Potential Energy: Associated with objects at rest but with the potential to do work.

For example, a
motionless wrecking ball suspended above the ground has potential energy due to its position. Other
examples include water behind a dam or a compressed spring.

Chemical Energy: Stored within the chemical bonds of molecules. When these bonds break, they
release energy, which can be harnessed for various cellular processes. Food molecules contain
chemical energy, which is released during digestion and cellular respiration.

Free Energy

Gibbs Free Energy (∆G): Measures the energy available to do work in a chemical reaction after
accounting for entropy. It quantifies the energy transfer in a reaction.

Exergonic Reactions: Release energy and have a negative ∆G. These reactions are spontaneous and
occur without the addition of energy into the system. Examples include the breakdown of glucose
during cellular respiration.

Endergonic Reactions: Require energy input and have a positive ∆G. The products have more free
energy than the reactants, making these reactions non-spontaneous. Anabolic processes, such as the
synthesis of complex molecules from simpler ones, are endergonic reactions.

Chemical Equilibrium: Most chemical reactions are reversible and can proceed in both directions,
reaching a state of equilibrium where the rates of the forward and reverse reactions are equal. In a
closed system, reactions would reach equilibrium, resulting in insufficient free energy to sustain life.
Living organisms constantly battle against equilibrium and entropy, requiring a constant energy
supply, often derived from sunlight through photosynthesis. Definition: Activation energy (EA) is the
minimum amount of energy required for a chemical reaction to occur. It represents the energy input
needed to transition reactant molecules to a high-energy, unstable state known as the transition
state.

Importance: Even exergonic reactions, which release energy overall, require an initial input of
energy to overcome the activation energy barrier and proceed with their energy-releasing steps.

Transition State: The transition state is a high-energy, unstable state that reactant molecules briefly
enter during a chemical reaction. It is necessary for the breaking and forming of chemical bonds.
 Source of Activation Energy: Activation energy typically comes from heat energy in the
surroundings. Increased heat speeds up molecular motion, increasing collision frequency and force,
and helping molecules reach the transition state.

Rate of Reaction: The activation energy of a reaction determines its rate. Reactions with higher
activation energies proceed more slowly. For example, iron rusting is a slow reaction due to its high
activation energy.

Catalysis: Lowering activation energy is essential for efficient cellular reactions. Catalysts, such as
enzymes, lower activation energy, thereby increasing the rate of reactions. Without catalysis, many
essential cellular processes would occur too slowly to sustain life.d High-Energy Bonds: The two
bonds between the phosphate groups (phosphoanhydride bonds) in ATP are high-energy bonds.
When these bonds are broken through hydrolysis, releasing one phosphate group and forming ADP
(adenosine diphosphate) and inorganic phosphate (Pi), a considerable amount of energy is released.

ATP Hydrolysis: The hydrolysis of ATP into ADP and Pi is an exergonic reaction, meaning it releases
energy. The calculated standard free energy change (∆G°) for this reaction is -7.3 kcal/mol, but under
cellular conditions, it is approximately -14 kcal/mol.

Energy Coupling: ATP hydrolysis energy is coupled with cellular work through processes like
phosphorylation. ATP transfers its phosphate group to other molecules, phosphorylating them and
providing the energy needed for various cellular activities.

Example: Sodium-Potassium Pump: One example of energy coupling using ATP is the sodium-
potassium pump, which transports sodium ions out of the cell and potassium ions into the cell
against their concentration gradients. ATP hydrolysis powers this pump, allowing it to undergo
conformational changes necessary for ion transport.

Importance in Metabolic Pathways: ATP hydrolysis plays a crucial role in metabolic pathways by
providing the energy needed for various reactions. For example, ATP is used to phosphorylate
glucose during glycolysis, initiating the breakdown of glucose into usable energy. Enzyme
Regulation:

Competitive Inhibition: Inhibitor molecules compete with substrates for binding to the active
site, reducing the enzyme's activity.

Noncompetitive Inhibition: Inhibitor molecules bind to allosteric sites on the enzyme, altering its
conformation and reducing substrate binding.

Allosteric Regulation: Allosteric inhibitors or activators bind to allosteric sites, affecting the
enzyme's affinity for its substrate.
 Feedback Inhibition: End products of metabolic pathways act as inhibitors, regulating their own
production by inhibiting key enzymes in the pathway.

Enzyme Cofactors and Coenzymes: Some enzymes require non-protein molecules called cofactors
and coenzymes for optimal activity. Cofactors are inorganic ions, while coenzymes are organic
molecules often derived from dietary vitamins.

