Metabolism Flashcards
What is anabolism?
synthesis of biopolymers
What is catabolism?
degradation of biopolymers
What is a metabolic pathway?
sum of all steps in the synthesis or breakdown of a product
What are the types of metabolic pathways?
linear, cyclic, branched converging, branched diverging, spiral
What are intermediates? What is another name for them?
a compound that isn’t the intial reactant or final product
metabolites
What is associated with catabolism?
breakdown of biomolecules, overall chemical oxidation that leads to reduced cofactors (NADH, NADPH, FADH2), releases energy for ATP, convergence of pathways
What is assocaited with anabolism?
synthesis of biomolecules, overall chemical reduction that leads to reduced cofactors (NAD+, FAD, NADP+), requires ATP, divergence of pathways
What is the most vs the least reduced form of carbon?
CH4 is most and CO2 is least
What enzymes carry out standard redox reactions?
dehydrogenases
For the reaction AH2 + B <–> A + BH2 what is AH2 and B?
AH2 is the reducing agent and B is the oxidizing agent
What is the major electron acceptor during the oxidiation of metabolites vs the major electron donor during the reduction of metabolites?
NAD+ vs NADPH
What are the chemical reactions involved in metabolism?
redox reactions, group transfer, hydrolysis, non-hydrolytic cleavage, isomerizations, bond formation coupled with ATP
What is a common example of a group transfer reaction?
transfer of PO3 group from ATP, trasnfer of acyl from carboylic acid derivative to SH group of CoA
What are hydrolysis reactions?
adding water to break up a covalent bond
Why is ATP so energetic?
- more resonance structures for ADP and Pi than ATP so they have less energy
- lot of negative charges cause charge repulsion, relieving this gives off energy
- products of atp hydrolysis are easily solvated
- icnrease in disorder
How can you get a reaction with a positive delta G to happen?
couple it with a reactiom with a negative delta G
What equation can be used to calculate Keq when given standard Gibbs and temperature?
deltaG=RTlnKeq
What are the two main phases of glycolysis?
preparatory phase and payoff phase
What is the first reaction of glycolysis? What is involved?
glucose to glucose-6-phosphate, uses hexokinase, uses one atp
What is the structure of glucose-6-phosphate?
normal 6 carbon ring (glucose) with a phosphate group attachted to the 6th carbon
What is the second reaction of glycolysis? What is involved?
glucose-6-phosphate to fructose-6-phosphate, uses phosphohexoisomerase (rearranged structure)
What is the third reaction of glycolysis? What is involved?
fructose-6-phosphate to fructose1,6-bisphospahte, uses phosphofructokinase, also uses another ATP
What is the priming steps in glycolysis?
1st, and 3rd, steps that activate the substrate for the enxt reaction
What is the fourth step of glycolysis?
fructose 1,6 bisphosphate is broken down into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate
What is the fifth reaction of glycolysis? Why does this reaction happen even though its endergonic?
converting dihydroxyacetone phosphate to glyceraldehyde 3-phospahte
in cells its closer to 0 and there is constant depletion of GAP which moves the reaction to the right
What is the sixth reaction of glycolysis?
glyceraldehyde 3 phosphate is oxidzed into 1,3 bisphosphoglycerate, NADH is produced
What is the seventh reaction of glycolysis?
phosphate group is removed from 1,3 bisphosphoglycerate and added to ADP, makes ATP and 3-phosphoglycerate
What is the eight reaction of glycolysis?
3-phosphoglycerate gets rearranged to 2-phosphoglycerate
What is the ninth reaction of glycolysis? (After 2-phosphoglycerate is made)
2-phosphoglycerate converted to phosphoenolpyruvate (PEP) through a dehydration reaction
What is the tenth reaction of glycolysis? (After PEP)
phosphate group from phosphoenolpyruvate to ADP, making pyruvate and ATP
What are the net products of glycolysis?
