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Metabolism > Fundementals of metabolism > Flashcards

Fundementals of metabolism Flashcards

1
Q

autotrophs (photosynthetic)

A

Use CO2 as their carbon source

Use sunlight as their energy source

Produce O2

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2
Q

Heterotrophs

A

Use complex organic compounds

  • as a source of carbon
  • as an energy source

Produce CO2

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3
Q

what is nitrogen required for

A

AA’s and nucleotides

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4
Q

autotrophs require what source of nitrogen

A

ammonia or nitrate

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5
Q

heterotrophs require what sources of nitrogen

A

AA’s, other N2 containing compunds

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6
Q

cyanobacteria get nitrogen by

A

fixing N2 to NH3

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7
Q

what do nitrifying bacteria do to get nitrogen

A

Oxidize NH3 to nitrates and nitrates

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8
Q

is energy cycled in metabolism?

A

no. energy enters as light and leaves as heat and chemical potential energy

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9
Q

catabolism consists of what

A

Breakdown of nutrients (e.g. glucose)

Releases energy for anabolic reactions

Releases heat

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10
Q

anabolism consists of

A

Synthesis of macromolecules

Requires energy

Releases heat

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11
Q

intermediary metabolism consists of

A

Metabolic pathways involving low molecular weight (<1000) compounds

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12
Q

what type of metabolism converges? what diverges

A

catabolism; anabolism (check if always true)

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13
Q

what drives anabolism

A

catabolism

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14
Q

how are anabolic rxns and catabolic rxns separated

A

unique enzymes, cofactors, compartmentalization

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15
Q

examples of regulation in 1st rxn of glycolysis

A

Glucose to G-6-P via glucokinase (catabolic) (uses ATP)
G-6-P to glucose by G-6-P phosphatase (uses Pi)
Differential regulation (usually one off, the other on)

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16
Q

Cellular Compartmentalization examples: fatty acids

A

Fatty acid catabolism in mitochondria
Fatty acid synthesis in cytoplasm
Different concentrations of products, reactants and regulators

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17
Q

unique cofactors

A

NADH for catabolism, NADPH for anabolism

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18
Q

when two metabolic pathways run simultaneously in opposite directions and have no overall effect other than to dissipate energy in the form of heat

A

futile cycle

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19
Q

a genetic disease in which anesthetic* triggers heat generation and muscle contraction with temperatures when uncontrolled rising to 110 F leading to death.

A

Malignant hyperthermia (mechanism not known)

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20
Q

what are malignant hyperthermia (MH) triggers

A

halothane, enflurane, isoflurane, sevoflurane and desflurane

as is the depolarizing muscle relaxant succinylcholine

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21
Q

what hormone controls metabolic rate? what is a clinical correlate

A

thyroid hormone

CC: hyperthyroidism, weight losss, heat intolerance

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22
Q

what are the classes of biochemical rxns ( give examples

A

Oxidation-reduction
-Lactate dehydrogenase

Cleavage of carbon bonds

- Adol condensations (aldose)
- Claison condensations (citrate synthase)
- Decarboxylations (acetoacetate decarboxylase)

Internal rearrangements, isomerizations and eliminations
-Phosphohexose Isomerase

Group transfers (eg acyl,glucosyl, phosphoryl)
    -Hexokinase

Free radical reactions
-Ribonucleotide reductase

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23
Q

list hydrocarbons from most reduced to least reduced

A

alkane

alcohol

aldehyde (ketone)

carboxylic acid

carbon dioxide

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24
Q

list redox enzymes and what they do

A

Dehydrogenases
Dehydrogenations - loss of 2 electrons & 2 hydride ions

Oxidases
Oxygen becomes bonded to carbon

Oxygenases
Oxidases that use molecular oxygen

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25
Q

describe phosphate and phosphate transfer rxns

A

involves nucleophilic attack (glucokinase) and a transient intermediate

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26
Q

phosphate shape

what stabilizes it

A

tetrahedral

resonance

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27
Q

what is lost when you go from catabolism to anabolism

A

energy (usually in form of heat

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28
Q

what is a type of non-converging or diverging pathway

A

TCA: Cyclic pathway

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29
Q

characteristics of a typical rxn

A

The reaction is reversible

Forward and backward reactions occur at the same time

The rate of each reaction is dependent on the concentration of reactants

As A and B are used up, the forward rate decreases, C and D increase and the rate of the reverse reaction increases

At the steady state, the forward and backward reaction rates are the same

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30
Q

what is the steady state

A

point at which the forward and backward reaction rates are the same

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31
Q

in typical enzymatic rxns, what kind of constants are K1 and k2?

