Download I-1 I. Introduction BIOCHEMISTRY = METABOLISM At first you may

I. Introduction
BIOCHEMISTRY = METABOLISM
At first you may be puzzled by this rather extravagant statement that would seem to oversimplify the reality
of living systems. However if we accept that Biochemistry is the description of life in chemical terms and if we equate
life with the existence, growth and survival of an organism, then the metabolic activity of that organism must
provide:
For the survival of the individual:
(A) The processing of foods to yield new cellular material.
(B) The provision of energy to support all biological activities.
For the survival of the species:
(C) The biosynthesis of the nucleic acids (for the transmission of genetic information from parent to
progeny).
However conventional metabolism (A) has acquired a somewhat pedestrian image while the latter two areas of
metabolism have been glamorized with more flamboyant names, such as BioEnergetics (B) and Molecular Biology
(C).
There are two basic resources necessary for a cell to survive. These are:
1) ENERGY. In maintaining its existence a cell consumes prodigious amounts of energy. This energy is
utilized in three major ways:
i). MECHANICAL WORK e.g. the contraction of muscles, locomotion and other physical activity.
ii). ELECTRICAL AND OSMOTIC WORK: a more subtle but undoubtedly much more important for
survival It consists of:
(a) The creation and maintenance of concentration gradients of inorganic ions that are crucial for the
viability of an organism. Typically H+ , Na + and Cl- are pumped out while K+ is pumped in.
(b) The transport of metabolites from one domain of the cell to another against a concentration
gradient.
It is estimated that at least one-third of the energy consumed by a living cell is expended in supporting
electrical and osmotic work. Thus a human that is quiescent (i.e. physically inactive) has a Basal Metabolic Rate of
about 1 kcal/hr per kilogram of body mass; this is a large fraction of a typical day’s calorie intake and much of this
BMR is used for electrical and osmotic work.
iii). CHEMICAL WORK: This is required to Drive Biosynthetic Processes resulting in the formation of
new cellular material. Most biosynthetic reactions are endergonic i.e. they require the input of energy to
proceed to a significant extent.
2). CHEMICAL BUILDING BLOCKS. These are certain elementary organic and inorganic molecules
that serve as the "raw" materials in the production of new cellular matter. Some of them (e.g. sugars, amino acids,
fatty acids) are obtained after rather minimal processing of food while others e.g. pyruvate, acetyl CoA, NADH
(usually after conversion to NADPH) and some tricarboxylic acid cycle (see below) intermediates are only obtained
after foodstuffs are subjected to fairly extensive processing. A particular limitation of mammals is the requirement that
nitrogen be provided in organic-as opposed to inorganic-forms.
The processes that are responsible for providing and consuming these resources are grouped together and
called metabolism. These metabolic processes or pathways proceed in a stepwise manner with only a simple
chemical change occurring at each step. Because of the existence of these intermediates metabolism is often called
intermediary metabolism and the compounds that are formed in these metabolic pathways are called metabolic
intermediates or metabolites.
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Metabolism is conventionally divided into two areas of activity; these are catabolism and anabolism.
Catabolism is the degradative phase of metabolism and consists primarily of those reactions whereby the
highly reduced organic compounds (i.e. containing many -C-H bonds) principally provided by the food we ingest are
degraded to the smaller molecules noted above, together with CO2 and NH3; some of the latter are re-utilized and some
excreted.
(The hierarchy of oxidation levels is methane < methanol < formaldehyde < formic acid < carbon
dioxide. Conversion of one of these to a more oxidized member (on the right) of the series
proceeds with the release of free energy. Thus a carbon compound that is hydrogen-rich is a
better "fuel" than one that is oxygen-rich. For example, the free energy arising from the
combustion of a mole of hexane (C 6H14) = 1000 kcal/mole (1000 Cal) while for glucose
(C6H12O6) it is 700 kcal/mole.)
This degradation is accompanied by the release of chemical free energy and it is an important aspect of
catabolic processes that they proceed in such a way that this chemical free energy is preserved in forms that can be
subsequently re–utilized by the cell. The primary way this is accomplished is by trapping reducing equivalents (i.e. H
or some variant) in the compound NADH (those organisms that possess a membrane bound electron transport chain
also utilize a lipid-soluble quinone called ubiquinol). The reducing equivalents in NADH can be utilized directly for
biosynthetic purposes or can be used to reduce oxygen to water. In this latter process the energy released is preserved in
concentration gradients of protons; these concentration gradients can be subsequently converted to the phosphodiester
bond energy of ATP, a more versatile metabolic "currency".