Enzyme Compartmentalization: Enzymes are often compartmentalized within organelles in

eukaryotic cells, allowing for efficient regulation and coordination of cellular processes.

Drug Discovery and Enzyme Inhibition: Understanding enzyme function and regulation is essential
for drug development. Many pharmaceutical drugs act as enzyme inhibitors, targeting specific
enzymes involved in disease pathways.

Enzymes play a crucial role in regulating cellular metabolism by facilitating biochemical reactions
with high specificity and efficiency. Their activity is tightly regulated through various mechanisms to
ensure proper cellular function and response to changing environmental conditions.vdv The energy is
used to do

work by the cell, usually when the released phosphate binds to another molecule, thereby activating
it. For example, in the

mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle
proteins. Recall the active

transport work of the sodium-potassium pump in cell membranes. ATP alters the structure of the
integral protein that

functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs
work, pumping ions

against their electrochemical gradients.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an

adenine molecule bonded to a

ribose molecule and to a single phosphate group (Figure 7.3). Ribose is a five-carbon sugar found in
RNA, and AMP is one of the

nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the
formation of adenosine

diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).

7.1 • Energy in Living Systems 181

Figure 7.3 ATP (adenosine triphosphate) has three phosphate groups that can be removed by
hydrolysis (addition of H2O) to form ADP

(adenosine diphosphate) or AMP (adenosine monophosphate). The negative charges on the

phosphate group naturally repel each other,

requiring energy to bond them together and releasing energy when these bonds are broken.

The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively
charged and thus repel one

another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP
and ATP molecules

inherently unstable. The release of one or two phosphate groups from ATP, a process called
dephosphorylation, releases energy.

Energy from ATP

Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is split,
or lysed, and the

resulting hydrogen atom (H+

) and a hydroxyl group (OH-

), or hydroxide, are added to the larger molecule. The hydrolysis of ATP

produces ADP, together with an inorganic phosphate ion (Pi

), and the release of free energy. To carry out life processes, ATP is

continuously broken down into ADP, and like a rechargeable battery, ADP is continuously regenerated
into ATP by the

reattachment of a third phosphate group. Water, which was broken down into its hydrogen atom and
hydroxyl group

(hydroxide) during ATP hydrolysis, is regenerated when a third phosphate is added to the ADP
molecule, reforming ATP.

Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come
from? In nearly every living

thing on Earth, the energy comes from the metabolism of glucose, fructose, or galactose, all isomers
with the chemical formula

C6H12O6 but different molecular configurations. In this way, ATP is a direct link between the limited
set of exergonic pathways of

glucose catabolism and the multitude of endergonic pathways that power living cells.

Phosphorylation

Recall that, in some chemical reactions, enzymes may bind to several substrates that react with each
other on the enzyme,
forming an intermediate complex. An intermediate complex is a temporary structure, and it allows
one of the substrates (such

as ATP) and reactants to more readily react with each other; in reactions involving ATP, ATP is one of
the substrates and ADP is a

product. During an endergonic chemical reaction, ATP forms an intermediate complex with the
substrate and enzyme in the

reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its
energy, to the substrate, a

process called phosphorylation. Phosphorylation refers to the addition of the phosphate (~P). This is
illustrated by the following

generic reaction, in which A and B represent two different substrates: Introduction to Cellular
Respiration

The conversion of energy from one form to another is a fundamental process in both natural and
engineered systems. In living organisms, this transformation is crucial for sustaining life processes.
Just like a power plant converts thermal energy into electrical energy, cells convert energy from
various sources into forms usable for cellular functions. This process is vital for providing energy to
fuel the activities of organisms.

Chapter Outline:

Energy in Living Systems

Glycolysis

Oxidation of Pyruvate and the Citric Acid Cycle

Oxidative Phosphorylation

Metabolism without Oxygen

Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

Regulation of Cellular Respiration

Energy in Living Systems:

Living systems rely on the transfer of electrons in biochemical pathways to produce energy.
Oxidation-reduction (redox) reactions play a central role in these processes. During oxidation, an
electron is removed from a molecule, reducing its potential energy. The electron is then transferred
to another molecule, which becomes reduced, storing the energy. Electron carriers, such as NAD+
and FAD+, shuttle electrons between molecules in metabolic pathways.
ATP in Living Systems:

Adenosine triphosphate (ATP) serves as the primary energy currency in cells. ATP stores energy in its
phosphate bonds, which can be readily broken to release energy for cellular work. Through the
process of hydrolysis, ATP is converted into adenosine diphosphate (ADP) and inorganic phosphate,
releasing energy. The regeneration of ATP from ADP involves phosphorylation, where a phosphate
group is added to ADP, requiring energy typically derived from glucose metabolism.

