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Biochem > Quiz 2 Reading Info > Flashcards

Quiz 2 Reading Info Flashcards

1
Q

Energy transductions

A

conversions of one form of energy to another

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2
Q

Antoine Lavoisier

A

French chemist who recognized that animals somehow transform chemical fuels (food) into heat and that this process of respiration is essential to life

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3
Q

First law of thermodyanmics

A

Total amount of energy in the universe is constant

The form of energy may change, but energy cannot be created or destroyed

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4
Q

Second law of thermodyanmics

A

in all natural processes, the entropy of the universe increases

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5
Q

What type of systems are living organisms?

A

they are open systems

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6
Q

Gibbs Free Energy, G

A

expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure

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7
Q

Exergonic and endergonic reactions refer to

A

Change in delta G

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8
Q

Endothermic and exothermic reactions refer to

A

Change in enthalpy (H)

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9
Q

Exothermic reactions

A

delta H is negative

heat is released

surroundings feel warm

ex: gas burning

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10
Q

Endothermic reactions

A

delta H is positive

heat is consumed

feels cold, since energy is taken from the environment

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11
Q

Enthalpy, H

A

is the heat content of the reacting system. it reflects the number and kinds of chemical bonds in the reactants and products

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12
Q

Entropy, S

A

quantitative expression for the disorder in a system

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13
Q

Units of G and H

A

joules/mole or cal/mole

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14
Q

Units of S

A

joules/moleKelvin (J/molK)

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15
Q

How do cells become so ordered and seem to disobey the second law of thermodyanmics?

A

the order produced within cells as they grow and divide is more than compensated for by the disorder they create in their surroundings in the course of growth and division

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16
Q

isothermal systems

A

function at essentially constant temperature and constant pressure

cells are isothermal systems

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17
Q

Is heat flow a source of energy for cells?

A

No

Cells only use free energy to do work

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18
Q

Standards condition for the cell

A

25ºC - temperature
101.3 kPa / 1 atm - pressure
pH 7 - [H+] concentration
55.5 M - constant water concentration

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19
Q

Standard transformed constants

A

use the prime ‘ mark because they are occuring in the biochemical standard state

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20
Q

What is not included when solving for Keq and the mass-action ratio, Q ?

A

H20, H+, and/or Mg2+

Their concentrations are not included

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21
Q

Relationship between K’eq and ΔG’º?

A

ΔG’º = -RTln(K’eq)

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22
Q

What happens when K’eq is >1.0?

A

ΔG’º is negative and the reaction proceeds forward

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23
Q

What happens when K’eq is <1.0?

A

ΔG’º is positive and the reaction proceeds in reverse

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24
Q

What happens when K’eq is 1?

A

ΔG’º is zero and the reaction is at equilibrium

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25
Q

What does the standard free-energy change tell us?

A

in which direction and how far a given reaction must go to reach equilibrium in the biological standard condition

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26
Q

Does ΔG change?

A

Yes, unlike ΔG’º

It is a function of reactant and product concentrations and of the temperature of the reaction

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27
Q

ΔG equation

A

ΔG = ΔG’º +RTlnQ

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28
Q

Mass-action ratio

A

Q

ratio of product to reactant concentrations at a given point in the reaction

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29
Q

What happens as a spontaneous reaction proceeds to ΔG?

A

Since the number of products increases and Q becomes a larger decimal, ΔG approaches 0

Makes sense. As the reaction approaches equilibrium, ΔG approaches 0

ln(1) = 0

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30
Q

What is the criterion for spontaneity of a reaction?

A

The value of ΔG NOT ΔG’º

Concerned with the current conditions

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31
Q

What happens when you immediately remove the products of a reaction?

A

the ratio of product/reactants remains a small decimal, so ΔG has a large negative value

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32
Q

What is the natural log of a decimal?

A

negative. the smaller the decimal, the more negative the log is

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33
Q

Do ΔG’º and ΔG represent the actual amount of free energy available for use?

