Download unit 1: introduction to biology

SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
CHAPTER 6: THE MAJOR PROCESSESS OF CELLULAR
RESPIRATION
6.1. INTRODUCTION TO CELLULAR RESPIRATION

In this Chapter we will have a close look at one of the most important biological
processes on planet Earth

This intricate process, called cellular respiration, is performed by the cells of
literally all biological organisms on Earth

It is the single most important process by which heterotrophic organisms, such as
animals and we humans, harvest taken up food energy to stay alive

Cellular respiration is the process in living organisms that extracts electron energy
stored in the chemical bonds of food molecules (e.g. glucose), and converts that
“tapped” chemical energy into the “high energy” chemical bonds of one of the most
important biological molecule, called ATP
Cellular respiration
food + oxygen  carbon dioxide + water + ATP + hheeaatt

Cellular respiration occurs in eukaryotic cells in the membranes and matrix of the
mitochondria
 in prokaryotic cells (e.g. bacteria), respiration happens in the cell membrane

Respiration is a synonym for ‘breathing’ and means in a more strict sense the
exchange of gases
 a respiring organism or cell obtains oxygen from its environment and releases
in exchange the gas CO2
 respiration in biological terms is the aerobic harvesting of energy from food
molecules by a living cell
 cellular respiration is therefore closely related to physiological (=body) respiration
or ‘breathing’
 in both cases O2 is taken up (by the cell or in the latter case by the lung),
transported (via diffusion or red blood cells, respectively) and transformed in
exchange with CO2 as waste product

The chemical net equation of cellular respiration is:
C6H12O6 + 6 O2
(glucose)

6 CO2 + 6 H2O + ATP
(chemical energy)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Cellular respiration occurs in three metabolic stages: glycolysis, the Krebs cycle,
and the mitochondrial electron transport chain (ETC) and oxidative
phosphorylation.

As a results of the cellular respiration process, part of the chemical energy of the
glucose molecule is converted and conserved in the chemical bonds of the ATP (=
adenosine-tri-phosphate) molecule, which is the ‘energetic currency’ of the cell
 a tablespoon (1 g) of glucose contains approx. 40 kcal of energy that is available
for ATP synthesis and cellular work
 during cellular respiration however only a small percentage (approx. 1%) of this
energy is finally saved as ATP
 while burning of glucose in a chemical lab releases 100% of its energy as heat,
the biological burning process ‘cellular respiration’ banks only about 40% of
glucose’ energy as ATP; the rest gets lost as (body)heat
 for comparison: an automobile engine converts only about 25% of the energy of
the burned gasoline into moving force (= kinetic energy!)

75% of our food’s energy is used to keep our life-sustaining activities in the body
running; is used as so-called maintenance energy
 e.g. heart beat, breathing and resting (or basal) metabolism
 the average human adult needs food that produces approx. 2200 kcal of energy
per day!
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
6.2. REDOX REACTIONS DURING RESPIRATION

During cellular respiration cells dismantle the 6 carbon molecule glucose in a series
of redox reactions (see Chapter 5) by transferring and rearranging electrons
coming from glucose into the chemical bonds of highly specialized redox
molecules ( NAD+, FAD, see sections below!)
- finally the electrons are shuttled through a series of energy-releasing (=
exergonic) reactions starting from a molecule with higher chemical energy (=
glucose) down to low energy molecules (pyruvate, oxalacetate, water)
- part of the energy difference between the starting molecule and the end
cleavage products is used by the cell to synthesize ATP

The major biomolecule involved in the cellular redox reactions which result from the
degradation of glucose is nicotineamide dinucleotide (or NAD+)

NAD+ shuttles the electrons retrieved from these redox reactions from one
molecule to another; it is the major key player of the redox reactions of cellular
respiration

When glucose gets metabolized in a living cell, at several steps along this
degradative (or catabolic) pathway, it is catalyzed by a class of enzymes, called
dehydrogenases; during each of these enzymatic or dehydrogenation steps,
glucose loses 2 electrons together with 2 H+-ions (= protons !) and becomes
oxidized to NADH + H+

Both (electrons and protons) are transferred onto NAD+, which functions as the coenzyme of the cellular dehydrogenases; NAD+ is located in close proximity to the
active site of this enzyme

During the catalytic turnover of the dehydrogenases, NAD+ becomes reduced to
NADH + H+
 along the degradation of the glucose molecule in the cytosol in a process called
glycolysis (see below for more details), the cell gains 2 NADH + H+ molecules
from each molecule of glucose

NADH + H+ carries the extra energy retrieved from the cellular redox reactions (in
form of 2 electrons and 2 protons) over to a so-called electron transport chain
(ETC), which is located in the mitochondrial membrane (see section below)

There NADH + H+ chemically interacts with so-called electron carrier proteins,
which are part of the ETC; the NADH + H+ molecule gives off its electrons (=
becomes oxidized) and is recycled to NAD+ again

The released electrons are handed down a so-called electron cascade within the
ETC which consists of several proteins and co-factors
 the interaction of NADH + H+ with the electron carrier protein triggers a series
of consecutive redox reactions within the ETC
 the different members of the ETC become reduced and oxidized again, while
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
the electrons lose energy along this energetic down-hill reaction
 in the final scenario of the ETC cascade, the 2 electrons are transferred onto
oxygen which becomes reduced to water
 parts of the released energy is used by the cell to make ATP