Substrate-Level Phosphorylation:

During glucose catabolism, ATP is generated directly through substrate-level phosphorylation. This
process involves the transfer of a phosphate group from an intermediate reactant to ADP, forming
ATP. This mechanism provides a rapid source of ATP for cellular energy needs.

Oxidative Phosphorylation: Electron Carriers:

Specialized compounds, such as NAD+ and FAD+, serve as electron shuttles in living systems. These
electron carriers facilitate the transfer of high-energy electrons between molecules in metabolic
pathways. NAD+ and FAD+ play crucial roles in energy extraction from sugars and other organic
compounds.

ATP in Living Systems:

Adenosine triphosphate (ATP) acts as the primary energy currency in cells, analogous to a
rechargeable battery. ATP stores energy in its phosphate bonds, which can be readily broken to
release energy for cellular work. The hydrolysis of ATP into ADP and inorganic phosphate liberates
energy for various cellular processes.

Phosphorylation:

Phosphorylation, the addition of phosphate groups to molecules, is a key mechanism for transferring
energy in cellular processes. Substrate-level phosphorylation directly generates ATP during the
breakdown of glucose, while oxidative phosphorylation, occurring predominantly in mitochondria,
produces the majority of ATP through chemiosmosis. Fat-Soluble Vitamins (A, D, E, and K):

Fat-soluble vitamins are absorbed along with dietary lipids in micelles via simple diffusion.

Micelles are tiny structures formed in the small intestine that contain lipids and fat-soluble
vitamins, allowing for their absorption into the intestinal cells.

It's recommended to consume some fatty foods when taking fat-soluble vitamin supplements to
enhance their absorption.

Water-Soluble Vitamins (B Vitamins and Vitamin C):

Most water-soluble vitamins are also absorbed by simple diffusion.

 Water-soluble vitamins dissolve easily in water and are absorbed directly into the bloodstream
through the intestinal cells.

Exception: Vitamin B12:

Vitamin B12 is a large molecule that requires a specific mechanism for absorption.

In the stomach, intrinsic factor, a protein secreted by gastric parietal cells, binds to vitamin B12.

This complex of vitamin B12 and intrinsic factor moves to the terminal ileum, the last part of the
small intestine.

In the terminal ileum, the complex binds to mucosal receptors on the surface of intestinal cells.

The complex is then taken up by endocytosis, a process by which cells engulf external materials,
allowing for the absorption of vitamin B12 into the bloodstream.Structure of the trp operon:

Coding region: This includes the genes necessary for synthesizing tryptophan. In the trp operon,
there are five genes responsible for encoding enzymes involved in tryptophan biosynthesis.

trp operator: This is a specific DNA sequence where a regulatory protein, called the trp repressor,
can bind.

Low Glucose: Conversely, when glucose levels are low, cAMP levels increase. This allows for the
formation of the cAMP-CAP complex. The cAMP-CAP complex binds to the CAP-binding site on the
lac operon promoter, facilitating RNA polymerase's binding to the promoter region. As a result,
transcription of the lac operon increases, allowing the cell to utilize lactose as an alternative energy
source.

Lactose Level:

Absence of Lactose: In the absence of lactose, the lac repressor protein binds to the lac operator
region. This binding prevents RNA polymerase from accessing the promoter region, leading to low
transcription of the lac operon genes.

Presence of Lactose: When lactose is present, it is converted to allolactose, which acts as an

inducer. Allolactose binds to the lac repressor protein, causing it to undergo a conformational change
that reduces its affinity for the lac operator. As a result, the lac repressor is unable to effectively bind
to the operator, allowing RNA polymerase to initiate transcription of the lac operon genes.

In summary, the levels of glucose and lactose determine the activity of the lac operon:
 Glucose levels regulate the formation of the cAMP-CAP complex, which enhances RNA polymerase
binding to the promoter.

Lactose levels regulate the binding of the lac repressor to the operator, allowing or preventing
transcription of the lac operon genes.. Chromatin Structure:

DNA in eukaryotic cells is organized into chromatin, which consists of DNA wrapped around
histone proteins.

Chromatin structure influences gene expression by regulating access to DNA. Nucleosome

complexes, formed by histones and DNA, control the accessibility of DNA regions to proteins involved
in transcription.

Chromatin Remodeling:

Chromatin remodeling involves changes in the positioning and spacing of nucleosomes along DNA.

