Fuel and Metabolism

Lecture-1
Steady State

Good Morning every one.

Slide-1: Today we are going to start with new part CMM course, related to biochemistry namely FUEL and
METABOLISM. This part provides you with all basics of internal medicine, basics to understand physiology,
pharmacology and related medical sciences.

Slide-2: poem I wrote for x-Medical students who joined medical school with previous bad experience about
biochemistry. To them biochemistry was a nightmare. My answer (the slide) is become a better clinician, and
to be able to diagnose you need to know and understand biochemistry. TOGETHER WE CAN MAKE IT A BETTER
EXPERIENCE

Slide-3: Fuel and metabolism part is composed of 5 sub-parts: as listed in slide 3 they deal with
BIOENERGETICS: energy production ATP production important property of living beings; Carbohydrate
Metabolism; Lipids and Fats metabolism; Amino acid Metabolism; and finally we will integrate all the
metabolic pathways together. Although here we are going to go through pathways and reactions, our goal is
not to memorize the pathways but to understand how is this pathway regulated and how does it relate to
other pathways and to the overall homeostasis leading to integration of metabolism .

Slide-4: of course each and every single one of you is asking why do we need to study biochemistry? My
answer is I DO NOT WANT YOU TO STUDY . I WANT YOU TO LEARN about you, about the normal you in order
for you to understand the abnormal situation. Keeping in mind there is a lot of biochemistry involved in our
daily life; that unknowingly we practice ; such as the making of: dough (fermentation of flour) , Yoghurt ,
vinegar and wine all are examples of biochemical processes. Moreover Biochemical reactions/ changes
underlie many of our activities. Behind any activity physical. Mental emotional there is a biochemical reaction.
If you walk if you sit, if you laugh or cry, if u love or hate there is a biochemical reaction. So we will learn more
about us, So What exactly are we going to learn?

Slide-5: This is a quite a busy slide covering all what we will learn. this should remain as your companion and
guide throughout the unit. It is true we are going to study each pathway independently but I will emphasize,
pinpointing how these pathways are linked and regulated. Pathways include RNA or DNA Purines and
pyrimidine biosynthesis to nucleotides where R5p (ribose 5-phosphate) and Glucose 6-P that is converted to
glycogen and other monosaccharides. From glucose 6-P it goes to trioses Phosphates (TP) that goes via PEP
and pyruvate to acetyl CoA then to fatty acids (triglycerides , phospholipids, cholesterol , sterols) or ultimately
pyruvate feeds into Tricarboxylic acid cycle . the important take home message is that bio-transformations of
all biomolecules (carbohydrates, lipids, sugars) will converge into 2 common pathways, the heart of
metabolism: tricarboxylic acid cycle (TCA)and oxidative phosphorylation. Both are strictly aerobic processes
and they are at the terminal stage of metabolism where the carbon skeleton of biomolecules gets converted
into CO2; this specifically occurs in TCA ; while oxygen reduction into water and occurs in the last pathway
oxidative phosphorylation with consequent production of energy (ATP) . These 2 pathways are tightly linked
where both will simply accomplish cellular combustion. Recall that combustion is burning of organic
molecules in presence of oxygen to CO2, Water while producing energy. This same process occurs in the cell,
but in 2 pathways: TCA and Oxidative phosphorylation.

Slide-6: the 2 basic dogmas that you need to consider and always remember during this unit are the
following: first Dogma NO ENERGY NO LIFE. All the pathways are induced and mobilized simply to maintain
ATP (energy) level. The cell can tolerate decrease/deficiency in a nutrient but not in energy (ATP). all metabolic
pathways are geared towards energy production. The second dogma is that CARBOHYDRATES MAY BE
CONVERTED INTO FATS but the other way round is not true. Therefore biochemistry deals with living
systems.

What are the properties of a living system??