2 mechanisms are used by cells to synthesize the cellular fuel ATP
1. by Chemio-osmotic phosphorylation or short: chemio-osmosis
 also called ‘Mitchell or chemio-osmotic theory’, named after the British
biochemist Peter Mitchell who first described this mechanism in the 1960s
 it is called osmosis since protons are separated by a biological membrane
which prevents free diffusion of these solutes cross this barrier; they can only
pass the membrane through selective membrane openings (= pores)
 cells tap the potential energy conserved in a proton (= H+) gradient to
synthesize ATP with the help of a highly specialized enzyme system, called
ATP-synthase (see section below for more details)
 the proton gradient is formed as a consequence of the delivery of NADH + H +
(together with another proton-loaded molecule named FADH2) to the
mitochondrial electron transport chain
 after feeding in the electrons and protons at the electron carrier proteins of
The ETC, they are recycled to NAD+ (and FAD) again, while the protons are
actively transported across the mitochondrial membrane; as a consequence
of this ‘proton-pumping’ process, a so-called proton gradient along the
membrane is formed
 these separated and accumulated protons can only go back (= diffuse) to the
side with the lower H+-concentration via a selective pore in the membrane
 this pore is part of the earlier introduced enzyme system called ATP-synthase
 this ATP-synthase uses the energy retrieved from the ‘gated degradation’ of
the H+-gradient to make ATP from the precursor molecule ADP
 since both, the ATP-synthase and the proton-gradient forming ETC, are
located in the mitochondrial membrane, they form an efficient cellular ‘ATPmanufactoring belt’
2. by Substrate level phosphorylation
 an enzyme transfers a phosphate group from a suitable organic substrate
molecule (= phosphate donor) to ADP to recover ATP
 an important phosphate donor, e.g. in the skeletal muscle is phosphocreatine
which quickly restores ATP after exhaustive physical exercise
 substrate level phosphorylation is simpler than chemio-osmosis and doesn’t
need a biological membrane as a ‘helper structure’
 it accounts for only a small percentage of cellular ATP synthesis
 it occurs at several steps during glycolysis and Krebs cycle
(see next section for details)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
6.3. THE THREE MAIN STAGES OF CELLULAR RESPIRATION

Cellular respiration dismantles glucose in a series of chemical reactions by
transferring and rearranging electrons coming from glucose into the chemical bonds
of highly specialized biomolecules (= NAD+ and FAD)

Cellular Respiration happens in 3 major steps:
11.. G
Gllyyccoollyyssiiss
22.. K
Krreebbss oorr C
Ciittrriicc A
Acciidd ccyyccllee
33.. E
Elleeccttrroonn ttrraannssppoorrtt cchhaaiinn

The function of 11 and 22 is to supply 33 with electrons and H+ coming from glucose
degradation
 the electrons and protons are shuttled to 33 in form of
the biological energy shuttles NADH + H+ and FADH2
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
 33 uses the incoming energy in form of the down-hill flow of electrons and the
established proton gradient to make ATP
Net complete net equation of respiration
C6H12O6 + 6 O2
glucose

oxygen
6 CO2 + 6 H2O + ATP + H
Heeaatt
carbon water
dioxide
The individual steps of Glycolysis

Glycolysis means literally translated “splitting of sugar”. It is the universal energy
harvesting process of life on planet earth. It is performed by bacteria, protists, fungi,
plants, animals and humans to dismantle glucose into two molecules of pyruvate.

During glycolysis, glucose, a six carbon-sugar, is split into two, three-carbon
sugars. These smaller sugars are oxidized and rearranged to form two molecules of
pyruvate. Each of the nine steps in glycolysis is catalyzed by a specific enzyme.

These steps can be divided into two phases: an energy investment or preparative
phase (= steps 1 – 4) and an energy pay-off phase (steps 5 – 9).
 input: 1 glucose (C6)
2 ADP + Pi
2 NAD+
Carbons:
output:
6
2 Pyruvate (C3)
2 ATP
2 NADH + H+
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Glycolysis Summary
 the energy retrieved from the sequential enzymatic breakdown of glucose is
banked in form of 2 ATP and 2 NADH + H+ molecules
 the energy of ATP can be used directly for other processes while the energy of
NADH + H+ first has to be transformed into ATP at the ETC
 along the chemical degradation of glucose to 2 pyruvate, 8 chemical
compounds are formed in between, they are also called intermediates
 each intermediate along the glycolytic path has a slightly lower chemical
energy than its precursor molecule
 there is no carbon loss in glycolysis and no oxygen is required!
P
Prreeppaarraattiivvee pphhaassee (= first graph)
1. glucose is energized by adding a phosphate from
ATP to form glucose-6-phosphate (Glc6P)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
2. Glc6P is subsequently transformed into fructose-6-phosphate (Fru6P)
in an enzymatic reaction
3. A second phosphate coming from ATP again is used to convert Fru6P into
Fructose-1,6-bisphosphate (Fru1,6P2)
4. The 6 carbon molecule Fru1,6P2 (C6) is cleaved into two 3-carbon (C3)
intermediates, called dihydroxyacetone-phosphate (DAP) and
glyceraldehyd-3-phosphate (GAP)
- glucose is trimmed (chemically energized) for degradation by adding
phosphate groups from ATP to glucose and derivatives thereof

Dihydroxyacetone-phosphate is converted into GAP by the enzyme isomerase. 2
molecules of the 3-carbon molecule glyceraldehyde-3-phosphate (GAP) is the end
product of the preparative phase of glycolysis
- at this point the cell invested 2 ATP molecules per molecule glucose
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
E
Enneerrggyy ppaayy--ooffff pphhaassee (= second graph)
1. In a redox reaction and in the presence of 2 phosphates, 2 molecules of G3P
are converted into 2 molecules of 1,3-phosphoglycerate (1,3PGA), while 2
NADH + H+ molecules are generated
2. In a series of enzymatically catalyzed chemical reactions, 1,3PGA is
converted (via 3 intermediate compounds) into the 3-carbon (C3) molecule
pyruvic acid or pyruvate (Pyr); along these chemical reactions 4 molecules
of ATP are formed per molecule of glucose
- during this step the cell gains 4 ATP and 2 NADH+H+ molecules
(= GAP)
Key Enzyme
Pay-Off: 1 ATP
Pay-Off: 1 ATP
(C3)
Coenzyme A
NAD+
(= HS-CoA)
Pyruvate
Dehydrogenas
NADH +
H+
Key Enzyme
CO
Acetyl-CoA
(C2)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

The 3-carbon (C3) molecule pyruvate is the ultimate end product of glycolysis.
The net yield from glycolysis is 2 ATP and 2 NADH + H+ for each molecule glucose
metabolized.

No CO2 is produced and no oxygen molecule (O2) was consumed during glycolysis.
Glycolysis occurs whether O2 is present or not.