Modifications to histone proteins, such as acetylation, methylation, and phosphorylation, affect

the tightness of DNA wrapping around nucleosomes.

These modifications are reversible and can alter the accessibility of DNA regions for transcriptional
machinery.

DNA Methylation:

DNA methylation occurs at specific regions called CpG islands, often found in gene promoter
regions.

Methylation involves adding a methyl group to cytosine nucleotides, which can lead to gene
silencing.

Methylation patterns can be influenced by environmental factors and can affect gene expression
patterns.. Regulation at Multiple Levels:

Eukaryotic cells have multiple levels of gene expression regulation, allowing for fine-tuned control
over gene activity. This regulation occurs at various stages, including transcription, RNA processing,
mRNA transport, translation, and post-translational modification.

Epigenetic Changes:
 Epigenetic changes refer to heritable alterations in gene expression that are not caused by changes
in the DNA sequence itself. Instead, they involve modifications to chromatin structure, such as
chromatin remodeling and DNA methylation.

These changes can influence gene expression patterns by regulating access to the DNA and
modulating the activity of specific genes.

Chromatin Structure and Nucleosome Complexes:

Chromatin consists of DNA wrapped around histone proteins, forming nucleosome complexes.

Nucleosomes control access to DNA regions by regulating the binding of proteins involved in
transcription. The positioning of nucleosomes along the DNA can be dynamically adjusted through
chromatin remodeling, allowing for the opening or closing of chromosomal regions as needed for
transcriptional activity.

Transcriptional Machinery:

RNA polymerase is the enzyme responsible for transcribing DNA into RNA. To initiate transcription,
RNA polymerase requires access to specific DNA regions. Chromatin remodeling allows for the
movement of nucleosomes to expose these regions and facilitate transcription. The inactivation of
one of the two X chromosomes in females during embryonic development involves epigenetic
changes to chromatin. Specifically, one of the X chromosomes becomes highly condensed and
transcriptionally inactive through a process called X chromosome inactivation.

In this context, the impact on nucleosome packing would likely involve the compaction of chromatin
on the inactivated X chromosome. This compaction would result in the close spacing of nucleosomes
along the DNA, making it less accessible for transcription factors to bind. Consequently, gene
expression on the inactivated X chromosome would be turned off due to the tightly packed
chromatin structure.

The epigenetic changes associated with X chromosome inactivation may involve modifications to
histone proteins and DNA methylation, which contribute to the formation of a closed chromosomal
configuration. These modifications signal transcriptional silencing, preventing RNA polymerase and
transcription factors from accessing the DNA and initiating transcription. As a result, the genes on the
inactivated X chromosome remain transcriptionally inactive during subsequent cell divisions.
Transcription Initiation in Eukaryotes:

Similar to prokaryotic cells, transcription in eukaryotes begins with the binding of RNA
polymerase to a DNA sequence upstream of a gene.

However, unlike prokaryotic RNA polymerase, eukaryotic RNA polymerase requires the
assistance of transcription factors to initiate transcription.
 Types of Transcription Factors:

There are two main types of transcription factors that regulate transcription in eukaryotes:

General (or Basal) Transcription Factors: These factors bind to the core promoter region
located upstream of the coding sequence. They assist in the binding of RNA polymerase to the
promoter and the initiation of transcription.

Specific Transcription Factors: These factors bind to regions outside of the core promoter and
interact with the transcriptional machinery to enhance or repress transcriptional activity.

Promoter Region:

The promoter region is located immediately upstream of the coding sequence of a gene.

It can vary in length, with longer promoters providing more space for protein binding and
additional control over transcription.

The core promoter region typically contains specific DNA sequences, such as the TATA box
(consensus sequence: 5’-TATAAA-3’), which serves as the binding site for transcription factor TFIID.

Transcription Initiation Complex:

The assembly of the transcription initiation complex involves the binding of transcription factors,
including TFIID, TFIIB, TFIIE, TFIIF, and TFIIH, to the core promoter region.

These factors help recruit RNA polymerase and facilitate its binding to the promoter, initiating
transcription.

Promoter-Proximal Elements:

Additional binding sites, such as the CAAT box (consensus sequence: 5’-CCAAT-3’) and the GC
box (consensus sequence: 5’-GGGCGG-3’), may be present in the promoter region.

Specific transcription factors can bind to these promoter-proximal elements and regulate gene
transcription.

Cis-Acting Elements:

Transcription factors bind to cis-acting elements located on the same chromosome, just
upstream of the gene they regulate.

