CLASS: 10-11
8-25-10
Popov
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VII.
Intro to Metabolism
Scribe: Jordan Heath Taylor VI
Proof: Lee Redditt
Page 1 of 5
Introduction to Metabolism [S1]
a. Focus on fundamentals of metabolism: Why do these pathways exist? What do they accomplish? How
they’re related…
Outline [S2]
a. Topics: Metabolism, High-energy compounds, ATP, redox rxns, vitamins
b. Ch. 17 of textbook
Cycling of Carbon Dioxide and Oxygen [S3]
a. Life on earth is carbon-based
b. All living things need a continuous supply of carbon (i.e. to build molecules)
c. 2 large groups of organisms:
i. autotrophs – (plants) receive carbon primarily from CO2 of atmosphere. They can build all of their
molecules out of this carbon.
ii. Heterotrophs – (like us) can’t utilize CO2 and rely on organic molecules produced by autotrophs
d. The goal of all metabolic transactions is to make our own molecules out of available sources, by way of
biosynthetic pathways
e. In order to build such molecules you need some source of energy
f. 2 main categories in respect to energy source used to build molecules
i. phototrophs (plants) use energy of light to drive biosynthetic reactions. A side product of these reactions is
Oxygen
ii. heterotrophs – use energy gathered from oxidation of compounds provided by plants in order to gain
energy for biosynthetic reactions.
g. Continuous cycle of carbon: CO2 from atmosphere is picked up by plants, incorporated in their molecules,
animals/humans use the plants’ compounds to build their own molecules/gain energy, release CO2 into
atmosphere, cycle starts over
Cycling of Nitrogen in the Biosphere [S4]
a. Most of our molecules are built of Carbon, Oxygen, Nitrogen
b. Nitrogen source cycle is a bit different from Oxygen cycle
c. Main source of nitrogen is nitrogen gas in the atmosphere, but this is not very reactive
d. We are lucky that certain bacteria in soil that are capable of reducing nitrogen (known as nitrogen fixation)
into Ammonia
e. Ammonia can be incorporated into biological molecules
f. Unfortunately, there is other bacteria that uses the NH4+ as an energy source and they rapidly oxidize it back
to nitrate
g. Nitrate is a “dead molecule” to us because there are no biochemical means to use it
h. Luckily plants are capable of converting nitrate back into ammonia
i. We as humans end up on the sidewalk of the cycle because our source of nitrogen is obtained from eating
molecules produced by plants
Relationship between Catabolic and Anabolic Pathways [S5]
a. In general, metabolism refers to the set of all chemical transactions that happen in the cell or organism.
b. Our goal is to synthesize complex molecules like proteins, polysaccharides, fats, DNA, etc.
c. Any anabolic reaction requires an input of energy. Therefore, there’s another side to the synthetic reactions
known as catabolic reactions.
d. The goal of catabolic reactions is to produce energy to drive the anabolic reactions.
e. Energy containing molecules are taken in, broken down, and eventually completely oxidized.
f. For us the primary energy fuels are carbs (about 50% of our intake), fats (about 30% of intake), and proteins
(about 20%).
Chemistry of ATP [S6]
a. The universal energy that is released during reactions is accumulated in the form of Adenosine triphosphate
b. This is the universal carrier of energy that couples catabolic and anabolic processes
c. Anabolic reactions are generally reductive. This reducing power is provided by catabolism in the form of
reduced electron carriers. (pyridine nucleotides, reduced form of NADH and NADPH, flavin
nucleotides:FADH)
Chemical basis of ATP Hydrolysis [S7]
a. ATP is a nucleotide built of adenine, ribose, and a polyphosphate tail
b. From a bioenergetic viewpoint, the important part is the polyphosphate tail, particularly the gamma and beta
phosphates
c. The phosphate bonds are known as anhydride bonds that are the product of a dehydration reaction between
2 acid molecules.