Slide-7: so what are the attributes of a living system? A living system obeys the physico-chemical laws, the
basic laws of thermodynamics. We are all made of periodic table elements (H,O,N,P,K,Na,Mg,Fe,Cu,Ni.Mo,Cl, F,
Mn, I, Ca…..etc) hence we obey the basic 1st and 2nd laws of thermodynamics. Energy is neither created nor
destroyed but is transformed from one form to another. For ex: the life cycle begins with CO2, & water,
where nitrogen assimilation via photosynthesis (light energy) are converted into carbohydrates, aas, and lipids.
Following ingestion of plants and oxidative pathways all of carbohydrates, lipids and proteins are oxidized to
CO2, water and new form of energy (ATP), chemical energy is generated. From CO 2 to biomolecules then to CO2
A living system is highly organized, precisely controlled and highly regulated. Specific structures within the
cells have evolved for specific function. The cellular compartments for instance, allows different pathways to
occur for ex: oxidation of fats occurs in the mitochondria, whereas synthesis of fats occurs in cytoplasm. the
occurrence of 2 pathways each in one compartment makes regulation possible, in some cases however we
may have 2 opposite pathways occurring in the same compartment and each is regulated differently, such as
glycolysis and gluconeogenesis.
A living system is self reproducing , self regenerating This occurs with utmost fidelity. Example wound
healing, scar reconstruction, involves genes, proteins that operate under strict mechanisms , and regulations
to heal injury
A living system is energy utilizing and synthesizing. We consume chemical energy in the form of ATP, the
advantage of using chemical energy is the fact it can be used isothermally (370C), at a constant temp. Living
cells cannot tolerate deficiency in cellular ATP level (no energy , no life)
a living system is an open system, a dynamic system that depends on efflux and influx . we inhale and exhale,
we drink we excrete, there is always an input and output that is continuously changing , moving in a controlled
manner. A dynamic system is an open system that survives on 2 contradictory currents or conflicting forces
that are balanced and in harmony. Anabolism and catabolism may take place in same compartment but
reversibly regulated. What is the importance of a dynamic system? It is continuously changing it looks the
same but it is not. We are not the same person every minute every second. Our cells are shed and new cells
are synthesized a dynamic system appears to be constant but it is not. Think of our body like a tank of water
which has water inlet and outlet flowing water in and out at a constant rate. If you add ink to the tank of
water, the color will fade away with time indicating the water is changing although the level remains the
same.

Slides 8-9: So a living system is an open and dynamic system , a flexible system that interacts and responds
to environmental factors by flexible I mean it may undergo minor fluctuation, changes but will always go back
to normal. If you eat chocolate the blood sugar will immediately rise but after half an hour (normal person) the
blood glucose level is re-established, and will go back to normal maintaining homeostasis and steady state.
Every intermediate in our cells is in steady state. That is it adapts, recycles back to steady state
concentration where rate of formation from different pathways is equal to the rate of breakdown.
Reactions maintaining homeostasis or SS involve both irreversible and reversible reactions . This IS NOT
EQUILIBRIUM . equilibrium is a closed system involving only reversible reaction with Keq that is constant
doesnot change. a steady state concentration however, can transiently change then goes back to normal or
basal level . a reaction at equilibrium has a ∆G = zero, incapable of doing work, whereas reactions in steady
state has ∆G# zero indicating it is capable of doing work. Take home message: living systems are open,
dynamic , not at equilibrium, rate of formation = rate of consumption , capable of doing work, responds to
environmental changes may change transiently but return to the basal level. How do we know it is a
dynamic system? what experimental evidence supports the dynamic system?

Slides10-11: Experimental evidence in support of living system being dynamic came from schoenheimer
expt and our daily ATP requirement . in slide 11 Rudolph schoenheimer, a pathologist in 1930 proposed the
idea that we continuously undergo degradation and synthesis of biomolecules while maintaining steady
state concentration (initially his idea was rejected by scientific community, but turned out correct ). To prove
the point he did the following expt. He fed mice deuterated water ( heavy water D 2O) for one month after
which mice were sacrificed and different intermediates and biomolecules were isolated and tested for the %
of incorporated deuterium, if any. Should our bodies be simply a black box, then deuterated water will be
excreted as is with being incorporated. Of the heavily labeled compounds identified were the fatty acids
palmitic acid and stearic acid, likewise the amino acids glycine and serine . on the other hand slightly
labeled compounds included the fatty acid linoleic and the aa valine. The fatty acids palmitate and stearate
as well as amino acids glycine and serine are non-essential fatty acid and aminoacids, respectively meaning
they are synthesized in the body from simple intermediates (involving elimination reduction by addition of
D2 or hydration adding D2O) which explains why they were heavily labeled. As far as linoleic and valine
both are essential and cannot be synthesized hence minimal D- label detected may be attributed to
exchange reactions involving reversible H-deuterium exchange at NH 2, COOH sites
In 1940 theory of dynamic state of the cell was established.

