Fundementals of metabolism Flashcards
1
Q
autotrophs (photosynthetic)
A
Use CO2 as their carbon source
Use sunlight as their energy source
Produce O2
2
Q
Heterotrophs
A
Use complex organic compounds
- as a source of carbon
- as an energy source
Produce CO2
3
Q
what is nitrogen required for
A
AA’s and nucleotides
4
Q
autotrophs require what source of nitrogen
A
ammonia or nitrate
5
Q
heterotrophs require what sources of nitrogen
A
AA’s, other N2 containing compunds
6
Q
cyanobacteria get nitrogen by
A
fixing N2 to NH3
7
Q
what do nitrifying bacteria do to get nitrogen
A
Oxidize NH3 to nitrates and nitrates
8
Q
is energy cycled in metabolism?
A
no. energy enters as light and leaves as heat and chemical potential energy
9
Q
catabolism consists of what
A
Breakdown of nutrients (e.g. glucose)
Releases energy for anabolic reactions
Releases heat
10
Q
anabolism consists of
A
Synthesis of macromolecules
Requires energy
Releases heat
11
Q
intermediary metabolism consists of
A
Metabolic pathways involving low molecular weight (<1000) compounds
12
Q
what type of metabolism converges? what diverges
A
catabolism; anabolism (check if always true)
13
Q
what drives anabolism
A
catabolism
14
Q
how are anabolic rxns and catabolic rxns separated
A
unique enzymes, cofactors, compartmentalization
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)
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
17
Q
unique cofactors
A
NADH for catabolism, NADPH for anabolism
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
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)
20
Q
what are malignant hyperthermia (MH) triggers
A
halothane, enflurane, isoflurane, sevoflurane and desflurane
as is the depolarizing muscle relaxant succinylcholine
21
Q
what hormone controls metabolic rate? what is a clinical correlate
A
thyroid hormone
CC: hyperthyroidism, weight losss, heat intolerance
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
23
Q
list hydrocarbons from most reduced to least reduced
A
alkane
alcohol
aldehyde (ketone)
carboxylic acid
carbon dioxide
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
25
describe phosphate and phosphate transfer rxns
involves nucleophilic attack (glucokinase) and a transient intermediate
26
phosphate shape
what stabilizes it
tetrahedral
resonance
27
what is lost when you go from catabolism to anabolism
energy (usually in form of heat
28
what is a type of non-converging or diverging pathway
TCA: Cyclic pathway
29
characteristics of a typical rxn
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
30
what is the steady state
point at which the forward and backward reaction rates are the same
31
in typical enzymatic rxns, what kind of constants are K1 and k2?
Forward Rate
Proportional to [A][B] = k1[A][B]
Reverse Rate
Proportional to [C][D] = k2[C][D]
32
what occurs at equilibrium
what 3 equations used for equilibrium states
forward rate = reverse rate
k1[A][B] = k2[C][D]
k1/k2 = [C][D] / [A]{B]
Kequ= [C][D]
[A][B]
33
Keq exist at what conditions, by convention
K'eq is rate constant only at pH7 (10 E-7 M H+) and 55.5 M H2O
34
what is dynamic equilibrium
when rate of formation of products = rate of formation of reactants
35
What kind of enzymatic rxns are reversible
ALL OF THEM
36
what drives a rxn
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)
37
what does delta G depend on
The ∆G depends on the concentrations of reactants and products, temperature and pressure
38
what is standard delta G (delta G naught)
delta G at the following conditions:
One molar reactants and products, 298 K (25 C), 1 atm
39
what is standard biological delta G (G naught prime)
delta G at conditions:
∆Gº at pH 7 (10-7 M H+), 55.5 M H2O, 1 mM Mg2+
40
can the standard free energy change be used to predict the net direction of a rxn in vivo?
not in vivo since the reactants and products are not at 1 Molar
41
what do enzymes do?
what do they change? what don't they change
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
42
what is released during oxidation? what is gained?
electrons and H+ in oxidation
electrons and H+ gained in reduction
43
what is the relationship between delta G and Keq
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
44
removing products at equilibrium does what?
removing reactants does what?
makes delta G neg (drive rxn forward)
makes delta G positive (drives rxn backward)
45
how are energetically unfavorable rxns pushed forward
they are coupled to favorable ones
46
give example of reaction coupling
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
47
delta G's can be what
added
48
Keq's are combined how
they are multiplicative
49
what are operational delta g's
observed versus biological standards
50
what are the differences between operational delta G's (in vivo)
Conditions vary, but in general the true ∆G of ATP hydrolysis in vivo is more negative than standard ∆G
51
law of mass action
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
how are products moved through pathwasy
Increasing the level of substrate
Decreasing the level of product
-Especially useful for energetically unfavorable reactions
53
what is ∆Gº’ when Keq is 1
0
54
what is Keq when ∆Gº’ is 0
1
55
what is Keq when ∆Gº’ is negative
greater than 1
56
what is ∆Gº’ when Keq is greater than 1
negative
57
what is Keq when ∆Gº’ is positive
less than 1
58
what is ∆Gº’ when Keq is less than 1
positive
59
what type of bonds between phosphates of ATP
phosphoanhydride bonds
60
what type of bond between ribose and phosphate
phosphoester bond
61
what is adenosine
ribose and adenine only
62
name of the phosphates on NTP;s based on their position
from closest to farthest from ribose
alpha, beta, gamma
63
what is ∆Gº’ of ATP hydrolysis
-30.5 kJ/mol
64
what happens with ATp hydrolysis
relief of charge repulsion
65
what stabilizes products of ATP hydrolysis
resonance stabilization
ionization
66
what does ATP form a complex with?
what purpose?