A

No! They represent the theoretical maximum amount

In reality, there is always less energy than these amounts

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34
Q

Does free energy change depend on the pathway?

A

No. All that matters is the starting and final products

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35
Q

Can enzymes change equilibrium constants?

A

No because equilibrium constants are not dependent on pathways

They can just change the rate/kinetics not thermodynamics

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36
Q

In energy coupling what do we do with K’eq and ΔG’º?

A

ΔG’º is additive

K’eq is multiplicative

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37
Q

What determines which reactions take place in biological systems and which do not?

A

1) their relevance to that particular metabolic system
2) their rates

even if useful to biological system, certain reactions may be too slow to use

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38
Q

5 categories of reactions for living cells

A

1) Reactions that make or break C-C bonds
2) International rearrangements, isomerizations, and eliminations
3) Free-radical reactions
4) Group transfers
5) Oxidation-reductions

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39
Q

Homolytic cleavage

A

each atom leaves the covalent bond carrying one unpaired electron (a radical)

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40
Q

Heterolytic cleavage

A

one atom retains both bonding electrons

this generates unstable carbanions, carbocations, and hydride ions

still, more common than homolytic cleavage

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41
Q

Nucleophiles

A

functional groups rich in and capable of donating electrons

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42
Q

Electrophiles

A

functional groups electron-deficient and seek electrons

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43
Q

Is the carbon atom a nucleophile or electroophile?

A

depends on which functional groups are attached to it! Can be both!

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44
Q

How are carbanion and carbocation intermediates created?

A

they are too unstable to be created alone, so functional groups containing electronegative species (O and N) help form them

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45
Q

Carbonyl groups

A

have a partial positive on carbon

can facilitate the formation of a carbanion on an adjoining carbon by delocalizing the carbanion’s negative charge through the carbonyl

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46
Q

What reactions is the carbonyl group essential to?

A

Aldol condensation
Claisen condensation
Decarboxlation reaction

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47
Q

Aldol condensation

A

common route to the formation of a C-C bond

carbanion attacks the carbonyl’s carbon. electron’s move through the carbonyl creating a negative charge on oxygen that changes to an alcohol

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48
Q

Claisen condensation

A

the carbanion is stabilized by the carbonyl of an adjacen thioester

similar to aldol condensation, except the thioester is the leaving group, so the carbonyl remains intact

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49
Q

intramolecular rearrangement

A

redistribution of electrons results in alterations of many different types WITHOUT a change in the overall oxidation state of the molecule

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50
Q

How do intramolecular rearrangements work?

A

different groups in a molecule may undergo oxidation-reduction with no net change in oxidation of the overall molecule;
undergo cis/trans rearrangement;
positions of double bonds may be transposed

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51
Q

Example of intramolecular rearrangement

A

fructose 6-phosphate to glucose 6-phosphate during glycolysis

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52
Q

Elimination reaction that does not effect overall reaction oxidation state

A

loss of water from an alcohol bond that results in a C=C double bond

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53
Q

How does acyl group transfer work?

A

involves the addition of a nucleophile to the carbonyl carbon of an acyl group to form a tetrahedral intermediate

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54
Q

How do glycosyl group transfers work?

A

nucleophilic substitution at C-1 of a sugar ring

this substitution could take place through SN1 or SN2 pathways

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55
Q

How do phosphoryl group transfers work?

A

they attach a good leaving group to a metabolic intermediate to “activate” the intermediate for subsequent reactions

for example, attaching a phosphoryl group to an otherwise poor LG like -OH

56
Q

How many covalent bonds can phosphorous form?

A

5

57
Q

What do the phosphorous bonds actually look like?

A

4 bonds with intermediate character between single and double bond character

Makes them tetrahedral

58
Q

What does Pi (orthophosphate) have?

