CELLULAR METABOLISM

Overview of Metabolism
 Metabolism is defined as the entire set of life-sustaining chemical reactions that
occur in organisms.
 These reactions number in the thousands and include reactions such as those
responsible for getting energy from food, processing and removal of waste, building
up muscles, growth, photosynthesis in plants, cell division, and reproduction. The
entire set of metabolic reactions is organized into smaller sets of sequential
reactions called metabolic pathways.
 Many of the reactions in metabolic pathways require enzymes; therefore, organisms
can control (accelerate or suppress) metabolic pathways, according to their current
needs, by upregulating, downregulating, inhibiting, or activating one or more of the
enzymes involved in the pathway
CELLULAR METABOLISM
 What is metabolism?
- How cells acquire, transform, store and use
energy
- Study reactions in a cell and how these
processes are coordinated and regulated

 Metabolic pathways can be linear, branched, cyclic or spiral

Catabolism and AnaBolism

 Metabolic pathways can usually be classified as catabolic (catabolism) or anabolic
(anabolism).
 Catabolic pathways involve the breakdown of larger organic compounds into smaller
compounds.
 Anabolic pathways involve biosynthesis of larger organic compounds from smaller
ones.
 An ultimate goal of these reactions is to convert the chemical potential energy
contained in food into chemical potential energy in the form of ATP.
CATABOLISM and ANABOLISM
 - CATABOLISM: Degradative Pathway

 Generating energy from macronutrients

 Formation of NADH, FADH2 and ATP
 § NADH and FADH2 are used to make ATP
 - ANABOLISM: Biosynthesis
o Synthesizing molecules and polymers that make up the cell
 § Uses NADPH, FADH2 and ATP
Catabolism and Anabolism

THE ATP ENERGY CYCLE

• Energy derived from metabolic fuels is largely recovered in the form of ATP
• Pathways of catabolism release free energy that is captured as ATP
- ATP – adenosine triphosphate
o Main source of energy for the body
o Not stored but used up rapidly and resynthesized
o Common to both aerobic (with oxygen) and anaerobic (without oxygen) organisms
o Phosphoanhydride bonds are energy rich – release energy when broken
Metabolism Proceeds by Discrete Steps
 Multiple-step pathways permit control of energy input and output
• Catabolic multi-step pathways provide energy in smaller stepwise amounts
• Each enzyme in a multi-step pathway usually catalyzes only one single step in the
pathway
•Control points occur in multi-step pathways: Regulation

 Regulation by Reversible Phosphorylation

• Protein kinases phosphorylate enzymes (+ ATP)
• Protein phosphatases remove phosphoryl groups
- Metabolism is highly regulated to permit organisms to respond to changing conditions
and most pathways are irreversible

Metabolic Fuels
 Three major nutrients consumed by mammals:
(1) Carbohydrates - provide energy
(2) Proteins - provide amino acids for protein synthesis and some energy
(3) Fats - triacylglycerols provide energy and also lipids for membrane synthesis

Three Stages of Metabolism

Catabolism
I. Breakdown of Macromolecules into Building Blocks
- Virtually no useful energy is released
- Preparing substrates for next stage
 II. Amino acids, Fatty acids and monosaccharides are OXIDIZED to a common
intermediate
- Common intermediate = ACETYL-CoA (acetyl coenzyme A)
- All building blocks converge to same pathway
- Some energy is released also small amount of energy is used

III. Acetyl-CoA enters the TCA CYCLE

- Oxidized further to CO2 – the end product of aerobic carbon metabolism
- Reduced NADH and FADH2 formed give up their electrons (are oxidized!) and the
electrons are transported through proteins and other molecules to O2 which is reduced
to water
- This produces a proton flow and a transmembrane potential
- The energy potential across the membrane is coupled DIRECTLY to ATP synthesis from
ADP and Pi. ADP + Pi === ATP