2 atp, 2 nadh, 2 pyruvate
What determines what happens to pyruvate after glycosis?
whether there are anaerobic vs aerobic conditions
What is gluconeogenesis? Where does it happen?
synthesis of glucose from pyruvate or lactate
mostly in liver cells
How is PEP made in gluconeogenesis?
using pyruvate or lactate, combines with bicarbonate to make oxaloacetate using pyruvate carboxylase (uses atp)
then using gtp its converted into PEP (phosphoenolpyruvate) by PEP carboxykinase
What cofactor is almost always involved when adding or removing a carbon?
biotin
What enzymes are a major point of regulation for glycolysis/gluconeogenesis?
phosphofructokinase (PRK-1) and fructose-1,6-bisphosphotase
What favours glycolysis vs gluconeogenesis? Why?
high atp favours gluconeogenesis (high energy levels) high amp favours glycolysis (low energy levels)
How does Fructose 2,6-bisphosphate mediate glucose metabolism?
activates PFK1 which activates glycolysis
The enzymes involved in the citric acid cycle are often associated in functional units called metabolons, what does this allow for?
substrate channelling
What is the oxidation of pyruvate to acetyl CoA performed by?
pyruvate dehydrogenase which is a multienzyme compelx
What is the first step of the pyruvate dehydrogenase cycle?
pyruvate is linked to pyruvate decarboxylase and then decarboxylates, remaining hydroxylethyl group bind to coenxyme TPP
What is the second step of the pyruvate dehydrogenase cycle?
the C2 of the hydroxethyl is oxidized into an acetyl group, this is done by reducing the disulfide bond of the lipoamide group of the second enzyme, this transfers the acyl group to the enzyme
What is the third step of the pyruvate dehydrogenase cycle?
acetyl coa is formed by trasnfering the acetyl group to the thiol group of pantothenic acid which contains coenzyme A
What is the fourth step of the pyruvate dehydrogenase cycle?
the lipoamide needs to be reoxidized, to do this FAD is reduced to FADH2
What is the fifth step of the pyruvate dehydrogenase cycle?
to regenerate FAD, FADH2 reduces NAD+ to make NADH
What are the names and functions of the enzymes in pyruvate dehydrogenase complex?
pyruvate dehydrogenase (decarboxylates pyruvate), dihydrolipoyl transacetylase (transfer of acetyl group to CoASH), dihydrolipoyl dehydrogenase (reoxidizes dihydrolipoamide)
What is the sum of the reaction of pyruvate dehydrogenase?
products are acetyl CoA, CO2, NADH, H2
What is the first step of the citric acid cycle?
acetyl group of acetyl CoA is added to oxaloacetate to make citrate, releases CoA and uses water
Why does the first step of the kreb’s cycle happen even though the concentration of oxaloacetate is very low?
first step is very exergonic
What is the second step of the citric acid cycle?
citrate is isomerized to form isocitrate, involves a dehydration and then a rehydration
What is the third step of the citric acid cycle?
isocitrate is oxidized to make a-ketoglutarate, releases a CO2 and reduces NAD+ to make NADH
What is the fourth step of the citric acid cycle?
a-ketoglutarate is oxidized to succinyl CoA by ketoglutarate dehydrogenase complex, releases a CO2 and reduces NAD+ to make NADH
What is the a-ketoglutarate complex similar to?
pyruvate dehydrogenase complex (almsot identical chemcial reaction with same cofactors)
What is the fifth step of the ctric acid cycle?
succinyl CoA is converted to succinate, releases CoA and makes GTP
WHat is the sixth step of the citric acid cycle?
succinate is oxidized to fumarate, reduces one FAD to FADH2
What is the seventh step of the citric acid cycle?
fumarate is converted to malate by fumarase using a water moelucle
What is the eigth step of the citric acid cycle?
malate is oxidized and turned into oxaloacetate, also NAD+ is reduced to NADH
Why does the last step of the kreb’s cycle happen even though its energetically unfavoured?
because the first step is so favoured it happens anyway
What inhibits pyruvate oxidation?
ATP, acetyl CoA, NADH, fatty acids
What stops the first step of the citric acid cycle?
NADH, citrate, succinyl CoA, ATP
Where is the electron transport chain found?
inner mitochondrial membrane
What equation can be used to relate standard reduction potentials to standard gibbs?
deltaG=-nFdeltaE
n=# of e- and F is faraday constant (96485 C/mol)
How can you calculate standard reduction potential?
Eacceptor-Edonor
Where does NADH and FADH2 enter the ETC?
NADH enters at complex I and FADH2 enters at complex II
How does complex I pass on electrons?