A

a partial positive charge on P to act like an electrophile

the oxygen groups take electron density away from the central P

59
Q

Kinases

A

family of enzymes that catalyze phosphoryl group transfers with ATP as a donor

60
Q

What is another type of group that activates molecules besides phosphoryl groups?

A

thioalcohols (thiols) -SH

activate carboxlyic acids by forming thioesters

61
Q

What is the most highly oxidized form of carbon?

A

O=C=O

carbon dioxide

62
Q

Dehydrogenation

A

common oxidation reaction where two electrons and two hydrogen ions are lost

63
Q

Oxidases/oxygenases

A

catalyze oxidations where the carbon atom is directly covalently bonded to an O2

64
Q

What generally happens in oxidation?

A

energy is released

Ex: campfires are oxidized by oxygen molecules in the air and release energy

65
Q

How do most living cells obtain the energy needed for cellular work?

A

by oxidizing metabolic fuels such as carboydrates or fats

66
Q

Catabolic pathways and oxidation

A

Catabolic pathways are oxidative reaction sequences that result in the transfer of electron from fuel molecules, eventually to oxygen

this process is highly exergonic, which provides energy to synthesize ATP, the goal of catabolism

67
Q

Cofactors

A

facilitate reactions in the form of coenzymes and metals

bind to enzymes (either reversibly or irrevisibly) and promote a particular kind of chemistry/reactions

68
Q

How does the role of ATP work from catabolism to anabolism?

A

Hetereotropic cells obtain free energy in a chemical form by catabolism of nutrient molecules

They use that energy to make ATP from ADP+Pi

ATP then donates some of its energy to endergonic processes, such as the synthesis of metabolic intermediates and macromolecules from smaller precursors

69
Q

Why is ATP hydrolysis exergonic?

A

electrostatic repulsion in ATP is lowered

Pi product is stabilized by the formation of several RESONANCE structures not possible in ATP

70
Q

phosphoryl-action potential ΔGp

A

the actual free energy of hydrolysis of ATP under intracellular conditions

for example, often times Mg is bound to ATP

71
Q

What concentrations do we take into consideration when calculating ΔGp?

A

Have to consider the free concentrations, not the total concentrations in a cell

This means that the energy released by ATP hydrolysis is greater than the standard free energy change ΔG’º

72
Q

Why is ATP used so frequently?

A

Besides its chemical properties, in the course of evolution, there has been a very strong selective pressure for regulatory mechanisms that hold cellular ATP concentrations far above equilbrium concentrations

important to be able to maintain high levels of ATP to drive hydrolysis of ATP forward

73
Q

Other phosphorylated compounds that have large free energies of hydrolysis

A

1) Phosphoenolpyruvate (PEP)
2) 1,3-biphosphoglycerate
3) Phosphocreatine

74
Q

Commonality between all phosphorylated compounds with large free energies of hydrolysis

A

several resonance forms of Pi available stabilize this product relative to the reactant

75
Q

Thioesters

A

sulfur replaces the usual oxygen in an ester bond

the sulfur has less resonance stabilization than oxygen in ester

this makes a greater free energy change with its hydrolysis products, that are stabilized

76
Q

Example of a thioester

A

acetyl-CoA

uses this property that its carboxylic acid product is more resonance stabilized than the original thioester

77
Q

How does ATP normally provide energy?

A

Normally involves group transfers, not just simple hydrolysis

78
Q

How does group transfer with ATP work?

A

A part of the ATP molecule (either Pi or PPi or AMP) is first transferred to a substrate molecule (covalently bonded)

This raises the molecules free energy content (more free energy to perform metabolic transformations)

Then, the transferred moiety transfered in the first step is displaced, released Pi PPi or AMP

79
Q

When does direct ATP hydrolysis occur?

A

muscle contractions

80
Q

High energy phosphate compounds

A

ΔG’º of hydrolysis is more negative than -25 kJ/mol

81
Q

Low energy phosphate compounds

A

ΔG’º of hydrolysis is less negative than -25kJ/mol

82
Q

Does energy of hydrolysis come from breaking the P–O bond?