CLASS: 10-11
Scribe: Jordan Heath Taylor VI
8-25-10
Proof: Lee Redditt
Popov
Intro to Metabolism
Page 2 of 5
d. The bond between the alpha phosphate and the ribose is an ester bond, which is another dehydration
reaction between an acid and an alcohol.
e. High-energy bond, in this case, refers not to the energy of the bond, but the energy that is released during
transfer reactions.
f. Here is a simple example of the gamma phosphate being transferred to another molecule via hydrolysis.
g. Notice that Gibbs free energy is a high (magnitude) negative number
h. Practically, if you put ATP in water, let it sit, then measured what happened…you would notice that most of
the ATP is now ADP + P. Which tells us that this reaction is irreversible.
i. This is because the molecule is highly charged and when you break it apart, you separate charges and
release repulsion. This actually promotes the breakdown of the molecule.
j. This hydrolysis leaves ADP in the form of an acid (H attached) but in neutral conditions the ADP will be found
in ionized form (H immediately dissociated)
k. Say we want to make Glucose-6P…Glucose and Phosphate energies are individually rather low, but
Glucose-6P is rather high. If you mix glucose and phosphate and let them sit, the reaction won’t occur (it’s
energetically unfavorable)
VIII. Energy Coupling in chemical process [S8]
a. This diagram shows the hydrolytic reaction of ATP: reactants are high energy and products are low energy,
indicating a spontaneous reaction.
b. If you use ATP as a source of phosphate to phosphorylate glucose, the energy of reactants is far greater than
the energy of products. This makes the reaction favorable. This is the background of energetic coupling.
c. ATP drives energetically unfavorable reactions.
IX. ATP Hydrolysis in Two Steps [S9]
a. It’s not enough to simply break phosphate off of an ATP and then attach it to another molecule somewhere
else.
b. ATP must physically participate in the reaction.
c. ATP must change the reaction mechanism.
d. Here’s an example of glutamine synthase. Ammonia is attached to glutamic acid to make glutamine.
e. This reaction requires ATP. ATP is hydrolyzed to synthesize another molecule.
f. First, ATP is used to phosphorylate glutamate to form an phosphoryl intermediate. Then the intermediate can
react with ammonia to release the phosphate.
g. ATP drives this reaction because it physically participates in this reaction and changes the reaction’s route.
X. Ranking of biological phosphate compounds [S10]
a. This begs the question: Why ATP?
b. ATP is positioned ideally among different phosphoryl-containing compounds. It’s easy to use gamma
phosphate to drive a variety of processes making compounds that have less energy.
c. Keep in mind, you have to make ATP too.
d. Make other high-energy phosphoryl compounds to transfer phosphate to ADP to make ATP, but remember
that these other compounds must be of even higher energy than ATP.
e. ATP is high enough to phosphorylate a variety of lower energy compounds that the body needs, but it’s still
low enough energy to be phosphorylated by other higher compounds (glycolysis products) that exist in the
cell.
XI. The Oxidation States of Carbon [S11]
a. Anabolic reactions also need a source of reducing power. This comes from the oxidation of carbon
containing compounds.
b. The least oxidized compound is the alkane. The most oxidized carbon compound here is CO2 (the final
product of catabolism)
c. These increased states of oxidation occur through electron extraction.
XII. An Oxidation-Reduction Reaction [S12]
a. This is a typical oxidative/reduction reaction that will encounter often. Lactate  pyruvate.
b. Oxidation takes place at the alpha carbon of lactate.
c. To make this conversion, you have to remove two hydrogens and two electrons at the same time. Then, you
can use these electrons to drive some synthetic reaction.
d. But electrons can’t survive alone in solution, so you must have a carrier: (NAD, NADP or flavin nucleotides)
XIII. NAD and NADP [S13]
a. NAD and NADP are commonly known as pyridine nucleotides. They are both dinucleotides: adenine and
nicotinamide are linked together.
CLASS: 10-11
Scribe: Jordan Heath Taylor VI
8-25-10
Proof: Lee Redditt
Popov
Intro to Metabolism
Page 3 of 5
b. This structure is important because it’s important in enzyme recognition. The nictotinamide ring is important
because it functions in electron carrying. It can accept hydrate ion: one proton and 2 electrons at the same
time. It can deliver electrons to another substrate with the help of an enzyme.
c. The nicotinamide ring is derived from a vitamin: niacin.
d. The difference between NAD and NADP is just one phosphate at a hydroxyl group. Their functions, on the
other hand, are principally different.
e. NAD is usually involved in catabolic processes. It becomes oxidized in the electron chain to make ATP.
f. NADP, in contrast, is a coenzyme that is specifically made in its reduced form to be consumed in anabolic
reactions.
g. NAD carriers are limited because it can only transport two electrons at one time. It can’t transfer one at a
time.