• Processes called: ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION

CHEMISTRY OF METABOLISM

Oxidation-Reduction Reactions
 REACTIONS OF CATABOLISM ARE OXIDATIVE!
• Also known as REDOX reactions
• Amino acids, monosaccharides and
lipids are oxidized in the catabolic
pathways
• These substrates are relatively reduced
substrates (sugars, fats)
• Oxidizing agent - accepts electrons, is
reduced
• Reducing agent - loses electrons, is oxidized

THE COENZYMES INVOLVED IN METABOLISM

A coenzyme is a species that must bind to an enzyme in order for the enzyme to function.
• In most cases, a coenzyme is actually one of the substrates (reactants) in the catalyzed
reaction.
• The reason that certain substrates are also referred to as coenzymes is that these
substrates are common substrates in many different enzymatic reactions in which they
 donate electrons, atoms, or groups of atoms to other substrates, or accept electrons,
atoms or groups of atoms from other substrates.

 The five group-transfer coenzymes that are central to the

metabolism of food, along with the species each transfers
are listed in the table on the right.

Phosphoryl Group-Transfer Coenzymes: ATP and ADP

 ATP and ADP are classified as coenzymes because they are involved in the transfer of
phosphoryl groups (PO3-) in many different enzymatically catalyzed reactions.
 When a compound gains/accepts a phosphoryl group in a reaction, we say that the
compound became “phosphorylated.”
 When a compound loses/donates a phosphoryl group in a reaction, we say that it was
 “dephosphorylated.”

ATP and ADP

 ATP and ADP are interconverted by the transfer
of a phosphoryl group,
 Adding a phosphoryl group to ADP produces
energy.
 • Removing a phosphoryl group from ATP
consumes energy
 ATP is often formed by the reaction of ADP with
hydrogen phosphate (HPO 42-) and an H+ ion,

 Energy is released from ATP

when it is converted to ADP.
This energy is used by
organisms to drive energy-
requiring reactions or physical
processes that would
otherwise not occur
spontaneously.
 One way that energy can be
released from ATP is by reacting it
with H2O to form ADP, inorganic
phosphate, and an H+ ion. Although
this reaction is spontaneous (ΔG is
negative), the reaction rate is quite
slow, therefore organisms employ enzymes in order for the reaction to proceed at a
useful rate.
 The chemical equation for this reaction is shown below.
 Another way that organisms extract energy from ATP is to “energize” organic
compounds by transfer ring a phosphoryl group directly to the compound.
  In this reaction, ATP is dephosphorylated and an organic compound is phosphorylated,
as shown in the reaction above
Electron-Transfer Coenzymes and Their Role as Oxidizing and Reducing Agents
 A reduction occurs when a hydride ion forms a
bond with an organic compound.
 Many of these reactions involve the transfer of
an electron by way of the hydride ion (H:-).
 For example, aldehydes or ketones are reduced
when a hydride ion forms a bond with them.
 Electron-Transfer Coenzymes and Their Role as
Oxidizing and Reducing Agents
 An oxidation occurs when a hydride ion (H:-) and
an H+ ion are removed from an organic compound.
 For example, 2o alcohols can be oxidized to
ketones, as shown in the chemical equation below.

NAD+
 Nicotinamide adenine dinucleotide (NAD+) and flavin
adenine dinucleotide (FAD) are classified ascoenzymes
because they are common substrates, involved in the
transfer of phoshoryl group, in many different
enzymatically catalyzed reactions.
 The
structural
formula of
NAD+ is
shown on the left. NAD+ contains two
nucleotide residues. One of the
nucleotides has an adenine base, and
the other contains a nicotinamide
base.
 When NAD+ accepts a hydride ion
from another species, it is reduced to
NADH.
 NADH is referred to as a reduced form of the coenzyme.
 The reduction of NAD+ requires energy.
 When NADH donates a hydride ion (to another species) it is oxidized to NAD+.
 NAD+ is referred to as the oxidized form of the coenzyme
 Oxidation of NADH releases energy.

