

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43
Q

is light a form of energy

A

yes - it can be used to perform work e.g. powering photosynthesis in green plants

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44
Q

can objects that are stationary possess energy

A

yes - they possess potential energy

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45
Q

what is potential energy

A

energy that matter possesses because of its location or structure

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46
Q

what is chemical energy

A

the potential energy available for release in a chemical reaction

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47
Q

complex molecules such as glucose are in high/low chemical energy

A

high

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48
Q

what is an isolated system

A

a system that is unable to exchange energy or materials with its surroundings

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49
Q

what is an open system

A

a system that is able to exchange energy or materials with its surroundings

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50
Q

are organisms open or closed systems

A

open - they can exchange energy and materials with their surroundings

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51
Q

In most energy transformations some energy is transferred to what type of energy which is then released as heat

A

thermal energy

52
Q

During energy transfers from food to an organism very little of the energy is transformed into motion - why is this

A

most of the energy is lost as heat which dissipates rapidly through the surroundings

53
Q

the loss of energy as heat by systems makes the surroundings more/less disordered

A

more - the entropy of the surroundings increases

54
Q

what is entropy

A

the measure of disorder - the more disordered the matter the greater the entropy

55
Q

if a process leads to an increase/decrease in the entropy the process will proceed spontaneously (energetically favourable)

A

increase

56
Q

non spontaneous reactions proceed only when what is supplied

A

energy

57
Q

living systems increase/decrease the entropy of their surroundings

A

increase

58
Q

why is heat energy lost during consumption of food

A

energy is released to the surroundings during the catabolic reactions that break down the food into its component parts
the energy of the component parts is less than the original food

59
Q

organisms are islands of low/high entropy in an increasingly ordered/disordered universe

A

low

disordered

60
Q

what is gibbs free energy

A

the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system

61
Q

what is the gibbs free energy of a spontaneous process

A

negative

62
Q

what is the gibbs free energy of a non spontaneous process

A

positive

63
Q

at what gibbs free energy does a reaction become spontaneous

A

0

64
Q

unstable systems have a higher/lower gibbs free energy

A

higher - they will change in a way to decrease their free energy

65
Q

when is a reaction said to be at equilibrium

A

when the forwards and backwards reactions are occurring at the same rate

66
Q

when a system proceeds towards equilibrium its free energy increases/decreases

A

decreases - it is becoming more stable

67
Q

what happens to the gibbs free energy when a system is pushed away from equilibrium

A

it increases

68
Q

why do systems never spontaneously move away from equilibrium

A

any change away from equilibrium has a positive change in free energy and so is not favourable
a process is spontaneous and can perform work only when it is moving towards equilibrium

69
Q

breaking bonds requires/releases energy

A

requires

70
Q

making bonds requires/releases energy

A

releases

71
Q

is a living cell in equilibrium

A

no -there is a constant flow of materials in and out of the cell, preventing pathways from ever reaching equilibrium

72
Q

animals and other nonphotosynthetic organisms must have a constant supply of free energy in the form of what

A

organic products of photosynthesis

73
Q

what are the three main type of work that a cell carries out

A

chemical work - the pushing of endergonic (nonspontaneous) reactions
transport work - the pumping of substances across membranes against the direction of spontaneous movement
mechanical work - e.g. the beating of cilia, contraction of muscle cells, movement of chromosomes

74
Q

what is energy coupling

A

the use of an exergonic process to drive an endergonic one

75
Q

what are the components of ATP

A

sugar ribose, nitrogenous base adenine and a chain of 3 phosphate groups

76
Q

in addition to its role in energy coupling ATP is also a component of which biological molecule

A

ATP is one of the nucleoside triphosphates used to make RNA

77
Q

the bonds between each phosphate group of ATP can be broken by what type of reaction

A

hydrolysis

78
Q

what happens when the terminal phosphate bond of ATP is broken by hydrolysis

A

an inorganic phosphate leaves ATP and the ATP becomes ADP

79
Q

is the reaction below endergonic or exergonic

ATP —> ADP + Pi

A

exergonic - releases energy

80
Q

why are the phosphate bonds of ATP sometimes referred to as high energy

A

Because the hydrolysis of ATP releases energy - ATP and water have high energy relative to the products (ADP + Pi)

81
Q

where does the energy released in ATP hydrolysis come from

A

the chemical change of the system to a state of lower free energy - NOT FROM THE PHOSPHATE BONDS

82
Q

why is ATP useful to a cell

A

because the energy released on losing a phosphate is larger than the energy most other molecules could deliver

83
Q

the 3 phosphate groups of ATP are negatively/positively charged

A

negatively - these like charges are crowded together and their repulsion contributes to the instability of this region

84
Q

if deltaG of an endergonic reaction is less/more than the amount of energy released by ATP hydrolysis then the two reactions can be coupled so that overall the coupled reactions are exergonic

A

less than - this usually involves phosphorylation

85
Q

what is phosphorylation

A

the transfer of a phosphate group form one molecule to another molecule - the recipient molecule is called the phosphorylation intermediate

86
Q

a phosphorylated intermediate is more/less reactive than the original unphosphorylated molecule

A

more reactive (less stable, more free energy)

87
Q

go over the conversion of glutamic acid to glutamine

A

the reaction in isolation is endergonic but by coupling with ATP can proceed

  1. ATP phosphorylates glutamic acid, making it less stable, with more free energy
  2. ammonia displaces the phosphate group, forming glutamine
88
Q