A

Forward Rate
Proportional to [A][B] = k1[A][B]

Reverse Rate
Proportional to [C][D] = k2[C][D]

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32
Q

what occurs at equilibrium

what 3 equations used for equilibrium states

A

forward rate = reverse rate

k1[A][B] = k2[C][D]

k1/k2 = [C][D] / [A]{B]

Kequ= [C][D]
[A][B]

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33
Q

Keq exist at what conditions, by convention

A

K’eq is rate constant only at pH7 (10 E-7 M H+) and 55.5 M H2O

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34
Q

what is dynamic equilibrium

A

when rate of formation of products = rate of formation of reactants

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35
Q

What kind of enzymatic rxns are reversible

A

ALL OF THEM

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36
Q

what drives a rxn

A

The free energy change drives a reaction

A negative ∆G drives the reaction forward (as written)

A positive ∆G drives the reaction backwards (as written)

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37
Q

what does delta G depend on

A

The ∆G depends on the concentrations of reactants and products, temperature and pressure

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38
Q

what is standard delta G (delta G naught)

A

delta G at the following conditions:

One molar reactants and products, 298 K (25 C), 1 atm

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39
Q

what is standard biological delta G (G naught prime)

A

delta G at conditions:

∆Gº at pH 7 (10-7 M H+), 55.5 M H2O, 1 mM Mg2+

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40
Q

can the standard free energy change be used to predict the net direction of a rxn in vivo?

A

not in vivo since the reactants and products are not at 1 Molar

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41
Q

what do enzymes do?

what do they change? what don’t they change

A

Enzymes work by lowering the activation energy

Therefore:

Enzymes increase the dynamics of a reaction

Enzymes may increase the net rate of product formation

Enzymes do not change the Keq

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42
Q

what is released during oxidation? what is gained?

A

electrons and H+ in oxidation

electrons and H+ gained in reduction

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43
Q

what is the relationship between delta G and Keq

A

delta G = delta G naught + RTln ([C][D]/[A][B])

where R= the gas content and T= temp in Kelvin

at equlibrium: delta G = 0

therefore: delta G naught = -RTlnK’eq

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44
Q

removing products at equilibrium does what?

removing reactants does what?

A

makes delta G neg (drive rxn forward)

makes delta G positive (drives rxn backward)

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45
Q

how are energetically unfavorable rxns pushed forward

A

they are coupled to favorable ones

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46
Q

give example of reaction coupling

A

glucose + inorganic phosphate yields G6P and H2O (delta G naught = +13.8)

ATP + H2O yields ADP and P (-30.5)

net rxn Glucose + ATP yields G^P and ADP -16.7 KJ/mol

hydrolysis drives rxn forward

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47
Q

delta G’s can be what

A

added

48
Q

Keq’s are combined how

A

they are multiplicative

49
Q

what are operational delta g’s

A

observed versus biological standards

50
Q

what are the differences between operational delta G’s (in vivo)

A

Conditions vary, but in general the true ∆G of ATP hydrolysis in vivo is more negative than standard ∆G

51
Q

law of mass action

A

a mathematical model that explains and predicts behaviors of solutions in dynamic equilibrium. It can be described with two aspects: 1) the equilibrium aspect, concerning the composition of a reaction mixture at equilibrium and 2) the kinetic aspect concerning the rate equations for elementary reactions. WIKIPEDIA