If O2 is present, pyruvate moves to the Krebs cycle and the energy stored in NADH
can be converted to ATP by the electron transport system and oxidative
phosphorylation.

Pyruvate is finally transformed (= oxidized) by the pyruvate dehydrogenase (=
PyrDH) enzyme under release of NADH + H+
 PyrDH is another glycolytic key-enzyme and strongly regulated

In a parallel reaction pyruvate dehydrogenase enzyme also catalyzes the release of
carbon dioxide (= CO2) in a so-called decarboxylation reaction yielding the highenergy 2-carbon compound acetyl-co-enzyme A (Acetyl-CoA)
- 1 molecule of NADH + H+ is formed and 1 molecule of CO2 is simultaneously
cleaved

The 3-carbon molecule pyruvate is the end product of glycolysis; it is finally
transformed (= oxidized) by a so-called glycolytic key-enzyme reaction into the
high-energy 2-carbon compound acetyl-co-enzyme A (Acetyl-CoA) which enters
the Krebs cycle
- 1 molecule of NADH + H+ is formed and 1 molecule of CO2 is simultaneously
cleaved from the pyruvate molecule in an enzymatic reaction called oxidative
decarboxylation
- the same enzyme also attaches a molecule called co-enzyme A, which is a
rather complex molecule which synthesis requires vitamin B5
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
The coenzyme A (HS-CoA) molecule
 “the big energizer”
Cysteine
Cysteamine
β-Alanine
O
C
CH2
Chemical
reaction
CH2
Pantothenic
Acid-P
(= Vitamin B5)
reactive
Sulfhydryl group
NH – CH2 – CH2 – SH
N–H
C
NH2
O
N
N
H – C – OH
 essential
e.g. Acetic acid
H3C – C – CH3 O
N
O
H2C – O – P – O – P – O CH2
O-
O-
N
O
O
Pantoic Acid-P
_
O
P
O
OH
O
Adenosine-3’,5’-P2
Covalent linkage creates molecules with a very high group transfer potential
Acetyl + HS – CoA

Acetyl – CoA + H2O : ΔG0’ = - 35 kJ/mol
At this point of cellular respiration, the energized (‘groomed’) pyruvate molecule is
ready for entering the final stage of the cellular glucose degradation machinery,
called the Krebs cycle
 pyruvate leaves the cytosol and enters the mitochondria as acetyl-CoA
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
6.4.
THE KREBS CYCLE (OR CITRIC ACID CYCLE)

Named after the German-British scientist Hans Krebs, who unraveled the cyclical
nature of this central part of cellular respiration (see Graphic below)

It is a cyclical, 8-staged chemical process which is started by entering of AcetylCoA into the mitochondrion

The 8 steps of the Krebs cycle
1. Co-enzyme A (HS-CoA) is cleaved from acetyl-CoA and recycled; only the 2carbon molecule acetic acid (C2) enters the cycle; the C2 compound is
covalently combined with the 4-carbon molecule oxal acetate (OxAc) to form
citric acid (= C6 compound!), which gets the energy of the acetyl group
- since citric acid (or citrate) is the first chemical product, the Krebs cycle is
also often referred to as the citric acid cycle
- this rate-limiting chemical reaction is a typical condensation reaction which
is catalyzed by the enzyme citrate synthase
- citrate synthase is a critical regulatory enzyme of the Krebs cycle
2. The enzyme aconitase catalyzes the reversible transformation of citrate into
isocitrate by reversible addition of water
 the chemical reaction is an addition reaction
 aconitase is an iron-containing enzyme with a iron-sulfur (Fe-S) cluster
3. In the next step isocitrate is dehydrogenated (loss of two hydrogens) and
simultaneously decarboxylated (loss of CO2) to the 5-carbon molecule alphaketoglutamic acid (= -KG or -ketoglutarate)
- this oxidative decarboxylation reaction is catalyzed by the enzyme
isocitrate dehydrogenase, an enzyme which contains NAD+ as co-enzyme
and requires magnesium (Mg2+) or manganese (Mn2+) as co-factors
4. In step number 4, -ketoglutarate is oxidized to succinyl-CoA and CO2 under
formation of the redox molecule NADH + H+ by the catalytic action of the ketoglutarate dehydrogenase enzyme complex; along the reaction, a highenergy bond ( symbolized by “~” in the Graphic below) between one carboxyl
group of ketoglutarate and coenzyme A is formed
- the chemical reaction is a oxidative decarboxylation reaction which is
similar to the one catalyzed by the pyruvate dehydrogenase complex (see
above)
- the enzyme complex is comprised of three sub-units and requires thiamine
pyrophosphate (TPP), Mg2+, coenzyme A, FAD, and lipoic acid
5. In step #5, the highly energized succinyl-CoA molecule is converted into
succinate in a coupled hydrolysis reaction which is catalyzed by the enzyme
succinyl-CoA synthetase
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
- succinyl-CoA synthetase couples the highly exergonic hydrolysis of
coenzyme A from succinyl-CoA with the endergonic formation of GTP from
the precursor molecule GDP; the cell is able to convert GTP into ATP in the
presence of ADP with the help of an enzyme called nucleoside
diphosphokinase (NDK)
(NDK)
GTP +
ADP