ATP hydrolysis changes in what properties of proteins

A

shape and binding affinities

89
Q

During transport work what is the effect of ATP hydrolysis

A

ATP phosphorylates transport proteins causing a shape change that allows transport of solutes

90
Q

During mechanical work what is the effect of ATP hydrolysis

A

ATP binds non covalently to motor proteins and then is hydrolysed releasing ADP and Pi causing a shape change that walks the motor protein forward along the cytoskeleton. Another ATP molecule can bind and the process repeats

91
Q

ATP hydrolysis is anabolic/catabolic

A

catabolic - energy released - exergonic

92
Q

ATP synthesis is anabolic/catabolic

A

anabolic - energy required - endergonic

93
Q

what is an enzyme

A

a macromolecule that acts as a catalyst

94
Q

what is the activation energy

A

the energy required to start a reaction

95
Q

what is activation energy often supplied by

A

heat in the form of thermal energy absorbed for the surroundings

96
Q

what is the state called when reactant molecules have absorbed enough energy for their bonds to break

A

transition state

97
Q

Proteins, DNA and other complex cellular molecules are rich in free energy and have the potential to do what

A

decompose spontaneously - these molecules only exist because the temperature of a normal cell doesn’t allow enough molecules to reach the activation energy

98
Q

enzymes lower what of a reaction

A

activation energy

99
Q

what is the complex called that occurs when an enzyme and substrate bind

A

enzyme-substrate complex

100
Q

what does reaction of sucrose with water and sucrase produce

A

glucose and fructose

101
Q

the specificity of an enzyme is a result of what property

A

its shape - a consequence of its amino acid sequence

102
Q

what part of the enzyme binds to the substrate

A

active site - a pocket or groove on the surface of the enzyme

103
Q

what happens when an enzyme and substrate react

A
  1. substrate enters the active site and forms weak bonds (hydrogen bonds, ionic bonds) with the enzyme - this induce a shape change
  2. additional weak bonds form sue to the shape change causing the active site to enfold the substrate, holding it into place.
104
Q

the tightening of binding after the initial contact of the enzyme and substrate is called what

A

induced fit

105
Q

what part of the active site catalyses conversion from substrate to product

A

the R groups of a few amino acids that make up the active site

106
Q

what mechanisms do enzymes use that lower activation energy

A
  1. when there are multiple reactants the active site provides a template so the substrates can come together in the correct orientation for reaction
  2. The enzyme can stretch the substrate towards its transition state form, stressing the bonds to be broken
  3. active site can provide a microenvironment e.g. the active site may be a pocket of low pH facilitating H+ transfer to the substrate
  4. amino acid in the active site directly participate in the reaction
107
Q

when is an enzyme said to be saturated

A

when adding more substrate does not increase rate

108
Q

which environmental factors can effect enzyme activity

A

pH
temperature
presence of detergents

109
Q

optimal conditions favour the most/least active shape of the enzyme

A

most active - this is why enzymes work better in optimal conditions

110
Q

temperature increase speeds up a reaction to a point because the molecules collide more frequently but after a certain point reaction rate drops why is this?

A

the enzyme becomes denatured - thermal agitation disrupts hydrogen bonds, ionic bonds and other weak interactions that stabilise the active shape of the enzyme

111
Q

what are optimal conditions for thermophilic bacteria

A

high temperatures like in hot springs

112
Q

many enzymes require non protein helpers for catalytic activity, what are these called

A

cofactors

113
Q

how are cofactors bound to the enzyme

A

tightly - as a permanent resident

loosely - reversibly along with the substrate

114
Q

if a cofactor is an organic molecule what is it referred to as

A

coenzyme

115
Q

if an inhibitor attaches to an enzyme via covalent bonds is this reversible

A

usually yes

116
Q

what is a competitive inhibitor

A

an inhibitor that binds to the active site, mimicking the substrate - this can be overcome by increasing thee concentration of the substrate

117
Q

what is a non-competitive inhibitor

A

they bind to the enzyme in a place other than the active site which changes the enzymes shape making the active site less effective

118
Q

toxins and poisons are often reversible/irreversible inhibitors

A

irreversible

119
Q

how does a cell control when and where enzymes are active

A

by switching on and off genes that encode enzymes or by regulating activity once the enzyme is made

120
Q

what is allosteric regulation

A

when the proteins function at one site is affected by the binding of a regulatory molecule to a separate site resulting in either inhibition or stimulation of enzyme activity

121
Q

most allosterically regulated enzymes have how many subunits and active sites

A

2 or more - the complex oscillates between the active and inactive shapes

122
Q

how does regulatory molecule binding of one subunit of an allosteric enzyme effect the enzyme as a whole

A

binding to one subunit changes the shape of the other subunits

123
Q

what is cooperativity

A

binding to one active site of a multisubunit complex changes a shape change in all the subunits - this amplifies the response

124
Q

why is cooperativity considered allosteric regulation

A

because even though the substrate binds to the active site, its binding effects catalysis in another active site

125
Q

what is feedback inhibition

A

a metabolic pathway is altered by the inhibitory binding of its end product to an enzyme that acts early in the pathway

126
Q

what is a multienzyme complex

A

a team of enzymes where the product from the first enzyme becomes the substrate for the adjacent enzyme

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