 The oxidation of an organic compound using NAD+

as the oxidizing agent:
  In this reaction, malate is oxidized and NAD+ is reduced

Biological Oxidation of Alcohol

How Does NAD+ oxidize a substrate

Glyceraldehyde 3- phosphate uses NAD+ to oxidize substrate

How does NADPH reduce a substrate?

FAD (Flavin Adenine di Nucleotide)

ribitol adenine
 When FAD accepts a hydride ion from
another species (and an H+ from
solution), it is reduced to FADH2.
 The reduction of FAD requires energy.
 FADH2 is oxidized to FAD by donating
two electrons (and two H+ ions) to other
species.
 The oxidation of FADH2 releases energy.

 FAD is used in some oxidations that involve carbonyl compounds

Mechanism proposed for the FAD catalyzed oxidation

ACYL-GROUP TRANSFER COENZYME: COENZYME A

 Coenzyme A is classified as a coenzyme because it is involved in the transfer of
an acyl group in many different enzymatically
catalyzed
reactions.
 An acyl
group
consists of

a carbonyl group bonded to an organic

group (R), as shown on the right.
 When coenzyme A (H-CoA) accepts an
acyl group, the acyl group replaces the
left-most hydrogen in the coenzyme A
structure.

 Acetyl groups are donated and accepted by coenzyme A, as shown.

The Organic chemistry of Coenzymes, Compounds derived from Vitamins

VITAMINS
 A vitamin is a substance needed in a small amount for normal body function that the
body cannot synthesize.
 Many enzymes cannot catalyze a reaction without the help of a cofactor
  Some cofactors are metal ions, while others are organic molecules. Many enzymes
cannot catalyze a reaction without the help of a cofactor . Some cofactors are metal
ions, while others are organic molecules.
 Cofactors that are organic molecules are called coenzymes . Coenzymes are derived
from organic compounds commonly known as vitamins.
 Some coenzymes function as oxidizing and reducing agents,some allow electrons to be
delocalized, some activate groups for further reaction, and some provide good
nucleophiles or strong bases needed for a particular reaction.

The absence of thiamine in the diet causes

a disease called beriberi, which damages the
heart, impairs nerve reflexes, and in extreme
cases causes paralysis

Vitamin B1. The vitamin needed for Acyl –group TraNSFER

Mechanism for the reaction catalyzed by pyruvate decarboxylase

VITAMIN H: The vitamin needed for Carboxylation of an alpha -carbon
 Biotin (vitamin H) is an unusual vitamin
because it is synthesized by bacteria
that live in the intestine. Consequently,
biotin does not have to be included in
our diet, and deficiencies are rare.
Biotin deficiencies, however, can be
found in people who maintain a diet
high in raw eggs.
Biotin

Mechanism for the reaction catalyzed by acetyl –CoA carboxylase

vitamin B 6 deficiency causes

anemia; severe deficiencies
can cause seizures and death.

Vitamin B6: The Vitamin needed for Amino acid transformations

PLP catalyze certain reactions of amino acids: decarboxylation, transamination, racemization, C a
— Cb bond cleavage, and a , b -elimination Humans must obtain all their vitamin B from their
12

diet, particularly from meat. A deficiency causes

pernicious anemia. Because vitamin B is needed in
12

only very small amounts, deficiencies caused by the

consumption of insufficient amounts of the vitamin
Vitamin B12: The vitamin needed for certain Isomerizations
are rare but have been found in vegetarians who eat
no animal products.

Enzyme-catalyzed reactions that require coenzyme B12 A tetrahydrofolate (THF)

coenzyme is required by
enzymes that catalyze the
transfer of a group containing
Folic Acid: The vitamin needed for one- carbon Transfer

Vitamin K: The vitamin needed for Carboxylation of glutamate

 Vitamin K is required for proper blood clotting.
 Vitamin K is found in the leaves of green plants.
 Deficiencies are
rare because the
vitamin is also
synthesized by
intestinal bacteria.
 Vitamin KH2 (the
hydroquinone of
vitamin K) is the
coenzyme form of
the vitamin
 Vitamin KH2 is
required by the
 enzyme that catalyzes the carboxylation of the alpha -carbon of a glutamate side
chain.