GDP +
ATP
- this is the only step of the Krebs cycle were substrate level
phosphorylation takes place and a net production of ATP is achieved
6. In the next step of the Krebs cycle succinate is dehydrogenated (removal of two
hydrogens and two electrons) to fumarate
- this dehydrogenation reaction (oxidation of succinate) is catalyzed by the
succinate dehydrogenase (SDH), an enzyme which is tightly associated
with the inner mitochondrial membrane where it forms the crucial component
of complex II of the mitochondrial electron transport chain (see sections
below)
- SDH is a large iron-sulfur protein (MW 100,000) which has a covalently
bound FAD molecule as essential co-enzyme (see Image below)
- The iron-sulfur (Fe-S) clusters of this interesting enzyme are known to
somehow transport and feed electrons into the connected protein
components of the electron transport chain
- It is competitively inhibited by the Krebs cycle blocker malonate, which
played an important role in the unraveling of the intricate chemical reactions
of the Krebs cycle
Succinate dehydrogenase, mitochondria & Aging theories
All multi-cellular biological organisms age for currently unknown reasons. Many
theories have been brought forth in the past to explain the cause of biological aging.
One of them is the free radical theory of aging. According to this currently popular
theory, scientists believe that more and more free radicals and reactive oxygen species
(ROS) accumulate in cells as living organisms age which eventually leads to
progressive destruction of the integrity of proteins and to DNA mutations. As one of the
suspected sources for these free radicals, a defective, “electron-leaking” electron
transport chain has been postulated which may trickle more and more free radicals
(unpaired electrons) into the cells. In the recent years - due to the fact that succinate
dehydrogenase is an integral part of the complex II of the mitochondrial electron
transport chain (ETC) and is an electron transporting Fe-S protein - scientists
suspected this mitochondrial enzyme to be a weak link in the ETC. According to the
popular “free radical theory of aging”, free electrons (= radicals) leaking from complex II
of the ETC may lead to hydrogen peroxide formation, peroxidation processes,
degradative oxidative stress in cells, cellular senescence … and – in the long haul – to
the demise of the whole body (commonly referred to as aging).
In the round worm Caenorhabditis elegans, scientists could show that mutations in the
mev-1 gene (which codes for the beta-subunit of the succinate dehydrogenase enzyme
= complex II of the mitochondrial ETC) leads to increased oxidative damage and a 37%
shorter lifespan.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
7. In the second last reaction, water is added to fumarate to form the 4-carbon
molecule malate (or maleic acid)
- this hydration reaction is catalyzed by the enzyme fumarate hydratase
8. In the last reaction of the Krebs cycle, malate is converted into the 4-carbon
molecule oxalate (= oxalic acid) is a typical dehydrogenation reaction
(transfer of 2 hydrogens onto NAD+) involving the co-enzyme NAD+
- the oxidation of malate to oxalate is catalyzed by the enzyme malate
dehydrogenase
- even though this reaction is highly endergonic (ΔG0’ = +7.1 kcal/mole) and
the equilibrium (under standard reaction conditions; 1 M, pH 7.0) is far to the
left, in intact cells, however, proceeds towards the product, since oxalate is
rapidly removed by the following citrate synthase reaction in a “fully
humming” Krebs cycle!

All chemical reactions of the Krebs cycle occur in the matrix of the mitochondria.
The mitochondrion: The place of the Krebs cycle within the cell
Matrix  Krebs cycle
Inner mitochondrial  Electron transport
membrane
chain (ETC)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Pioneers in
-Hans Adolph Krebs –
(1900 – 1981)
- Born in Hildesheim, Germany
- Died in Oxford, England
- 1926-1930: studies in the lab of Otto Warburg
- 1931: discovery of the ornithine cycle at the medical
faculty at the University of Freiburg, Germany
- 1933: escapes Nazi terror in Germany and flees to
the University of Cambridge, England where he continues
his studies with the support of a Rockefeller fellowship
- 1937: publishes his famous findings about the chemical
center piece reaction of cellular metabolism in the Dutch
journal ‘Enzymologia’
- 1953: wins the Nobel prize in Physiology for his groundbreaking work on the Citric Acid or Krebs cycle in cells
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
The 8 steps of the Krebs cycle
Glycolysis
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

The Krebs cycle pays big energy dividend to the cell: the overall energy bilance
after degradation of 1 molecule of glucose is:
 2 ATP, 6 NADH + H+ and 2 FADH2 molecules are retrieved after two complete
rounds of the cycle
 Degradation of 1 molecule glucose during glycolysis in comparison brings the
cell only 2 ATP and 2 NADH + H+

The biggest energy profit the cell gains after ‘cashing-in’ the 6 NADH + H+ and 2
FADH2 molecules (retrieved from two complete rounds of the Krebs cycle) at the
earlier introduced eelleeccttrroonn ttrraannssppoorrtt cchhaaiinn ((E
ETTC
C)) located in the inner
mitochondrial membrane

There the ‘high-energy load’ of these two molecules is used in the cellular process
called chemio-osmosis (see earlier section above) to synthesize ATP
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
6.4.
The mitochondrial electron transport chain (ETC)

The vast majority of the ATP generated within a cell comes from the energy in the
electrons carried by NADH + H+ (and FADH2). The energy in these electrons is
used in the electron transport chain (ETC) to power ATP synthesis.

The ETC is an assembly of closely packed so-called electron carrier proteins
located in the mitochondrial membrane (see Graphics below)

Four of these electron carrier proteins, named complex I, II, III and IV, are
embedded into the inner mitochondrial membrane; one electron carrying protein,
called cytochrome c, is associated with the membrane between complex III and IV
- cytochrome c shuttles electrons from complex III over to complex IV

Thousands of copies of the electron transport chain are found in the extensive
surface of the cristae, the inner membrane of the mitochondrion. Most components
of the ETC are iron-containing proteins that are bound with prosthetic groups that
can alternate between reduced and oxidized states as they accept and donate
electrons.
- Electrons drop in free energy as they pass down the electron transport chain.