Slide-12: the second evidence was suggested from calculating our daily requirement of ATP. The free energy
change released from ATP hydrolysis is 7 Kcal/mole. If you estimate the amount of calories needed by an
adult/day to be 1000 KCal, this will be equivalent to 140 moles of ATP (1000/7 moles of ATP). An ATP MWT
is around 500 g/mole which means the mass of ATP needed is 500 x 140=70000g or 70 Kg. More than your
own body weight, suggesting that ATP is not stored but is continuously being synthesized and consumed
dynamically to meet cellular needs and requirements. The ATP as we shall see in coming lectures is
generated by oxidative phosphorylation which carry on the oxidation of the 2 reducing cofactors NADH and
FADH2.

Side 13-14 : ATP is a molecule composed of adenine (base) , Ribose (sugar) and 3 phosphate residues linked by
anhydride bonds. The anhydride bond is quite reactive center. The hydrolysis of ATP to ADP and Pi will
generate more stable products and energy that can be coupled to other reactions. ATP is termed as high
energy molecule. Keep in mind that High energy is not synonymous with stability, ATP is very reactive tends
to hydrolyze, it is unstable molecule. A Favorable reaction is one which yields a more stable product. In the
following table a list of biochemical are mentioned with the amount of energy generated from their
hydrolysis indicated (structures are presented on slide 14 do not memorize but look at their structures). In
general compounds belong to class of : phosphoanhydrides (ATP) , including mixed anhydride ( anhydride
made of phosphoric acid and organic acid) , guanidino phosphates ( creatine P later ), phospho enols(PEP in
glycolysis), and thio esters. Please compare the amount of energy generated from their hydrolysis.We are
going to see all these molecules in future lectures just know the general classes and the importance of these
compounds in driving reactions that are endergonic (coupled ) or in phosphorylation of ADP into ATP

Slides 15-16: The 2 slides are to refresh your memory about bioenergetics of the cell. the Gibbs free enegy
change of a reaction depends on enthalpy change ( exothermic ∆H <0, Endothermic ∆H > 0 ) and entropy (∆s
>0 spontaneous , more disorder) . Remember the second law of thermodynamics states that a spontaneous
process increases entropy of universe (∆S>0), more disorder
If Gibbs free energy change is 0 it is equilibrium no work, while when ∆G <0 it is spontaneous and it is constant
for a reaction regardless of the path (S going into P).
In addition slide -16, the free energy change is also related to the `keq of the reaction if Keq is <1 meaning C
and D concentration are low, the change in free energy will be +ve. While when Keq>1, meaning more of C
and D then free energy change is going to be negative and spontaneous.

Slide-17, 18: in fuel and metabolism we are going to move quite rapidly with pathways. You may think
biochemistry is simply to memorize structures and study by heart. My advice you do not need to memorize,
you simply need to familiarize yourself with the structures identify the functional groups in each molecule
which dictate the types of reactions these groups undergo .
Let us consider for example a simple molecule at the heart of different pathways; pyruvate. What are the
functional groups in a pyruvate? There are 3 functional groups; COOH, Carbonyl (alpha keto) and alpha H that
is acidic ( generating a carbanion, a nucleophilic center) the possible reactions that this molecule undergoes
will yield almost most of the important biochemicals.
Decarboxylation : pyruvate will become acetyl CoA. In turn can be converted into fatty acids and cholesterol
Transamination : alanine typical reaction that yield all non-essential aa
Reduction of keto of pyruvate: lactate. very important reaction with important clinical relevance in many
disorders
Carboxylation at the alpha H carbanion center: oxaloacetate. Oxaloacetate can be reduced …..malate or it
may undergo transamination to form aspartic acid.
Pyruvate can be converted to glucose and vice versa.
My advice is to look for the possible transformation occurring in the molecule this will guide and allow you to
predict, rather than memorize pathways, the reactions that will take place as well as the type of reaction.
 On your moodle there is a problem to solve on the advantage of having an open system in maintaining steady
state.