NADH gives 2e- to flavin mononucleotide (FMN) which then passes those electrons onto an iron-sulfur and then onto coenzyme Q
What is another function of compelx I aside from passing on electrons?
moves 4 H+ into intermembrane space against concentration gradient
What are the types of Coenzyme Q?
ubiquinone (Q, fully oxidized), semiquinone (*QH, half reduced), ubiquinol (QH2, fully reduced)
How does complex II pass on electrons?
takes electrons from succinate via FADH2, passes onto iron-sulfur cluster and then onto coenzyme Q
Does complex II move protons into intermembrane space?
no
How does complex III receive electrons?
iron-sulfur clusters containing cytochromes receive e- from CoQ
Why does the Q cycle exist?
cyt c1 only takes 1 e- but CoQ has 2e-
How does the Q cycle work?
ubiquinol gives 1 e- to uniquinone which becomes semiquinone and the other to cyctochrome c
the other electron is given to semiquinone to make ubiquinol and other goes to cyt c
What do the iron-sulfur clusters in cytochromes resemble?
heme groups
What is the function of complex IV?
transfers electrons from cyt c to O2 via cyt a and a3 (also pumps 2 H+)
What are some examples of chemicals that can stop the ETC?
cyanide, carbon monoxide, rotenone, antimycin A
How many protons do each complex pump?
1- 4 H+
2- none
3- 4 H+
4- 2 H+
What does protons moving through the pore of atp synthase cause?
rotation of the y subunit, this causes conformational changes in the beta subunits that drive atp synthesis
How does NADH from glycolysis get into the mitochondria?
malate-aspartate shuttle
How does the malate-aspartate shuttle work?
NADH is used to reduce oxaloacetate to malate, malate enters matrix in exchange for a-ketoglutaraete, malate is oxidized to oxaloacetate and forms NADH, oxaloacetate is converted to aspartate which flows out in exchange for glutamate
How many ATP per glucose?
30-32
What is the differnce between saturated and unsaturated fats?
saturated have no double bonds and unsaturated do
What are triglycerols broken down by/into?
by lipases into glycerol and fatty acids
What are some sources of fatty acids for energy metabolism?
dietary triacyclglycerols, triacyclglycerols synthesized in the liver, triacyclglycerols stored in adipocytes
How are triacyclglycerols absorbed by small intestine?
they are broken down into fatty acids and absorbed by the mucosa, which are remade into triacyclglycerols and combined with lipoproteins and cholesterol into chylomicrons which are distributed to cells
After chlymicrons are distributed to cells what happens?
broken back down by lipoprotein lipase and fatty acids are used for energy or storage
How are fatty acids marked to be catabolized in the mictochondria?
they are activated by a thioester linkage to CoA, making acyl-CoA
What allows for the passage of fatty acid through the inner mitochondrial membrane?
linkage to carnitine via carnitine acyltransferase I, once inside caritine acyltransferase II reverses the reaction making acyl CoA again
What is the beta oxidation spiral? What are the products for each turn?
break down of fatty acids, two carbons from acyl CoA are removed at a time
each turn makes an acetyl CoA, NADH, and a FADH2
Can beta oxidation happen with a fatty acid with an odd number of carbons?
yes
What is the substrate for fatty acid syntehsis? What is this syntehsis performed by?
malonyl CoA
fatty acid synthase
Are fatty acids made in the cytoplasm are what?
palmitate (palmitic acid)
What are chlyomicrons?
made in intestinal mucosa, transport triacyclglycerols to tissues
WHat is VLDL?
very low density lipoprotein, made in liver and deliver liver synthesize triacyclglycerols to adipose tissue
What is LDL?
low density lipoprotein, major cholesterol carrier, moves from liver to tisse
What is HDL?
high density lipoprotein, highest protein content, moves cholestreol from tissue to lvier
Can N2 gas be reduced to NH3 enzymatically?
yes only by certain species, for example rhizobium which forms nodes in roots of legumes
What do all nitrogen fixing enzymes contain?
nitrogenase complex, made up of a Fe-S that contains dinitrogenase reductase and a molybdenum-iron cofactor which has a protein called dinitrogenase
How much atp is used to fixate 1 n2?
16
NH4 cannot be free flowing in system, so how does it exist in our bodies?
glutamate is aminated to make glutamine
What is alpha-ketoglutarate the carbon skeleton of?
glutamate, glutamine, proline, arginine
What is pyruvate the carbon skeleton of?
alanine, valine, leucine, isoleucine
What is oxaloacetate the carbon skeleton for?
aspartate, asparagine, methionine, threonine, lysine
What is 3-phosphoglycerate the carbon skeleton of?
serine, glycine,cysteine