Some of the members of the ETC have docking/interaction sites for the
electron/proton-loaded (= reduced) NADH + H+ and FADH2 molecules

NADH + H+ delivers the electrons and protons to complex I of the ETC, while
FADH2 docks further downstream at complex II of the ETC where it gives off its 2
electrons and protons

In the course of the “electron de-loading process” of NADH + H+ and FADH2, which
is chemically spoken an oxidation, each of these two molecules gives up 2
electrons and 2 H+-ions (= protons)

the 2 freed electrons are handed down between the different electron carriers along
a down-hill energy gradient (see Graphics below); at the end of this energy
cascade the electrons finally interact with an oxygen atom and reduce it under
consumption of 2 protons (H+) to water!
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
The enzymes & the flow of electrons and protons along the Electron Transport
Chain (ETC) in the inner mitochondrial membrane
•
The electrons carried by FADH2 have lower free energy and are added to a later
point (= complex II) in the ETC. These given off electrons will allow the cell only to
generate 2 ATP molecules for each FADH2 molecule.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Complex I
Complex III
Complex IV
gain
3 ATP
2 ATP
Complex II
•
2 electrons
The electron transport chain does NOT generate ATP directly, but generates a
proton gradient between the inner mitochondrial membrane and the inner
mitochondrial space. The ETC’s function is to break the large free energy drop from
food to oxygen into a series of smaller steps that release energy in manageable
amounts.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Components and energetics of the mitochondrial
electron transport chain (ETC)
2 H+
Reduction Potential (Eo’) [ V ]
electron flow
2 H+
- 0.32
FMN
FeS
2 e-
CoQ
FeS
CoQH2
CoQH2
NADH
H + H+
NAD+
NADH-CoQ
reductase
Cytochrome c
2 H+
Cyt b
Cyt c
Cyt c1
Cyt b FeS
Cyt c
+ 0.04
Cytochrome c
oxidase
+ 0.26
H+
2H
Cyt a
UbQ-Cytochrome c
reductase
½ O2 + 2 H+
+ 0.29
Cyt a3
2 e-
Mitochondrial Matrix
Graphic©E.Schmid/2003

H2O
+ 0.82
Along the serial redox reactions between the electron carrier proteins and as a
consequence of the permanent removal of protons in the mitochondrial matrix due
to formation of water at complex IV, a proton (H+) gradient is build up between the
inner mitochondrial membrane space and the matrix
- a high concentration of protons builds up in the inner mitochondrial space; the
space become acidic over time
20
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
M
Miittoocchhoonnddrriioonn


from
G
l
y
c
o
l
y
Glycolyssiiss & K
Krreebbss ccyyccllee

In the final pay-off scenario of glycolysis and cellular respiration, the potential
energy stored in the mitochondrial H+-gradient (often referred to as proton motive
force or “pmf”) is used to synthesize new ATP molecules starting from ADP (
chemio-osmotic theory)
(see Graphics below)

Energy released by the "downhill" passage of electrons is conserved in form of a
proton gradient across the inner-mitochondrial membrane
Potential Energy


Chemical Energy
ATP is made (= synthesized) by an enormously large and complex cellular enzyme
called ATP-synthase which has dual properties:
1. it is a proton-selective pore protein
 the accumulated protons flow back into the mitochondrial matrix through a
pore-like protein structure
2. it possesses enzymatic activity
 it is capable to use the H+-driving force as energy source to synthesize ATP
from the low-energy precursor molecule ADP
21
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
The proton gradient-drive mitochondrial ATP synthase
22
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Formation of a proton (= H+) gradient at the electron transport chain in the inner
mitochondrial membrane

Matrix
K
Krreebbss C
Cyyccllee

As the protons flow back to the inner space (= matrix) of the mitochondrion, the
energy of their movement is used by an enzyme called ATP-synthase to add one
phosphate (= PO42-) to ADP to form the life-essential ATP molecule
23
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
A proton gradient is used by the ATP-synthase enzyme to make ATP from ADP
and phosphate (= chemio-osmotic theory)
24
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
TToottaall A
ATTP
P ggaaiinn ffrroom
m aaeerroobbiicc rreessppiirraattiioonn ooff 11 m
moolleeccuullee ooff gglluuccoossee
G
Gllyyccoollyyssiiss
1 Glc  2 Pyr

2 NADH + H+
2 ATP
P
Pyyrruuvvaattee D
Deehhyyddrrooggeennaassee &
&K
Krreebbss ccyyccllee
2 Acetyl-CoA  6 CO2

8 NADH + H+
2 FADH2
2 ATP
E
Elleeccttrroonn ttrraannssppoorrtt cchhaaiinn
10 NADH + H+  10 NAD+ 
2 FADH2
 2 FAD

½ O2 + 2 H+
30 ATP
4 ATP
 H2O
Total Gain
max. 38 ATP
(Energy content: 277 kcal/mole)
25
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Under optimum conditions, for each molecule NADH + H+ delivering electrons and
protons to the electron transport chain, the cell is able to retrieve 3 molecules of
ATP, while for each FADH2 molecule the cell is able to synthesize 2 ATPs with the
help of the ATP synthase enzyme
1 NADH + H+
1 FADH2
-- ETC 
-- ETC 
3 ATP
2 ATP

Aerobic cellular respiration is a remarkably efficient cellular process; under
optimum conditions, more than 40% of the chemical energy of glucose is converted
into the high energy chemical bonds of the ATP molecule
- the Gibbs Free Energy of 1 mole of glucose (= 686 kcal/mole) is converted into
38 moles of ATP with a total Gibbs Free Energy of 277 kcal
- this calculates into a (theoretical) efficiency coefficient of 277/686 = 0.404 (see
Figure and individual calculations) below

The non-ATP-fixed energy from cellular respiration (= 409 kcal/mole glucose) is
released as (body) heat. This (unavoidable) heat release is due to the second law
of thermodynamics, which cannot be circumvented by living organisms
 heat release occurs whenever any form of energy is
transformed ( changed) into another form
 heat release is a consequence of conversion of food energy into the chemical
energy of ATP

Endotherm organisms, including humans, in contrary to ectotherm species use
the released heat to keep their body temperature at a constant, moderately high
level (= 370C in case of humans)
 the higher body temperature in endotherms enables them to
run their metabolism and their biological activities at a higher rate!
26
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

In contrary, ectoderm organisms (Greek: ecto = from outside) , e.g. amphibians
and reptiles, raise its body temperature passively, with the help of heat taken up
from the environment, mostly the sun (for more info see Metabolism section below)
 ectoderms have a much lower metabolic rate than endotherm organisms
 the body temperature of an ectoderm is warm when the environment
is warm, and vice versa
Glycolysis & the Electron Transport Chain are vulnerable to many toxins or
poisons!