Catabolism also includes those processes whereby previously synthesized cellular material is broken down
again for subsequent re-use. Most cellular material does not exist forever but continually undergoes cycles of synthesis
and degradation.
The lifetimes of different cellular components are dramatically different. For example, some species of
mRNA have a lifetime as short as a few seconds, while mitochondria persist for a few weeks and red blood
cells typically survive for about half-a-year. Thus living tissue is in a steady-state in which cellular material is
continually being synthesized and degraded.
Anabolism consists of those metabolic processes responsible for the de novo synthesis of cellular material
relying primarily on the raw materials and energy that were produced by the reactions of catabolism.
A simple comparison of catabolism and anabolism is as follows:
Catabolism
Anabolism
Degradative
Synthetic
Oxidative
Reductive
Energy-yielding
Energy-consuming
Large variety of starting
materials
Few, well-defined starting
materials
Few, well-defined end-products.
Large variety of
end-products.
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In summary:
FOOD
Building Blocks + Energy
New Cellular Material
Cellular Activity
The Main Metabolic Pathways
You may have had a chance to inspect a drawing called a metabolic map–a pictorial summary of the
various degradative and synthetic pathways present in a typical living cell. Such a map shows the intermediates present
in each pathway and the manner in which each pathway interacts with the other pathways present in the cell. (An
example can be found in V & V, p. 413.)
These maps are rather intimidating for there are more than 2000 enzymes present in a typical cell - and,
consequently, a comparable number of metabolic steps.
We will not study all of these pathways in this course! Rather we will restrict our attention to certain of
those pathways that form the central reactions of metabolism and that are found in most living systems. Consideration
of those pathways responsible for the production and processing of specialized metabolites that are needed in only
small amounts is the domain of more advanced courses. [By analogy to a highway map we are going to focus on the
Interstate System and ignore state and county roads.]
We will begin with a study of the metabolism of glucose–the most abundant monosaccharide present in the
cell and an acknowledged 'core' compound in metabolism. The degradation of glucose in most organisms proceeds with
the formation of pyruvate (the anion of pyruvic acid, CH3COCOOH) via the action of the glycolytic or sugarsplitting pathway. Glycolysis is a linear pathway.
The fate of pyruvate depends upon a number of considerations which include:
1) Availability of oxygen.
2) The nature of the tissue (e.g. muscle vs. yeast)
3) Whether-or-not there are energy demands upon the organism.
When the organism is inactive the pyruvate is diverted into the synthesis of storage materials such as liver glycogen
(animal starch) and body fat. However an active organism converts the three-carbon pyruvate to an activated two-carbon
species; this is a derivative of acetate called acetyl-CoA. Acetyl CoA is the substrate for the next major metabolic
pathway.
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Proteins
Polysaccharides
Amino Acids
Glycerol, fatty acids
β−Oxidation
Glucose
Fats
Glycolysis
Pyruvate
Acetyl CoA
Citric Acid
Cycle
NADH
Oxidative
Phosphorylation
ATP
O2
NH3
H2O
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CO2
The processing of acetyl CoA occurs by a cyclic reaction sequence alternatively called the Tricarboxylic
Acid Cycle (TCA cycle), Citric Acid Cycle or the Krebs' Cycle (regrettably to be confused with the Krebs’
Urea Cycle, that was actually discovered first). In this cycle the two carbon acetyl portion of acetyl-CoA is completely
oxidized to produce carbon dioxide and water with the production of large quantities of a reduced nucleotide, NADH.
The NADH, together with succinic acid (an intermediate of the TCA cycle), functions as electron donor to
the electron transport system of the mitochondrial inner membrane. The transport of electrons through this
system leads to the synthesis of ATP by means of the activity of the oxidative phosphorylation enzyme
apparatus. The ATP is then utilized either to service the energetic and biosynthetic needs of the cell - or converted into
storage forms such as phosphocreatine. The electron-transfer and ATP-synthesizing enzymes are integrated into the
inner membrane of the mitochondrion, and they depend upon the integrity and properties of that membrane for their
function; consequently the structure and properties of membranes will also be considered in this course.
The following areas of metabolism will be covered in the second half of the semester.
a) When the amount of pyruvate and/or acetyl CoA exceeds that needed to service the cell's energy
needs, these compounds can be converted back to glucose, a process called gluconeogenesis. In this pathway
pyruvate is converted to glucose by a pathway that is similar but not identical to glycolysis (when run in reverse). The
excess glucose produced by gluconeogenesis is not accumulated but polymerized to form starch-which is the normal
storage form of carbohydrate.
