CHAPTER 6 – Single circular DNA molecule present
BIOCHEMICAL ENERGY PRODUCTION near center of the cell called
By Anacita Albos nucleoid.
23.1 METABOLISM • Eukaryotic Cell: Multi-compartment cell
Sum total of all chemical reactions in a living – DNA is present in the membrane
organism. enclosed nucleus.
Metabolism will provide the source of – Cell is compartmentalized into
energy we need for all our activities such as cellular organelles.
thinking, moving, breathing, walking, – ~1000 times larger than bacterial
talking, etc. cells.
Energy is also needed for many of the Schematic Representation of a Eukaryotic Cell
cellular processes such as protein synthesis,
DNA replication, RNA transcription and
transport across the membrane, etc.
Catabolism and Anabolism
• Catabolism: All metabolic reactions in which
large biochemical molecules are broken
down to smaller ones
– Usually, energy is released in these
reactions.
– Example: Oxidation of glucose
Eukaryotic Cell Organelles and their Function
• Anabolism: All metabolic reactions in which
• Nucleus: DNA replication and RNA synthesis
small biochemical molecules are joined to
• Plasma membrane: Cellular boundary
form larger ones
• Cytoplasm: The water-based material of a
– Usually require energy.
eukaryotic cell
– Example: The synthesis of proteins
• Mitochondria: Generates most of the
• Metabolic Pathway: Series of consecutive
energy needed for cell.
biochemical reactions used to convert a
• Lysosome: Contain hydrolytic enzymes
starting material into an end product.
needed for cell rebuilding, repair, and
• There are two types of metabolic pathways.
degradation.
– Linear
• Ribosome: Sites for protein synthesis.
– Cyclic
Mitochondria
• The major pathways for all forms of life are
• An organelle that is responsible for the
similar:
generation of most of the energy for a cell:
– Outer membrane: Permeable to
small molecules: 50% lipid, 50%
protein
– Inner membrane: Highly
impermeable to most substances:
20% lipid, 80% protein
23.2 METABOLISM AND CELL STRUCTURE – Inner membrane folded to increase
• Knowledge cell structure is essential to the surface area.
understanding of metabolism. – Synthesis of ATP occurs.
• Prokaryotic Cell: Single compartment 23.3 Important Intermediate Compounds in
organism Metabolic Pathways
– No nucleus -- found only in bacteria. • Adenosine Phosphates (AMP, ADP, ATP,
cAMP)
• Monophosphate (AMP): one phosphate – Flavin subunit is the active form –
group accepts and donates electrons.
Phosphate-Ribose-Adenine – Ribitol is a reduced form of ribose
• Diphosphate (ADP): Two phosphate groups sugar.
Phosphate-Phosphate-Ribose-Adenine
• Triphosphate (ATP): Three phosphate
groups
Phosphate-Phosphate-Phosphate-Ribose-
Adenine
• Cyclic monophosphate (cAMP): Cyclic
structure of phosphate Cellular Reaction
• AMP: Structural component of RNA • A typical cellular reaction in which FAD
• ADP and ATP: Key components of metabolic serves as oxidizing agent involves
pathways conversion of an alkane to an alkene
• Phosphate groups are connected to – FAD is oxidized form
AMP by strained bonds which – FADH2 is reduced form
require less than normal energy to – In enzyme reactions FAD goes back
hydrolyze them. and forth (equilibrium) from
- Phosphoanhydride bond is a chemical bond oxidized to reduced form.
formed when 2 phosphate groups react with each • NAD+: coenzyme
other, and a water molecule is produced • NADH is reduced form
ATP + H2O ADP + PO43- + Energy • 3 Subunit stucture:
ADP + H2O AMP + PO43- + Energy – Nicotinamide - ribose - ADP
Overall Reaction: ATP + 2H2O AMP + 2 – 6 Subunit structure: Nicotinamide --
PO43- + Energy ribose -phosphate --phosphate -
The net energy produced in these reactions is used ribose – adenine
for cellular reactions. • A typical cellular reaction in which NAD+
• In cellular reactions ATP functions as both a serves as the oxidizing agent is the oxidation
source of a phosphate group and a source of a secondary alcohol to give a ketone.
of energy. • NAD+: coenzyme
– E.g., Conversion of glucose to • NADH is reduced form.
glucose-6-phosphate Coenzyme A
• A derivative of vitamin B
• Three Subunit Structure:
– 2-Aminoethanethiol - pantothenic
acid - phosphorylated ADP
Role of Other Nucleotide Triphosphates in • Six Subunit structure:
Metabolism – 2-Aminoethanethiol - pantothenic
• Uridine triphosphate (UTP): involved in acid -phosphate - phosphate
carbohydrate metabolism phosphorylated ribose - adenine
• Guanosine triphosphate (GTP): involved in • Active form of coenzyme A is the sulfhydryl
protein and carbohydrate metabolism group (-SH group) in the ethanethiol subunit
• Cytidine triphosphate (CTP): involved in lipid of the coenzyme.
metabolism • Acetyl-CoA (acetylated)
Flavin Adenine Dinucleotide (FAD)
• A coenzyme required in numerous
metabolic redox reactions
Classification of Metabolic Intermediate
Compounds
• Metabolic intermediate compounds can be
classified into three groups based on their
functions.
23.5 High-Energy Phosphate Compounds
• Several phosphate containing compounds
found in metabolic pathways are known as
high energy compounds.