Group Transfer Reaction:

 Group Transfer Reaction:
oPhosphorylation is one of the most common group
transfers
 Usually the first step in nutrient entering metabolism
 Glucose gets into cells via glucose transport proteins in the
cell membrane
 Phosphorylation of glucose inside cells adds charge and
prevents glucose from exiting
 Kinases are the subclass of transferases that catalyze
ophosphorylation

Isomerization and Rearrangement Reactions

- Two kinds of chemical transformations:
1. Intramolecular hydrogen atom shifts
a. Results in changing location of double bonds
2. Intramolecular rearrangement of functional groups (b)

Hydrolysis Reactions
- Water is used to split a molecule into TWO distinct
molecules
- ESTER HYDROLYSIS: Hydrolytic release of FA from TAG
- AMIDE HYDROLYSIS: Peptidase reaction; Cleaving
peptides into amino acids
- GLYCOSIDIC BOND HYDROLYSIS: Glycosidic bonds in
sugars hydrolyzed by glucosidases
- Opposite of nutrient formation which releases water
via dehydration reactions
- Recall lipid and disaccharide formation – Lost water in
those reactions

Non-hydrolytic Cleavage Reactions:

 - Molecules split WITHOUT use of
o water
o Most prevalent are carbon-carbon
o cleavages
o Enzymes called LYASES
 o May also include:
 Addition of functional groups to double
o bonds
 Enolase: water removed to form the
o double bond (b)
 Reverse of aldolase : Addition of
o Dihydroxyacetone phosophate to
carbonyl of glyceraldehydes 3-
o phosphate to make fructose 1,6-
bisphosphate (a)000

Bond Formation Using Energy of ATP Combination of acetyl-CoA and OAA to make citryl-CoA

 Enzymes that catalyze the joining of

two separate molecules using the
energy from ATP hydro lysis
 - For example, ligases and synthetases
 - Carbon – carbon bonds formed by
reaction of stabilized carbanion with the carbonyl groups of ketones, esters or CO 2
 - Carbanions are stabilized by the presence of electron-withdrawing groups such as acyl
groups. Inductive withdrawal of electrons or resonance stabilization of the negative charge.

REACTION EXAMPLES:
 Carboxylation of pyruvate to make oxaloacetate

Reactions types can be combined in a single metabolic step:

THERMODYNAMICS OF METABOLISM
 Overall process of catabolism RELEASES energy
 Overall process of anabolism REQUIRES energy input
 How do we define amount of energy?
  The quantity of usable energy (chemical potential) in a reaction is called the Gibbs Free
Energy (ΔG).
 ΔG is the difference between the energy contained in the products of a reaction and the
reactants:
 ΔG = (energy of products) - (energy of reactants)

Use ΔG – Thermodynamic term

ΔG°’ VALUES ARE ADDITIVE!
 • Reactions that are not spontaneous can
be coupled to spontaneous reactions
 • Under these conditions, the overall
reaction can be spontaneous (favorable)
When systems are not at equilibrium, the
reactants experience a driving force to reach their
equilibrium values. This force is the standard free
energy of change for the reaction ΔG°’ = -RTlnKeq
ΔG°’ > 0; not spontaneous (Endergonic) ; ΔG°’ < 0, spontaneous (exergonic).
For reaction: A + B  C + D
Actual free energy change ΔG for a reaction is a function of the actual concentrations of the
reactants and the temperature and is related to ΔG°’ by:
ΔG = ΔG°’ + RT ln [C][D] /[A][B]
o A + B → C + D ΔG°’ reaction 1
o D+E→F ΔG°’ reaction 2
o A+B+E→C+F
o ΔG°’ overall reaction
o ΔG°’ overall reaction = ΔG°’ reaction 1 + ΔG°’ reaction 2
Chemical reactions are classified as being either exergonic or endergonic. That just means that a reaction can either
release energy useful for work (an exergonic reaction) or requires energy to proceed (an endergonic reaction).
ATP AS AN ENERGY SOURCE
• ATP is a common form of “energy currency”
within cells
• Commonly use ATP hydrolysis to drive unfavorable
reactions
ATP + H20 → ADP + Pi +H+
• ATP hydrolysis has a high ΔG°’ (-30.5 kJ mol-1)
• The equilibrium for this reaction lies heavily towards the products
• Thioesters formed when a thiol (R – SH) joins with a carboxylic acid (R’COOH)