Due to the coordinated and serial action of many enzymes (= enzyme
cascades), glycolysis and, most of all, the mitochondrial electron transport chain
are vulnerable to many toxins or poisons
 many of these inhibitors are critical environmental pollutants
released through industrial or technological processes

Most of these poisons block enzymes, which are responsible for the coordinated
flow of the electrons between the electron carrier proteins of the ETC
G
Gllyyccoollyyssiiss
e.g.
arsenate (As)
fluoride, IAA
K
Krreebbss ccyyccllee
e.g.
fluoroacetic acid
E
ETTC
C
e.g.
 arsenate prevents the formation of P2GA from
GAP
 extremely poisonous molecule
 prevents the formation of citrate from acetyl-CoA
and oxalate
 produced by plants indigenous to Africa and
Australia, e.g. “Gifblaar” (Dichapetalum
cymnosum)
 it was once used in form of agent “1080” in
the U.S. to kill coyotes and rodents
 a potent, widely used pesticide
 an extremely toxic compound; already low doses
are lethal to mammalians and humans!
 used by the Nazis in form of “Zyklon B” in the
1940s to commit mass murder of the Jewish
population imprisoned in the concentration camps
( “Holocaust”)
Methyl isocyanate  a neuro-toxic chemical which blocks the
mitochondrial electron transport chain at complex
I
carbon
 odor-less, toxic gas
monoxide (CO)
 released in in-complete combustion reactions,
e.g. of car engines
rotenone
cyanide
27
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
 all prevent the reduction of oxygen to water, the build-up of the H+-gradient and
….. finally the synthesis of ATP
In 1984, in one of the worst industrial accidents in human history, the toxic
cyanide derivative methyl isocyanate killed 3,000 people and injured more than
100,000 humans after a catastrophic gas leak in a chemical factory in Bhopal,
India.

Other respiratory poisons directly inhibit the ATP-synthase
e.g.
oligomycin
 an antibiotic; used as anti-fungal drug
 prevents the cell from using the established H+-gradient to make ATP

Poisons which are also known as so-called uncoupler compounds
- they are able to shuttle H+-ions cross biological membranes (see Graphic
below) as a consequence, they destroy the mitochondrial proton gradient but
leave the electron flow along the ETC intact
- in the presence of an uncoupler, cells have a normal electron transport along
the ETC and continue to consume oxygen but they cannot make ATP
- almost all chemical energy is lost as (body)heat
e.g.
Dinitrophenol
(DNP)
Dinitro- o-Cresol
(DNOC)
CCCP
“Roundup”
 highly toxic compound;
used in the 1940s in low doses
in commercial weight-loss pills!
 a pesticide which may be
released to water in industrial
effluents or runoffs
 a synthetic uncoupler, widely
used in scientific research
 herbicide, which blocks mitochondrial
oxidative phosphorylation in plants
Natural uncouplers & Biology
In the recent years, scientist discovered a series of uncoupling proteins
(= UCPs) in cells of different organisms, which seem to play a crucial role
in the “natural uncoupling” of the mitochondrial electron transport chain,
e.g. in hibernating animals and in the brown fat tissue of infants
28
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Effect of a proton gradient-destroying molecule (= uncoupler) on the
mitochondrial electron transport chain
Heat Energy
Cytoplasm
H+
H+
+
H
Inner mitochondrial
membrane space
H+
H+
H+
+
H
H+
Uncoupler
H+
H+
ETC
Matrix
+
H
+
H
Destruction of
proton gradient
CO2
NADH +H+
-
e
H+
H+
e-
ATPsynthase
e+
H
FADH2
H+
O2
H2O
ATP
Krebs cycle
Glycolysis
Heat
Food
Graphic E.Schmid/2004
6.5 Metabolism & Caloric content of food molecules

Even though the Citric Acid or Krebs cycle is the center piece chemical reaction
pathway of cellular respiration, cells are able to perform many more chemical
reactions; in the past 100 years, scientist discovered thousands of chemical
reactions and metabolic pathways in cells which are able to form new molecules or
to break down larger molecules into smaller ones

Without these metabolic activities cells and living organisms wouldn’t be able to
sustain their vital activities

Metabolism is the sum of all chemical processes by which cells either degrade
materials or produce new materials and (ATP-) energy to sustain the life functions

Metabolism has two phases which happen in parallel and constantly in all living
organisms
1. Anabolism or constructive metabolism
 build-up of new substances and molecules from smaller precursor molecules
 e.g. the build-up of muscle protein from amino acids or the synthesis of fat
from acetyl-CoA and glycerol
2. Catabolism or destructive or degradative metabolism
 degradation of existing (food)-molecules
 e.g. metabolism of glucose and fatty acids down to carbon dioxide and water
29
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Since almost all chemical processes in living beings, whether catabolic or anabolic,
are catalyzed by enzymes, the metabolism is slowed down by cold temperatures
and can be influenced by many other factors

the conditions and factors which affect the cellular metabolism and control the
metabolic rate in organisms are:

1.
external temperature
- metabolism slows down at low temperatures
- metabolism increases at high temperatures and ceases at
very high temperatures due to heat destruction of
necessary enzymes and proteins
2.
length of day light
- in day-active organisms, e.g. humans, metabolism is slowed
down during night and high during the day
- the metabolic activity in many biological organisms follows
oscillating, so-called diurnal cycles ( bio-rhythm)
3.
biological activity
- the higher the physical activity, e.g. running, cycling, the
more cellular respiration occurs within the cells, the higher
the oxygen demand of cells will be
4.
respiratory efficiency
- the better the cells can be supplied with the necessary
oxygen, minerals and co-factors to conduct cellular
respiration, the higher the respiratory efficiency will be
- in this respect, optimum cellular metabolism is dependent
on the proper biological function of respiratory organs, such
as gills or lungs, the vascular system, e.g. blood vessels
and oxygen transporting proteins, such as hemoglobin
5.
body size
- smaller sized mammalian animals, e.g. a mouse, have a
faster metabolism (= higher metabolic rate) than
mammalian animals with larger body sizes, e.g. a human
The rate of respiration or also called the metabolic rate is the amount of food
metabolized within a certain time
 the respiration rate is usually measured as the amount of oxygen
(in mL) consumed by an organism within a certain time (in seconds)
 the metabolic rate is usually given in:
milli-liters oxygen / hour per gram weight
(ml O2 / hr x g)
30
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

in our own body, the metabolic rate is strongly controlled by special molecules
called hormones
 e.g. Thyroxine produced in the thyroid gland of humans
 e.g. Insulin and Glucagon produced in cells of our pancreas

the metabolism of many organisms, e.g. bears, hedgehogs, is controlled by
seasonal changes; these animals go into a state of torpor
 e.g. during the long winter sleep or during hibernation,
the metabolism of these species is dramatically slowed down
 the mitochondria are naturally un-coupled with the help of uncoupler proteins and
produce more heat for survival instead of ATP

due to the second law of thermodynamics, heat release occurs whenever any
form of energy is transformed ( changed) into another form
 heat release is a consequence of conversion of food energy
into the chemical energy of ATP