These elements play a crucial role in responding to environmental stimuli and initiating
transcription of the corresponding gene. Regulation at Multiple Levels:
 Eukaryotic cells can regulate gene expression at multiple levels, including transcriptional, post-
transcriptional, translational, and post-translational regulation. This multi-level regulation provides
flexibility and fine-tuning of gene expression in response to various internal and external signals.

Epigenetic Changes:

Epigenetic changes refer to heritable alterations in gene expression that do not involve changes in
the DNA sequence itself. Instead, they involve modifications to chromatin structure, such as
chromatin remodeling and DNA methylation.

Chromatin remodeling changes the way DNA is associated with histone proteins, affecting access
to DNA regions by transcription factors and RNA polymerase.

DNA methylation involves the addition of methyl groups to DNA, which can influence gene
expression patterns, often leading to gene silencing.

Nucleosome Dynamics:

DNA is packaged into chromatin, which consists of DNA wrapped around histone proteins to form
nucleosomes. Nucleosomes can slide along DNA to expose or conceal specific DNA regions.

When nucleosomes are closely spaced, transcription factors cannot bind effectively, resulting in
gene expression being turned off. Conversely, when nucleosomes are spaced far apart, transcription
factors can bind, allowing gene expression to occur. Histone Modifications:

Histone proteins can undergo chemical modifications such as phosphorylation, methylation, or

acetylation.

These modifications occur primarily on the "tails" of histone proteins, which protrude from the
nucleosome core.

The addition or removal of chemical groups alters the charge and structure of histones,
influencing their interactions with DNA.

Impact on Chromatin Structure:

DNA is negatively charged, while histones are positively charged. Changes in histone charge
affect how tightly DNA is wound around the histone proteins.

For example, adding acetyl groups to histones reduces their positive charge, loosening their grip
on DNA and allowing for a more open chromatin structure.

Alterations in chromatin structure, such as nucleosome spacing, determine whether specific

DNA regions are accessible for transcription or not.
 DNA Methylation:

DNA can also undergo chemical modification through methylation, where methyl groups are
added to cytosine bases, particularly in CpG islands.

Methylation of DNA is associated with gene silencing, as it can inhibit the binding of
transcription factors and RNA polymerase to the promoter region.

DNA methylation patterns can be influenced by environmental factors and are involved in
processes such as imprinting, where genes inherited from one parent are preferentially expressed or
silenced.

Interplay Between Histone Modifications and DNA Methylation:

Changes in chromatin organization, influenced by histone modifications, can interact with DNA
methylation to regulate gene expression.

Highly methylated DNA regions with deacetylated histones tend to be tightly packed and
transcriptionally inactive.

Epigenetic Regulation:

Epigenetic changes are reversible modifications that can persist through multiple cell divisions
and even across generations.

Chromatin remodeling, driven by histone modifications and DNA methylation, plays a crucial role
in regulating access to DNA for transcription.

Open chromatin configurations allow RNA polymerase and transcription factors to bind to the
promoter region and initiate transcription, while closed configurations silence gene expression. RNA
Polymerase and Transcription Factors:

Eukaryotic transcription requires RNA polymerase, similar to prokaryotic cells. However, eukaryotic
RNA polymerase cannot initiate transcription on its own.

Transcription initiation in eukaryotes involves the assistance of other proteins called transcription
factors.

There are two main types of transcription factors:

General (or basal) transcription factors: These factors bind to the core promoter region of genes
to assist RNA polymerase binding and initiation of transcription.

Overall, RNA stability is a critical aspect of post-transcriptional gene regulation, and it can be
modulated by various factors, including RNA-binding proteins and microRNAs, to finely tune protein
expression levels in the cell. Increased phosphorylation levels of eIF-2, as observed in patients with
neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s, would have a
significant impact on protein synthesis. Phosphorylation of eIF-2 prevents its binding to GTP, leading
to impaired formation of the translation initiation complex and subsequently inhibiting translation.
This means that the initiation of protein synthesis would be disrupted, resulting in reduced
production of proteins necessary for normal cellular functions.

In neurodegenerative diseases, where protein aggregates and misfolded proteins are common
pathological features, impaired protein synthesis due to increased phosphorylation of eIF-2 could
exacerbate cellular dysfunction and contribute to disease progression. Since protein synthesis is
essential for maintaining neuronal function and survival, the impairment of translation initiation can
lead to neuronal degeneration and cognitive decline characteristic of these diseases.

Disease Implications: Dysregulation of these mechanisms can contribute to the pathogenesis of

diseases, including neurodegenerative disorders, highlighting the importance of understanding
protein synthesis regulation in health and disease.