A

No! Breaking one bond requires an input of energy actually

It is the overall change from products to reactants that releases energy

83
Q

List phosphate compounds in terms of decreasing energy

A

PEP>1,3- biophopho..>PCr>ATP>glucose 6-phophate>glycerol

ATP’s intermediate position is useful

84
Q

Why does ATP not dissociate in water?

A

Although thermodynamically unstable, it is kinetically stable

Takes a while to overcome activation energy, without an enzyme

85
Q

Adenylylation

A

nucleophilic attack of ATP at the alpha position displaces PPi and transfers AMP as an adenlyl group

86
Q

Why is adenylyation often the mechanism of breaking ATP for energy coupling?

A

can break the PPi to release even more extra energy by using a inorganic pyrophosphatase enzyme

87
Q

How does polymerization of nuclei acids work?

A

Cleave the phosphate groups in the nucleoside triphosphate monomers

88
Q

How does polymerization of amino acids work?

A

donation of adenlyl groups from ATP to activate them

89
Q

Overall how does polymerization work?

A

couple endergonic reactions with exergonic breakdown of a nucleoside triphospate

90
Q

How is energy used in transport processes across cell membranes, like Na+ and K+?

A

ATP interacts with the enzyme, not the substrates

the transport of Na+ and K+ is driven by cyclic phosphorylation and dephosphorylation of the transporter protein, with ATP as the phosphoryl group donor

91
Q

How does muscle contration work?

A

direct hydrolysis of ATP

Mysosin contracts to hold ATP and then when it dissociates into ADP+Pi the muscle relaxs until another ATP molecule binds

92
Q

Nucleoside diphosphate kinase

A

carries phosphoryl groups from ATP to other nucleotides

93
Q

Adenylate kinase

A

during periods of intense demand for ATP, the cell lowers the ADP concentration and at the same time replenishes ATP

enzyme helps

94
Q

Phosophocreatin

A

PCr reservior can quickly replenish ATP

creatine kinase helps in this exergonic reaction

95
Q

polyP

A

a linear compound composed of many tens or hundreds of Pi residues, linked through phosphoanhydride bonds

96
Q

Polyphosphate kinase 1 and 2 (PPK-1, PPK-2)

A

PPK-2 is believed to act primarily in breaking down polyP to generate GTP and ATP

PPK-1 is believed to act primarily in breaking down ATP to form polyP longer chains

97
Q

polyP and bacteria

A

high levels of polyP correspond to greater expression of genes in adaptation to threats

in making new antimicrobial drugs, could attack the PPK enzymes to diminish the amount of polyP available

98
Q

Electromotive force (emf)

A

the force proportional to the difference in electron affinity

the spontaneously flow of electrons to a species with a high electron affinity has the ability to do work

99
Q

Glucose serves as …

A

a source of electrons

as glucose is enzymatically oxidized, the released electrons flow spontaneously through a series of species to O2

100
Q

Examples of using electron flow to do work

A

flow of electron provides energy for ATP synthesis

enzymes couple electron flow to the production of a transmembrane pH difference

flagellar motion in E. coli

101
Q

Reducing agent

A

electron donating molecule

will give up electrons to reduce another

102
Q

Oxidizing agent

A

electron accepting molecule

will accept electrons to oxidize another

103
Q

Conjugate redox pair

A

involve an electron acceptor and an electron donor

104
Q

Examples of conjugate redox pairs

A

Fe3+(electron acceptor) and Fe2+(electron donor)

Cu+(electron donor) and Cu2+(electron acceptor)

NADH(electron donor) and NAD+(electron acceptor)

105
Q

General trend of conjugate redox pairs

A

the electron acceptor is more positive

it wants an electron

106
Q

Order of increasing electronegativity

A

H

107
Q

How can you determine the oxidation of carbon?