Endotherm organisms, including humans (in contrary to ectotherm species)
use the released heat to keep their body temperature at a constant, moderately
high level ( 370C !!)
 the higher body temperature in Endotherms enables them to
run their metabolism at a higher rate!

the amount of heat released or energy output as a consequence of chemical
reactions can be measured most accurately with the help of an insulated
container called calorimeter
 a calorimeter is a specially isolated and water-surrounded
combustion chamber, which measures the amount of heat given
off by different foods when they burn

the amount of heat produced (in a calorimeter or body) is measured by food
(or nutritional) scientists in calories
 calorie in Latin means ‘heat’
 the unit calorie belongs to the metric system of measurement
Definition: Calorie
One physical calorie (1 cal) is the amount of energy needed to raise the temperature of
1 gram (= 1 ml) of water by 10C
 another metric unit used to measure heat energy is the ‘Joule’;
One Joule (1 J) equals 0.239 calories

another, less elaborate and expensive method to measure a body’s energy
output is via measurement of the oxygen consumption
 in cellular respiration and most combustion reactions, the amount of oxygen
used is directly proportional to the amount of (food) energy used by a body
during an activity or the amount of burned substances
31
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

the molecules of taken up foods (= nutrition) supply heterotrophic organisms
with the (chemical) energy for every action we perform; it also provides the
building blocks and substances that the body needs to build up and repair its
tissues and body parts

but the different food molecules of nutrition supply biological organisms with
different amounts of usable energy (given in “nutritional” Calories), which is
shown in the Tables I and II below
- Notice: the word Calorie (Cal) is capitalized and represents 1000 times the
value of a single physical calorie (= cal)!
1 Cal = 1,000 cal or 1 kcal

Today, the energy content and the major nutrients of our modern food sources
can be taken from the ‘standard food labels’ printed on all packaged and
processed foods sold in the US
 fresh fruits and vegetables and raw-meats are not required to carry labels

all body actions, e.g. sleeping, reading, shopping, physical exercise, etc., use
up ingested or stored food energy
- the longer the action or the exercise the more energy is needed and the more
ingested or stored food energy is burned through cellular respiration
32
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Table I: Energy content of major molecules in different nutritional components
N
Nuuttrriieenntt
E
Enneerrggyy ccoonntteenntt
E
Exxaam
mpplleess
(Cal / gram)
C
Caarrbboohhyyddrraatteess
4
FFaattss//O
Oiillss
9
P
Prrootteeiinnss
4
Alcohol
7
(Ethanol)
Water

0
all sugars and starches
 the main sugars in food
are sucrose, fructose
and lactose
made of glycerol and
fatty acids
 certain so-called
polyunsaturated fatty
acids cannot be
manufactured by our
body and must be taken
up by food (e.g. fish)
provide energy and 20
amino acids
(= the essential building
blocks for enzymes,
structure protein, etc.);
 9 amino acids are socalled essential amino
acids
Content of alcoholic
beverages in different
volume percentages
- Beer (5 – 7%)
- Wine (12%)
all life processes are carried
out in it
 an adult human should
consume 21/2 quarts (2.4
liters) of water per day!
Depending on the chemical composition, different food sources supply the human
body with different amounts of caloric energy which is strictly dependent on the
amounts of carbohydrates, proteins, fats and other nutritional molecules
 (for an overview of the energy content of different popular food sources see the
Table below)
33
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
6.6. Metabolism of other food molecules than sugar: Introduction to metabolic
pathways other than glycolysis

In the previous section you learned that humans are not only receiving food energy
from the mono-sugars of our ingested carbohydrates, such as glucose or fructose,
but also from the proteins and fats of the taken up food sources

Cells are not only able to make ATP starting from glucose (which is rarely the only
component of our human food sources!), but also from amino acids and fatty acids,
the monomers of proteins and fats

In order to retrieve the chemical energy intrinsic to fatty acids and amino acids, cells
rely on a series of other metabolic pathways (other than glycolysis) to tap these
nutritional energy sources for ATP production

The primary chemical reaction which prepares amino acids for its metabolic use
within cells is called transamination; during transamination reactions, the amino
group of amino acids is transferred onto the amino acid glutamate with the help of a
class of enzymes called transaminases (see Graphic below)
- the conversion of glutamate into glutamine during this reaction is reversible
- the collected metabolic nitrogen in form of glutamine is finally converted into the
nitrogenous waste products uric acid (birds) or urea ( animals and humans)

the amino acid products after transamination are fed into different stages of the
glycolytic pathway and/or the Krebs cycle an further metabolized down to carbon
dioxide, NADH + H+, FADH2
- since there are 20 different amino acids available for metabolic degradation,
different transamination products, such as acetyl-CoA, pyruvate or oxalate, are
received after transamination reactions
- each transamination product is “funneled” into distinct stages of the cellular
respiration pathways (see Graphic below)

for each metabolized molecule of amino acid a cell gains an average of 40
molecules of ATP
34
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Metabolic degradation of proteins
 Transamination
Fats/
Lipids
Fatty Acids
Glycerol
Carbohydrates
Glucose
(Glc)
Cell
Ac yl-CoA
Glc
Urea
Glc-6P
CO2
Pyr
NH4+
Acetyl-CoA
L-glutamate
Amino
Acids
Aminotransferases
Transamination
Amino
Acids
OxAc
Krebs
cycle
CO2
NADH + H+
FADH2
Citrate
α-KG
½ O2
ETC
~ 40 ATP
H2O
Proteins
©E.Schmid/SWC2002