XIV.
Structures of oxidized and reduced FAD and FMN [S14]
a. FMN and FAD have parts that are derived from riboflavin vitamin
b. The difference between pyridine and flavin nucleotides is the ability of flavin nucleotides to accept/transfer 1
or 2 electrons at one time.
c. These can accept 2 electrons from NADH and donate these 1 at a time.
d. Unlike pyridine nucleotides, flavin nucleotides are tightly bound to their protein counterparts. They’re not
mobile carriers. They accept from mobile/soluble carrier, NADH, and donate electrons downstream in the
ETC.
XV. Recycling of cytosolic NAD [S15]
a. In order to regenerate NAD+ when mitochondrial ETC relief is not available, there must be other options.
b. Often pyruvate is converted to lactate in lactate fermentation.
c. NADH is recycled as it builds up in the cytosol.
XVI.
Transfer of reducing equivalents via NADP cycle [S16]
a. NADPH is made specifically to serve synthetic pathways that need reducing power.
b. NADPH is produced by its own specialized set of reactions
XVII. General Scheme of Pentose Phosphate Pathway [S17]
a. NADPH is produced in this way most commonly.
b. This NADPH produced will later on be used by other biosynthetic pathways.
XVIII. Three Stages of Cellular Respiration S18]
a. Consider a bonfire…much heat/light/energy is produced from oxidation of fuel, but when this exergonic
reaction occurs in uncontrolled fashion, all the energy is wasted.
b. The same “burning” is happening in metabolism, but it occurs in very tiny, controlled steps. This allows our
bodies to capture the energy efficiently.
c. Initial carbs, fatty acid fuels are broken down into simple precursors, such as acetyl-CoA. By uniforming all
the different compounds we are able to utilize one common pathway
d. The major output of the Citric Acid Cycle is electrons, in the form of reduced NADH or FADH2. Carbon
compounds leave in the form of CO2.
e. In the last stage, the ETC, electrons are fed in and energy is used to make ATP.
f. Some amounts of ATP will be made in the preliminary processes (glycolysis and CAC) as well.
XIX.
Types of nonlinear metabolic pathways [S19]
a. All catabolic processes aim at bringing complex carbon molecules down to simpler molecules. This is a
converging scheme.
b. All anabolic processes aim at taking simple precursors and building more complex, diversified compounds.
This is a diverging scheme.
XX.
Enzyme-limited and substrate-limited reactions [S20]
a. How do we control all of these chemical reactions?
b. Pathways are just sequences of reactions that utilize different enzymes.
c. Most reactions occur very quickly because enzymes are very active. These steps are known as substratelimited.
d. Some steps will occur relatively slowly and these are known as enzyme limited. This step has an enzyme
that is not as active. These steps are also known as rate-limiting steps. These reactions are often used to
control the entire pathway, these are the sites of pathway regulation.
XXI.
Feedback Inhibition [S21]
a. If enough isoleucine is produced, then no more isoleucine is needed.
b. It’s inefficient to produce isoleucine if you already have enough. So we want to shut down this pathway.
c. Very common to use the end product of the pathway to go back and inhibit a previous step (often near the
first or second reaction)
d. If isoleucine concentration goes down, then inhibition is lifted and the pathway resumes.
CLASS: 10-11
Scribe: Jordan Heath Taylor VI
8-25-10
Proof: Lee Redditt
Popov
Intro to Metabolism
Page 4 of 5
e. Most real-life situations are more complex than this simple example.
XXII. Regulation of Phosphofructokinase-1 [S22]
a. Here’s an example of regulation in the glycolytic pathway.
b. The rate-limiting step is regulated by a variety of factors, this allows more options for pathway rate.
c. ATP inhibits because if you have plenty of energy, you don’t need to produce more.
d. Thus, ADP and AMP stimulate this pathway for the opposite reason.