Mg2+
stabilizes partial neg charges on adjacent phosphate hydrogens
67
list high energy compounds in decreasing order of potential energy ( most neg ∆Gº’ )
phosphoenolpyruvate, 1,3- bisphosphoglycerate, phosphocreatine, ATP, glycerol phosphate, Glucose 6 phosphate and Pi
first 3 used to make ATP
68
what is ATP used for
Biosynthesis of compounds such as G6P and Gycerol phosphate (low energy compounds)
69
what does tautomerization do?
stabilizes molecule, releasing energy
70
give example of tautomerization
PEP hydrolyzed to form pyruvate in enol form which interconverts with keto form
71
compare energy from hydrolysis with energy from tautomerization
-16 vs -46
tautomerization releases more energy thatn hydrolysis itself
72
how is 1,3-BPG hydrolyzed and stabilized to release energy?
what is the ∆Gº’ ?
after hydrolysis, 3-phosphoglyceric acid ionizes (releases H+) and it is then stabilized by resonance of the carboxyl group
-49.3
73
how is phosphocreatine hydrolyzed and stabilized to release energy?
what is the ∆Gº’ ?
2 adjacent H2N groups undergo resonance stabilization
-43.0
74
what is the purpose of phosphocreatine
what is the ∆Gº’ of its transphosphorylation what enzyme is used
it is an energy reservoir
-12.5; creatine kinase
75
name 2 other enzymes used in transphosphorylations
what are the ∆Gº’?
adenylate kinase
nucleoside diphosphate kinase
∆Gº’ is about 0
76
how is acetyl CoA hydrolyzed and stabilized to release energy?
∆Gº’ ?
hydrolyzed to acetic acid;
ionized to acetate
acetate has resonance stabilization on carboxyl group
∆Gº = -32.2
77
thioesters release more energy than oxygen esters? (Double check)
why?
no resonance stabilization
78
what powers the Na+K+ ATPase?
how?
ATP hydrolysis
-phosphorylation changes the confromation of the pump.
79
Ouabain
blocks ATPase pump
poisonous cardiac glycoside.
used to be used as ionotropic effect (sodium calcium exchanger (NCX) )
80
what is conjugation rxn
These reactions involve covalent attachment of small polar endogenous molecule such as glucuronic acid, sulfate, or glycine to form water-soluble compounds.
81
what happens in Palmitoyl-CoA Synthesis
∆Gº’?
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
what are used in RNA elongation
2 high energy bonds
between alpha and beta carbons and then the pyrophosphate anhydride bond is broken
83
what is like electrical motor
Food for work
Electromotif Force (emf)
- battery,(electrons), electric motor, (physical coupling), work
- food (electrons), mitochondria/proton motive force, (ATP) , Work
84
what metal ion can reduce sugars
cupric ions
85
organic redox reactions
yields 2 H+ and 2 e- for oxidation
consumes 2 H+ and 2 e- for reduction
86
in oxidation what can "replace" H+
OH to form OH group and an H20 product along with 2 e-
87
for redox rxns
2 e- + 2OH- + 2Cu2+ yields
Cu2O + H2O
subreactions:
2 Cu2+ + 2 e- yield 2Cu+
then 2 Cu+ + O2- yields CU2O
88
oxidation states of carbon:
ownership of electrons ranking
Ownership of Electrons H< C < S < N < O
89
what are 4 methods of electron flow
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
what does a hydrogen electrode measure
it measure reduction potential
91
what gas is pumped into one of the beakers of hydrogen electrode
H2 gas is pumped into one beaker at standard pressure
92
what connects the 2 solutions
a salt bridge (KCl)
93
what is the probe and device measuring in a hydrogen electrode
emf
94
what forced is involved in hydrogen electrode
reduction potential (E)
95
what is the value of the hydrogen electrode
0.00
96
what value is represented by a tendancy to remove electrons
positive number
97
what value is represented by a tendancy to donate electrons
negative number
98
what is the reference cell of known emf
the hydrogen electrode in which H2 gas at 101.3 kPa is equilibrated at the electrode with 1 M H+
99
what is the test cell?
a cell containing 1 M concentrations of the oxidized and reduced species of redox pair to be examined
100
What does the Nernst equation relate?
it relates standard reduction potential to true reduction potential
101
what is the nerst equation? Both versions
explain the variables
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
what is the relationship between delta G and delta E
Delta G = -nF*delta E
or
delta G naught prime = -nF*delta E naught prime
103
hardest question on exam will be
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
how many electrons does NAD+ accept? what are they transfered as?
2 electrons: transferred as a hydride Ion (H-)
H+ is released in the medium
105
what 2 sides are electrons added to NAD+?
either side A or B
106
what affects NAD+ reduction
only the substrates
107
at what wavelength is NADH absorbed
what can this be used for?
340 nm
can be used to measure conc.
108
what are the symptoms of pellagra
dermatitis, diarrhea, dementia, death
109
what are the precursors of NAD+
trp --> Niacin (nicotinic acid) --> Nicotinamide --> NAD+
110
what plant is deficient in trp and niacin
Maize
111
what demographic has reduced absorption of niacin
alcoholics
112
where was pellagra common in the past
southern US
113
Who went to find cure in 1914? what did he believe was the cause? how did he figure it out?
joseph Goldberg
nutrition
trials in orphanage and convict camps induced pellagra through restricted diet
114
what was eventually determined to be the cause?
In 1937 vitamin B3 was identified
115
why did native americans not suffer from pellagra?
because they treated their corn with lime which made the niacin available
116
what does FAD stand for
Flavin adenine dinucleotide
117
how many e- can FAD accept?
one or two