• Most common thioesters in cells are produced from the thiol Coenzyme A (CoA-SH)

Energy Diagram for ATP hydrolysis:

• The products (ADP and Pi) are at a lower energy level than the reactants. ADP and Pi are
made less reactive by resonance stabilization. Higher degree of electron delocalization –
more stable.
• Phosphoanhydride bonds are relatively reactive. Release energy upon cleavage. A large
amount of energy is released in the hydrolysis of the phosphoanhydride bonds of ATP
THIOESTERS: Other “highly reactive” or “energy rich” molecule.

First Step of Metabolism: Digestive Systems and Digestive Juices

 Digestion is the process in which the body breaks down carbohydrate, protein, and
triglyceride polymers into their small residues.
  Digestion occurs in the digestive system.
 The digestive system, sometimes referred to as the digestive track or gastrointestinal
(GI) track, includes the organs that are responsible for digesting food and eliminating
the undigestible components of food. The major organs of the human digestive system
are shown on the right
Digestion of Carbohydrates
 During the digestion of carbohydrate polymers, most oligosaccharides (2-10
monosaccharide residues) and polysaccharides (> 10 monosaccharide residues) can be
broken down to monosaccharide.
 Approximately 50% of our dietary carbohydrates are in the form of starch.
 Starch has two components, amylose and amylopectin, both of which are composed
entirely of glucose residues.
 Digestion of amylose and amylopectin (starch) begins in the mouth.
 Saliva contains salivary amylase enzymes, which catalyze the hydrolysis of some of the
α-(1→4) glycosidic bonds in amylose and amylopectin.
Hydrolysis of Carbohydrates

 Salivary amylase catalyzes the hydrolysis of amylose and amylopectin to form maltose
(an α-(1→4) glucose-glucose disaccharide) and small oligosaccharides called dextrins.
 Dextrins are oligosaccharides that generally contain between three and eight glucose
residues.
 The maltose, dextrins, and other nonstarch dietary carbohydrates then pass through the
stomach, where carbohydrate digestion temporarily stops because the salivary amylase
is denatured by the stomach’s low pH (very acidic) environment
 Digestion continues in the small intestine with the help of more digestive enzymes.
 Pancreatic amylase catalyzes the hydrolysis of dextrins to form maltose and isomaltose.
 Isomaltose is an α-(1→6) glucose-glucose disaccharide that comes from the branching
points in amylopectin.
 Maltase and isomaltase enzymes catalyze the hydrolysis of maltose and isomaltose
(respectively) into glucose.
 The non-starch dietary carbohydrates, lactose and sucrose, are converted to
monosaccharides with the help of lactase and sucrase enzymes, respectively.
  Lactose is hydrolyzed to galactose and glucose.
 Sucrose is hydrolyzed to fructose and glucose.
 It is critical that oligosaccharides and polysaccharides be converted to monosaccharides
in order for the sugars to pass through the intestine wall and into the bloodstream so
that they are available to cells throughout the body.
 Monosaccharides are transported into the cells by passive diffusion through
transmembrane proteins.
 Not all dietary carbohydrates can be digested.
• For example, cellulose cannot be digested because humans do not have a dietary
enzyme capable of hydrolyzing β- (1→4)glucose-glucose glycosidic bonds.
 Cellulose cannot pass through the small intestine and therefore passes through the
digestive track until it is excreted in feces.