XXIII. Relative Changes in ATP Derivatives [S23]
a. Under most circumstances, the concentration of ATP is very high and doesn’t change much in the cell.
b. This small 10% change is ideal because it is not large enough to cause detrimental changes to the cell, but it
is just enough to allow us to use ATP to regulate many enzymes in our body.
c. ADP doesn’t change at all, but AMP changes significantly.
d. When ATP drops 10%, AMP increases by 600%.
e. The increase in AMP relieves the inhibitory effect of ATP
XXIV. Role of fructose 2,6-bisphosphate in PFK-1 regulation [S24]
a. Here we are measuring a rate limiting step of glycolysis: regulation of phosphofructokinase-1
b. Fructo-2,6-bisphosphate (F2,6BP) is an allosteric regulator of the enzyme
c. This graph shows 2 situations: presence of F26BP (red) and absence of F26BP (blue)
d. In the absence of F26BP there is only enzyme activity over a small range of [substrate] (x-axis)
e. There has to be a high conc. of substrate to notice any activity
f. In contrast, there is more sensitivity to the substrate over a wider concentration range in the presence of
F26BP
g. The F26BP allosteric activator allows the enzyme to work at very low substrate concentrations
XXV. Glycolysis and Gluconeogenesis [S25]
a. Catabolic and Anabolic pathways share several steps
b. Many pathways are antiparallel like traffic on a two-way street
c. Many cells, especially liver and kidney cells, can not only break down glucose, but also synthesize glucose in
a process known as gluconeogenesis
d. Up to 7 steps in both pathways are shared, they are catalyzed by the same enzymes
e. How do we control the direction that this pathway goes?
f. For example, in a well-fed condition our cells will be running glycolysis
g. In starvation, our bodies must run gluconeogenesis in order to make glucose to feed organs such as the brain
h. In order to operate the direction of this pathway, we must have at least one step that uses 2 different
enzymes
i. In this particular example, PFK1 (the rate limiting reaction in glycolysis) is opposed by Phosphotase (in
gluconeogenesis)
j. At this point, the pathway takes two different paths, depending on direction
k. This is also the point that the pathway is regulated, in opposite manner.
l. When one path is being stimulated, the other pathway is being inhibited, and vice-versa.
XXVI. Compartmentalization of Metabolism [S26]
a. To keep all these reactions under check, they are compartmentalized separately in the cell
b. Glycolysis in the cytosol, CAC takes place in mitochondrial matrix, ETC takes place in mitochondrial
membrane
c. Physical separation of these processes allows for better individual control of each system
XXVII. Vitamins and Coenzymes [S27]
a. Nutrition provides several vital components in the form of metals and vitamins
b. These are small organic molecules and are consumed by us in much smaller quantities
c. These can be categorized into: water-soluble and lipid-soluble
d. Most water-soluble vitamins are part of different coenzymes. These assist in catalysis of certain biological
reactions..
e. Niacin and Riboflavin are part of NAD and FAD enzymes, respectively
XXVIII. Thiamine pyrophosphate’s role in decarboxylation [S28]
a. Thiamine (vit B1) is active in the form Thiamine pyrophosphate. The active part of this compound is the
diazonium ring. This is a very strong nucleophile. It functions in the stabilization of intermediates.
b. Pyruvate dehydrogenase  decarboxylation of pyruvate
XXIX. The structure of coenzyme A [S29]
a. Another vitamin that’s water soluble is Pantothenic Acid, which is part of the larger molecule: coenzyme A
b. This functions in the carrying of acyl groups. It provides acyl groups for various processes such as: beta
oxidation, pyruvate dehydrogenation, and others
c. It has an adenine nucleotide. This part functions in its recognition by enzymes.
CLASS: 10-11
Scribe: Jordan Heath Taylor VI
8-25-10
Proof: Lee Redditt
Popov
Intro to Metabolism
Page 5 of 5
d. Notice the sulfhydryl group on the terminal end of the carbon chain. This is a high-energy bond like the
gamma phosphate on ATP. It allows for coenzyme A to drive many reactions.
XXX. Enzyme-catalyzed transaminations [S30]
a. The aldehyde group can react with an amine group forming a Schiff base. This allows for a transamination
reaction. The amine group is transferred to a vitamin coenzyme, then given to Ketoglutarate forming
Glutamate in this example.
[End 48:11 mins]