• High energy compounds have greater free
energy of hydrolysis than a typical
compound:
– They contain at least one reactive
bond -- called strained bond
– Energy to break these bonds is less
than a normal bond -- hydrolysis of
high energy compounds give more
energy than normal compounds
– More negative the free energy of
hydrolysis, greater the bond strain
– Typically the free energy release is An Overview of Biochemical Energy Production
greater than 6.0 kcal/mole • Energy needed to run human body is
(indicative of bond strain) obtained from food.
– Strained bonds are represented by • Multi-step process that involves several
sign ~ (squiggle bond) different catabolic pathways
Free Energies of Hydrolosis of Common • There are four general stages in the
Phosphate-Containing Metabolic Compounds biochemical energy production process:
– Stage 1: Digestion
– Stage 2: Acetyl group formation,
– Stage 3: Citric acid cycle
– Stage 4: electron transport chain
and oxidative phosphorylation,
• Each stage also involves numerous
reactions.
Stage 1. Digestion
• Begins in mouth (saliva contains starch
digesting enzymes), continues in the
stomach (gastric juice), completed in small
intestine:
– Results in small molecules that can
cross intestinal membrane into the
blood
• End Products of digestion: the reduced coenzymes FADH2 and NADH
– Glucose and monosaccharides from are produced
carbohydrates • Also know as tricarboxylic acid cycle (TCA)
– Amino acids from proteins or Krebs cycle:
– Fatty acids and glycerol from fats – Citric acid is a tricarboxylic acid –
and oils TCA cycle
• The digestion products are absorbed into – Named after Hans Krebs who
the blood and transported to body’s cells elucidated this pathway
Stage 2. Acetyl Group Formation • Two important types of reactions:
• The small molecules from Stage 1 are – Oxidation of NAD+ and FAD to
further oxidized. produce NADH and FADH2
• End product of these oxidations is acetyl – Decarboxylation of citric acid to
CoA produce carbon dioxide
• Involves numerous reactions: – The citric acid cycle also produces 2
– Reactions occur both in cytosol ATP by substrate level
(glucose metabolism) as well as phosphorylation from GTP
mitochondria (fatty acid • Summary of citric acid cycle reactions:
metabolism) of the cells. Acetyl CoA + 3NAD+ + FAD + GDP + Pi + 2H2O
Stage 3. Citric Acid Cycle 2CO2 + CoA-SH + 3NADH + 2H+ + FADH2 + GTP
Takes place in inside the mitochondria.
First intermediate of the cycle is citric acid –
therefore designated as Citric acid cycle.
In this stage acetyl group is oxidized to
produce CO2 and energy
The carbon oxide we exhale comes
primarily from this stage.
Most energy is trapped in reduced
coenzymes NADH and FADH2
Some energy produced in this stage is lost in
the form of heat.
Stage 4. Electron Transport Chain and Oxidative
Phosphorylation
Takes place in mitochondria.
NADH and FADH2 are oxidized to release H+
and electrons.
H+ are transported to the inter-membrane
space in mitochondria. Reactions of the Citric Acid Cycle
Electrons are transferred to O2 and O2 is Step 1: Formation of Citrate
reduced to H2O. a. Condensation of acetyl CoA and
H+ ions reenter the mitochondrial matrix oxaloacetate to form citryl CoA catalyzed by
and drive ATP-synthase reaction to produce citrate synthase.
ATP. b. Hydrolysis of the thioester bond in Citryl
ATP is the primary energy carrier in CoA to produce CoA-SH and citrate.
metabolic pathways. Step 2: Formation of Isocitrate
23.6 The Citric Acid Cycle Citrate is converted to its isomer isocitrate
• Citric acid cycle: A series of biochemical catalyzed by aconitase that involves a dehydration
reactions in which the acetyl portion of then followed by hydration where –OH group in
acetyl CoA is oxidized to carbon dioxide and citrate is moved to a different carbon atom.
Step 3: Oxidation of Isocitrate and Formation of
CO2: involves oxidation–reduction as well as
decarboxylation catalyzed by isocitrate
dehydrogenase.
a. The alcohol group in isocitrate is oxidized to
a ketone (oxalosuccinate) by NAD+ releasing
2 hydrogens.
b. One Hydrogen and two electrons are
transferred to NAD+ to form NADH, and
the remaining Hydrogen is released.
c. The oxalosuccinate remains bound to the
enzyme and undergoes decarboxylation (loses
CO2).
Step 4: Oxidation of Alpha-Ketoglutarate and
Formation of CO2
The second oxidation reaction which
involves one molecule of NAD+, CoA—SH,
and alpha-ketoglutarate catalyzed by alpha-
ketoglutarate dehydrogenase complex. The
products formed are CO2, NADH, and
Succinyl CoA.
Step 5: Thioester bond cleavage in Succinyl CoA
and Phosphorylation of GDP.
a. Succinyl CoA is converted to succinyl
phosphate (a high energy phosphate
compound) and formed CoA-SH
b. The phosphoryl group in succinyl phosphate
is transferred to GDP to produced GTP and
succinate.
The entire reaction is catalyzed by succinyl-
CoA synthetase.
Step 6: Oxidation of Succinate
In this step 2 Hydrogen atoms are
released from succinate to produce
fumarate, (a C4 species with a trans
double bond) and FADH2.
The oxidizing agent is FAD and the enzyme
involve is succinate dehydrogenase.
Step 7: Hydration of Fumarate
The enzyme fumarase catalyzes the
addition of water to the trans double
bond of fumarate to produced malate.
Step 8: Oxidation of L-Malate to Regenerate
Oxaloacetate