52
Q

how are products moved through pathwasy

A

Increasing the level of substrate

Decreasing the level of product

   -Especially useful for energetically unfavorable reactions
53
Q

what is ∆Gº’ when Keq is 1

A

0

54
Q

what is Keq when ∆Gº’ is 0

A

1

55
Q

what is Keq when ∆Gº’ is negative

A

greater than 1

56
Q

what is ∆Gº’ when Keq is greater than 1

A

negative

57
Q

what is Keq when ∆Gº’ is positive

A

less than 1

58
Q

what is ∆Gº’ when Keq is less than 1

A

positive

59
Q

what type of bonds between phosphates of ATP

A

phosphoanhydride bonds

60
Q

what type of bond between ribose and phosphate

A

phosphoester bond

61
Q

what is adenosine

A

ribose and adenine only

62
Q

name of the phosphates on NTP;s based on their position

A

from closest to farthest from ribose

alpha, beta, gamma

63
Q

what is ∆Gº’ of ATP hydrolysis

A

-30.5 kJ/mol

64
Q

what happens with ATp hydrolysis

A

relief of charge repulsion

65
Q

what stabilizes products of ATP hydrolysis

A

resonance stabilization

ionization

66
Q

what does ATP form a complex with?

what purpose?

A

Mg2+

stabilizes partial neg charges on adjacent phosphate hydrogens

67
Q

list high energy compounds in decreasing order of potential energy ( most neg ∆Gº’ )

A

phosphoenolpyruvate, 1,3- bisphosphoglycerate, phosphocreatine, ATP, glycerol phosphate, Glucose 6 phosphate and Pi

first 3 used to make ATP

68
Q

what is ATP used for

A

Biosynthesis of compounds such as G6P and Gycerol phosphate (low energy compounds)

69
Q

what does tautomerization do?

A

stabilizes molecule, releasing energy

70
Q

give example of tautomerization

A

PEP hydrolyzed to form pyruvate in enol form which interconverts with keto form

71
Q

compare energy from hydrolysis with energy from tautomerization

A

-16 vs -46

tautomerization releases more energy thatn hydrolysis itself

72
Q

how is 1,3-BPG hydrolyzed and stabilized to release energy?

what is the ∆Gº’ ?

A

after hydrolysis, 3-phosphoglyceric acid ionizes (releases H+) and it is then stabilized by resonance of the carboxyl group

-49.3

73
Q

how is phosphocreatine hydrolyzed and stabilized to release energy?

what is the ∆Gº’ ?

A

2 adjacent H2N groups undergo resonance stabilization

-43.0

74
Q

what is the purpose of phosphocreatine

what is the ∆Gº’ of its transphosphorylation what enzyme is used

A

it is an energy reservoir

-12.5; creatine kinase

75
Q

name 2 other enzymes used in transphosphorylations

what are the ∆Gº’?

A

adenylate kinase

nucleoside diphosphate kinase

∆Gº’ is about 0

76
Q

how is acetyl CoA hydrolyzed and stabilized to release energy?

∆Gº’ ?

A

hydrolyzed to acetic acid;

ionized to acetate

acetate has resonance stabilization on carboxyl group

∆Gº = -32.2

77
Q

thioesters release more energy than oxygen esters? (Double check)

why?

A

no resonance stabilization

78
Q

what powers the Na+K+ ATPase?

how?

A

ATP hydrolysis

-phosphorylation changes the confromation of the pump.

79
Q

Ouabain

A

blocks ATPase pump

poisonous cardiac glycoside.

used to be used as ionotropic effect (sodium calcium exchanger (NCX) )

80
Q

what is conjugation rxn

A

These reactions involve covalent attachment of small polar endogenous molecule such as glucuronic acid, sulfate, or glycine to form water-soluble compounds.

81
Q

what happens in Palmitoyl-CoA Synthesis

∆Gº’?