A

often, if carbon has less Hydrogens, species are pulling electrons from carbon and it is being oxidized

ex: H3C-CH3 is less oxidized than H2C=CH2 (less hydrogens)

108
Q

dehydrogenation

A

often synonymous with oxidation

as you lose hydrogens, something is oxidized

109
Q

How are electrons transferred from one molecule to another? (4 ways)

A

1) Directly as electrons
2) As hydrogen atoms (proton+electron)
3) Hydride ion
4) Direct combination with oxygen

110
Q

Reducing equivalent

A

term used to designate a single electron equivalent participating in an oxidation-reduction reaction

111
Q

standard reduction potential

A

Eº

affinity of the electron acceptor of each redox pair of electrons

112
Q

Relationship between Eand flow of electrons

A

Electrons will flow to more positive E’º

E’º has a greater ability to be reduced (gain electrons)

113
Q

ΔE’º

A

given as E’º of the electron acceptor - E’º of the electron donor

*this occurs at typical biological standard conditions

114
Q

ΔE

A

gives the strength of the tendency for electrons to flow to the electron acceptors

115
Q

n in oxidation/reduction calculations

A

n is the number of electrons transferred in the reaction

116
Q

How is the ΔG’º so largely negative for oxidation of glucose to CO2? Like more than ATP synthesis needs?

A

this occurs in a series of controlled reactions, some of which are oxidations, rather than one big reaction

117
Q

Types of Coenzymes

A

NAD, NADP, FMN, FAD

118
Q

NAD+ or NADP+

A

accept a hydride ion and are reduced

makes no charge on the ring nitrogen (called the quinonoid form)

119
Q

Is NAD+ overall positive?

A

no! Just indicates the charge on the ring

actually, these molecules are overall negative

120
Q

NAD versus NADP

A

NAD is used mostly in oxidizations because it has a high concentration of NAD+ which makes it being reduced favorable

NADP is used mostly in reductions because it has a high concentration of NADPH which makes it being oxidized favorable

121
Q

When are reductions seen?

A

in anabolic reactions

(NADPH) is used

122
Q

When are oxidations seen?

A

in catabolic reactions

NAD is used

123
Q

Oxidoreductase

A

catalyzes reactions involving NADPH and NAD

124
Q

Rossman fold

A

NAD and NADPH coenzymes, losely bind to this fold in electrons. They are able to move around

125
Q

Is there a net production of coenzymes?

A

No! They are used catalytically

126
Q

niacin

A

vitamin that NAD and NADPH derive their rings from

get vitamin from tryptophan

definciny leads to pellagra

127
Q

Flavoproteins

A

enzymes that catalyze oxidation-reduction reactions using either FMN or FAD as coenzyme

128
Q

Flavin nucleotides

A

FMN or FAD coenzymes

129
Q

Why are flavin nucleotides used more than NAD and NADPH?

A

they have the ability to be involved in either one or two electron transfers

130
Q

Does the Eº change for flavin nucleotides?

A

yes! Depends on if they are tightly bound to an enzyme or not

131
Q

Cryptochromes

A

a family of flavoproteins that mediate the effects of blue light on plant development and the effects of light in circadian rthymns

eukaryotic cells

132
Q

Photolyases

A

found in prokaryotic cells

use the energy of absorbed light to repair chemical defects in DNA

133
Q

Fatty acid oxidation / B-oxidation

A

make a carbon that wasn’t a good electrophile into a good electrophile by creating a carbonyl group

then you can break up the hydrocarbon chains of fatty acids

134
Q

Why is it surprising to see methane on mars?

A

methane less oxidized than CO2 and is higher in energy than CO2

135
Q

What is the terminal electron acceptor?

A

oxygen

136
Q

Where does the energy go when it moves to O2 in the electron transport chain?

A

energy is pumped as protons to form a concentration gradient

from this concentration gradient we can power ATP synthase

137
Q

What do we do to keep high concentration of NAD+ in the electron transport chain?

A

dump electrons into the chain

Biochem (20 decks)

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