STUDY GUIDE: WEEK 1 (3 hours) OVERVIEW OF THE METABOLIC PATHWAYS

Read.

1. Read Chapter 15 “The Importance of Energy Changes and Electron Transfer and

Metabolism” pages 435-457 of Campbell, and Farrell. Biochemistry 8th Edition (2015)

or other editions.

2. Read pages 91-96 of Chapter 8 “Introduction to Metabolism and Glycolysis” of Ferrier,

Lippincott’s Illustrated Reviews Biochemistry 7th ed. (2017)

Khan academy: https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-energy/

a/atp-and-reaction-coupling

Remember:

Coenzyme: A substance that enhances the action of an enzyme. (An enzyme is a protein that functions
as a catalyst to mediate and speed a chemical reaction). Coenzymes are small molecules. They cannot by
themselves catalyze a reaction but they can help enzymes to do so. It is not active on its own. While
enzymes are proteins, coenzymes are small, nonprotein molecules. Coenzymes hold an atom or group of
atoms, allowing an enzyme to work. Examples of coenzymes include the B vitamins and S-adenosyl
methionine. Examples of coenzymes: nicotineamideadenine dinucleotide (NAD), nicotineamide adenine
dinucelotide phosphate (NADP), and flavin adenine dinucleotide (FAD). These three coenzymes are
involved in oxidation or hydrogen transfer.

Writing Biochemistry (For submission) What does it mean when we say that “In metabolism, ATP is
the universal carrier of biochemical energy?” Discuss your answer in at least 100 words using
appropriate reactions

This generally means that ATP can be thought as the energy currency of cells and living
organism to power several biochemical pathways. One of the main concepts in metabolism is the
coupling of energy-producing reactions (catabolism) and energy requiring reactions (anabolism).
ATP, as by far the most important compound containing essential high energy bond has been the
bank of useful energy. At standard and molecular states our cells energy coupling, in which an
energetically favorable reaction such as the ATP hydrolysis provides energy, which drives the
unfavorable endergonic reaction to spontaneously occur. Since free energy changes of coupled
reactions are additive hence long as the overall ΔG is negative these reactions indeed occur. For
instance, the reaction of glucose and fructose to produce sucrose, an endergonic reaction with a
ΔG =+27 kJ/mol is innately unfavorable under standard condition but coupling it with the
hydrolysis of ATP makes the former reaction thermodynamically possible. This reaction
involves utilization of the energy released in ATP hydrolysis; ΔG =+30 kJ/mol, to produce a
favorable yield of sucrose molecules with a ∆ G=−3 kJ .

Glucose + Fructose↔ C12 H 22 O11 ∆ G=+27 kJ

ATP+ H 2 O ↔ ADP+ P i ∆ G=−30 kJ

Glucose + Fructose+ ATP ↔ C12 H 22 O11+ ADP+ Pi ∆ G=−3 kJ

In the coupling of biochemical reactions, the energy released by one reaction, such as ATP hydrolysis, provides
energy for another

-Both ATP and electric current must be produced when they are needed—by organisms or by a power
plant, as the case may be. The cycling of ATP and ADP in metabolic processes is a way of shunting energy
from its production (by oxidation of nutrients) to its uses (in processes such as biosynthesis of essential
compounds or muscle contraction) when it is needed. The oxidation processes take place when the
organism needs the energy that can be generated by the hydrolysis of ATP.

 The energy that must be supplied for the many endergonic reactions in life processes comes
directly from the hydrolysis of ATP and indirectly from the oxidation of nutrients. The latter
produces the energy needed to phosphorylate ADP to ATP.
 The role of ATP as energy currency in processes that release energy and processes that use
energy.
 In addition to its key role in bioenergetics, ATP can do many other things, especially in the realm
of intercellular communication
 The role of ATP in generating and using energy within cells is a fundamental and well known
fact. Cells produce ATP in their mitochondria and use it to provide energy for their activities,
such as protein synthesis.
 It is less well known that ATP is widely involved in chemical signaling between cells. For
example, during the transmission of nerve signals, ATP is released along with neurotransmitters.

ATP in cells

 An ATP molecule stores energy in the bonds between its three phosphates. The phosphates are
anchored to adenosine, which belongs to the purine class of molecules
 Cells manufacture ATP constantly in their mitochondria, which build it from such raw materials
as protons (H+) derived from glucose that has undergone several stages of processing. Inside
mitochondria ,
1. protons power the addition of a phosphate to adenosine diphosphate (ADP); the
resulting ATP is delivered into the cytoplasm .
 2. Cellular activities such as protein manufacture draw energy from ATP molecules when
the terminal phosphate is released .
3. ADP and free phosphates are then recycled into ATP .

ATP in Neuron Signaling

 During the transmission of nerve signals, ATP is released along with neurotransmitters. It is
hydrolyzed by enzymes to ADP, AMP, and adenosine.
 Specific receptors exist on the surface of receiving cells: P2X receptors for ATP itself, P2Y
receptors for ATP and ADP, and P1 receptors for AMP and adenosine.
 The binding of ATP and its degradation products to their individual receptors sets off a response
within the cell.

Detailed process;

ATP often becomes a signal when a firing neuron releases it from vesicles ,

1. along with neurotransmitter molecules; many nonneuronal cells also release ATP using
vesicles or similar mechanisms.
2. Enzymes soon start breaking ATP down , sequentially removing phosphates to produce ADP,
adenosine monophosphate (AMP) and adenosine.
3. ATP and its breakdown products convey messages by binding to specific receptors on cells .
Two distinct receptor types, called P2X and P2Y, recognize ATP. P2Y receptors also recognize
ADP. AMP and adenosine bind to P1 receptors.
4. As ATP is degraded, signaling by its breakdown products can offset or enhance ATP’s effects;
for example; adenosine may also bind to P1 receptors on the releasing cell, suppressing
further ATP release.

Reviewing Concepts (Self-Assessment).

1. What does it mean when one is said to be a fast metabolizer? A slow metabolizer?

2. The following terms can be used to characterize catabolism and anabolism. Assign

each term to the proper direction of metabolism:

 Reduction reactions Biosynthesis

 Energy input necessary Oxidation reactions
 Energy release Production of ATP
 Convergence of reactions Divergence of reactions
 Cleavage of ATP Degradation

3. Describe the six basic types of chemical reactions encountered in cellular metabolism.

4. Discuss the three major mechanisms for the regulation of metabolism.

5. Discuss the coenzymes in biologically important oxidation-reduction reactions.

6. Describe energy coupling.

7. Define compartmentalization.

8. Describe the structure of coenzyme A (CoA) and its role as a carrier of acetyl or acyl

groups.

9. What is the common structural feature in NAD+, FAD, ATP, and CoA? Do they have any

common biological function?

10.Why is it an advantage to the cell for the mainstream catabolic reactions to converge

to the common intermediate acetyl CoA?

Note that catabolism is a convergent process—that is, a wide variety of molecules are transformed into
a few common end products. By contrast, anabolism is a divergent process in which a few biosynthetic
precursors form a wide variety of polymeric or complex products