A

AMP is conjugated to palmitate and pyrophosphate made and broken down by inorganic phosphatase

then CoA is added from CoASH formeing AMP and Palmitoyl-CoA

∆Gº’ = -32.5

82
Q

what are used in RNA elongation

A

2 high energy bonds

between alpha and beta carbons and then the pyrophosphate anhydride bond is broken

83
Q

what is like electrical motor

A

Food for work

Electromotif Force (emf)

  • battery,(electrons), electric motor, (physical coupling), work
  • food (electrons), mitochondria/proton motive force, (ATP) , Work
84
Q

what metal ion can reduce sugars

A

cupric ions

85
Q

organic redox reactions

A

yields 2 H+ and 2 e- for oxidation

consumes 2 H+ and 2 e- for reduction

86
Q

in oxidation what can “replace” H+

A

OH to form OH group and an H20 product along with 2 e-

87
Q

for redox rxns

2 e- + 2OH- + 2Cu2+ yields

A

Cu2O + H2O

subreactions:

2 Cu2+ + 2 e- yield 2Cu+

then 2 Cu+ + O2- yields CU2O

88
Q

oxidation states of carbon:

ownership of electrons ranking

A

Ownership of Electrons H< C < S < N < O

89
Q

what are 4 methods of electron flow

A
  1. direct electron transfer
  2. use of hydrogen atoms
  3. use of hydride ions
  4. Direct Oxidation by oxygen to give a covalently bound oxygen
90
Q

what does a hydrogen electrode measure

A

it measure reduction potential

91
Q

what gas is pumped into one of the beakers of hydrogen electrode

A

H2 gas is pumped into one beaker at standard pressure

92
Q

what connects the 2 solutions

A

a salt bridge (KCl)

93
Q

what is the probe and device measuring in a hydrogen electrode

A

emf

94
Q

what forced is involved in hydrogen electrode

A

reduction potential (E)

95
Q

what is the value of the hydrogen electrode

A

0.00

96
Q

what value is represented by a tendancy to remove electrons

A

positive number

97
Q

what value is represented by a tendancy to donate electrons

A

negative number

98
Q

what is the reference cell of known emf

A

the hydrogen electrode in which H2 gas at 101.3 kPa is equilibrated at the electrode with 1 M H+

99
Q

what is the test cell?

A

a cell containing 1 M concentrations of the oxidized and reduced species of redox pair to be examined

100
Q

What does the Nernst equation relate?

A

it relates standard reduction potential to true reduction potential

101
Q

what is the nerst equation? Both versions

explain the variables

A

E = E naught + RT/nF *ln (electron acceptor/electron donor)

E = E naught + (0.026 V/n) ln (electron acceptor/ electron donor)

n= no. of e- per molecule

F = Faraday’s constant

T = Temp (K)

R= gas constant

E naught prime = biological redction potential ( pH 7)

102
Q

what is the relationship between delta G and delta E

A

Delta G = -nF*delta E

or

delta G naught prime = -nF*delta E naught prime

103
Q

hardest question on exam will be

A

given 2 rxns, learn how to predict favorable direction of reaction; what becomes oxidized and what is reduced:

work problems in leningher 510/1

104
Q

how many electrons does NAD+ accept? what are they transfered as?

A

2 electrons: transferred as a hydride Ion (H-)

H+ is released in the medium

105
Q

what 2 sides are electrons added to NAD+?

A

either side A or B

106
Q

what affects NAD+ reduction

A

only the substrates

107
Q

at what wavelength is NADH absorbed

what can this be used for?

A

340 nm

can be used to measure conc.

108
Q

what are the symptoms of pellagra

A

dermatitis, diarrhea, dementia, death

109
Q

what are the precursors of NAD+

A

trp –> Niacin (nicotinic acid) –> Nicotinamide –> NAD+

110
Q

what plant is deficient in trp and niacin

A

Maize

111
Q

what demographic has reduced absorption of niacin

A

alcoholics

112
Q

where was pellagra common in the past

A

southern US

113
Q

Who went to find cure in 1914? what did he believe was the cause? how did he figure it out?

A

joseph Goldberg

nutrition

trials in orphanage and convict camps induced pellagra through restricted diet

114
Q

what was eventually determined to be the cause?

A

In 1937 vitamin B3 was identified

115
Q

why did native americans not suffer from pellagra?

A

because they treated their corn with lime which made the niacin available

116
Q

what does FAD stand for

A

Flavin adenine dinucleotide

117
Q

how many e- can FAD accept?

A

one or two

Metabolism (8 decks)

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