Metabolic pathways are essentially irreversible. While most of the individual steps are close to
equilibrium there is always at least one step, usually appearing near the beginning of the
pathway that is practically irreversible. This step is called the committing step for this
pathway. Because of this characteristic the processes of degradation and synthesis cannot
simply be the exact reverse of one-another. For example the pathways for glycolysis and
gluconeogenesis contain three steps in the sequence that are quite different in the forward and
reverse direction. The committing steps exist because they provide a place in the sequence by
which the overall activity of the pathway can be controlled.
b) The second major area of metabolism is the degradation and biosynthesis of fatty acids. These involve
pathways that are spiral. The catabolism of long chain fatty acids proceeds by oxidation and results in splitting the
carbon skeleton of the fatty acid into the same two-carbon fragment that is the product of aerobic glycolysis (acetylCoA); at this point the carbon atoms have lost their identity and their further metabolism follows the pathways
outlined above for glucose.
The biosynthesis of fatty acids begins with acetyl-CoA but, again, the details of the reaction are
significantly different from the oxidative, degradative pathway. (Synthesis occurs in the cytosol, oxidation in the
mitochondrial matrix space.)
c) You will also study selected pathways in the catabolism and synthesis of amino acids and you will
find that the TCA cycle serves as an important staging area for receiving (catabolism) and providing (anabolism)
intermediates that are important in these pathways.
d) Finally you will learn about the metabolism of purines and pyrimidines.
Before we actually embark on the metabolic pathways themselves there is a body of background material to
be covered. This is:
1). A knowledge of the chemistry of carbohydrates.
2). Some of the history of the elucidation of the glycolytic pathway.
Following that we will
3). Review aspects of thermodynamics relevant to a study of metabolism and bioenergetics.
4). Consider the structure and properties of ATP and NAD, molecules that we will meet very
early in this course.
(In this course we will not cover the structure and chemistry of all of the coenzymes and cofactors in one
section. Rather we will deal with them individually as the need arises.)
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There may be time to cover one other important metabolic sequence. This is Photosynthesis, whereby plants and
certain micro-organisms utilize the energy provided by the sun as the driving force to biosynthesize reduced carbon
compounds such as glucose. As you surely know this is the ultimate source of energy for all life processes.
Over the course of these lectures you will find that the individual reactions that occur in metabolic pathways
can be categorized into a small number of reaction types. These are detailed in the following table.
Classification of Types of Biochemical Reactions.
A. Group Transfer
a) Acyl Transfer (from one nucleophile to another) e.g. acetyl CoA synthetase.
b) Phosphoryl Transfer (usually from ATP) e.g. hexokinase.
c) Glycosyl Transfer e.g. UDP-glucose transferase
B. Oxidation-Reduction.
a) Loss or gain of electrons usually with C-H bond cleavage; requires cofactor (NAD, FAD, heme).
C. Elimination, Isomerization and Rearrangements.
a) Elimination (double bond creation). e.g. fumarase.
b1) Isomerization moves H to different atom (aldose <-> ketose) e.g. phosphoglucose isomerase, aconitase.
b2) Racemization moves H on same atom inverting chiral center.
c) Rearrangements (of carbon skeleton) e.g. methyl malonyl CoA mutase
D. Carbon-Carbon Bond Making and Breaking.
a) Breaking.
b) Making.
e.g. Aldolase (reverse of aldol condensation).
e.g. Pyruvate Decarboxylase (eliminates CO2 with chain shortening).
e.g. Citrate Synthase (Claisen condensation).
e.g. Pyruvate Carboxylase (incorporates CO2 with chain lengthening).
By the end of this semester we will have:
•
Studied most of the important metabolic pathways.
•
Learnt about the two remaining major classes of biomolecules (carbohydrates and lipids).
•
Discovered a variety of small molecules that facilitate enzyme-catalyzed reactions.
Coenzymes
NAD, ATP, CoA
Prosthetic groups
FAD, heme, TPP, B12,
biotin, folic acid, FeS clusters, Cu.
•
Seen many examples of the most common biochemical reaction types.
•
Been introduced to the bases of metabolic regulation and cellular physiology.
Our first task will be to acquire some knowledge of the structures and chemical properties of
carbohydrates commonly found in biochemical systems.
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