Fatty acids, e.g. palmitic acid or stearic acid, are the main components of nutritional
fats or oils, which are usually 12 – 22-carbon compounds

Fatty acids, once taken up by a cell and transported into the mitochondria, are
quickly degraded in a serial chemical “dismantling” process called beta- (β)oxidation into the C2-molecule acetyl-CoA

The β-oxidation end product acetyl-CoA is readily available for complete
metabolism within the Krebs cycle

since the cell gets e.g. 9 (!!) acetyl-CoA molecules from the degradation of one
saturated C18 fatty acid molecule, it obtains about 130 molecules of ATP for each
metabolized fatty acid molecule; this is more than 3 times the amount of ATP a cell
retrieves after degradation of 1 molecule of glucose (only 2 acetyl-CoA molecules!)
- therefore it is now better understandable (from a molecular point of view) why
fats are generally known to be a high-energy nutritional source
35
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
- a nutrition high in fats and oils, such as French fries, fried meats, lard or butter
supply a cell with lots of chemical energy which is metabolically converted into
high concentrations of ATP
Metabolic degradation of fats and lipids
 beta-oxidation
Fats/
Lipids
Fatty Acids
Glycerol
Acyl-CoA
Acyl-CoA-DH
Carbohydrates
Glucose
(Glc)
C e ll
Glc
β-Oxidation
Glc-6P
FADH2
Pyr
NADH + H+
Acetyl-CoA
OxAc
Citrate
Krebs
cycle
CO2
NADH + H+
FADH2
½ O2
131 ATP
H2O
ETC
©E.Schmid/SWC2002

Summarized, cells evolved different chemical pathways which shuttle degradation
products of amino acids and fatty acids into known stages of the cellular respiration
machinery, most prominently the Krebs cycle (see Graphics)
1. Polysaccharides, Disaccharides
 sugars (C5, C6)  glucose
 GLYCOLYSIS
2. Fats, Oils
 fatty acids
 Acetyl-CoA
 KREBS CYCLE
 Glycerol
 G3P
 GLYCOLYSIS
3. Proteins
 amino acids
 different derivatives
 KREBS CYCLE, PYRUVATE

But not all food molecules or nutritional components are destined to be oxidized as
fuel to make ATP
36
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Food delivers also the molecular raw materials a cell uses for an important cellular
process called biosynthesis

Amino acids retrieved after degradation of nutritional proteins are directly re-used
by the body for synthesis of novel proteins with the help of cellular ribosomes

Other biosynthesis pathways have been identified with which help cells can make
three classes of macro-molecules under consumption of ATP
1. Glucose synthesis (= gluconeogenesis)
 starting from pyruvate to make C5 and C6-sugars
2. Build up of fatty acids and fats (= fatty acid synthesis)
 starting from Acetyl-CoA

The capability of cells to do biosynthesis of fats or proteins from components of the
glycolytic pathway or the Krebs cycle, has intricate consequences for our human
diet, nutritional behavior and weight control
- even a low fat and primarily carbohydrate-based diet can lead to fatty acid
synthesis and finally fat storage (adipositas  see section 6.7. below),
especially if the ingested food intake is excessive and/or not counter-balanced
by energy-consuming physiological work or exercise e.g. biking, swimming,
jogging, etc.
- the saying ‘the best exercise is to push off the dining table’ shows awareness of
our body’s biosynthetic potential and makes perfect sense in this respect!
37
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Table: Food Composition Table
(approximate amounts of carbohydrates (C), protein (P) and fats (F) in the foods listed)
FFoooodd
Bread (1 slice)
Noodles (Wheat; 3/4 cup)
Tortilla Chips (9 chips)
Butter (1 pat)
Cheese (1 ounce)
Cracker (1 saltine)
Egg (1 medium-sized)
Grapefruit
¼ pound Hamburger
Jam (1 tbl. spoon)
Lettuce (1 leaf)
Mayonnaise (1 tbl. spoon)
Orange
Peanuts (1 cup)
Salad Greens (no dressing)
Salad Oil (1 tbl. spoon)
Sirloin Steak (3 ounces)
Tuna (2 ounces)
Whole Milk (8 ounce cup)
C
C
P
P
FF
[ grams ]
[ grams ]
[ grams ]
12
42
20
trace
1
3
trace
24
0
14
trace
trace
16
27
7
0
trace
0
12
2
7
1
trace
7
0.4
6
2
28
trace
trace
trace
1
37
2
0
20
15
9
0.7
1
8
4
9
0.5
6
trace
23
trace
trace
11
trace
11
trace
14
27
1
9
 use this table to calculate the total calories taken up by your test person
in the assigned classroom or laboratory activities!
Food
Taco salad (w. shell)
French fries (medium)
Chicken burrito
Big Mac
Whopper (w. cheese, no mayo)
Jack’s Chicken Supreme
Ice cream
Cream cake
Coke or Beer
Quantity
Total Calories
1
1
1
1
1
1
150g
120g
0.5l
(Cal/kcal)
840
450
760
590
530
830
350
420
250
For caloric calculations:



1 gC
Caarrbboohhyyddrraattee
1 gP
Prrootteeiinn
F
1 g Faatt
=
=
=
4 Calories of energy input
4 Calories of energy input
9 Calories of energy input
38
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
6.7. Health aspects of cellular metabolism: overweight, obesity and health
disorders

in the past 20 years we observed a steady increase in overweight people and
people suffering from obesity in the U.S. and in other developed countries; many
scientists begin to speak of an obesity epidemic which is expected to take its
future toll on general human health, the health care system and our society in
general

So when is someone considered to be overweight, what means obesity and how do
both conditions have to do with cellular respiration and metabolism?
Overweight and obesity in the U.S. numbers:
- between 1999-2002, 65.1% of U.S. adults aged 20 years and older were identified as
overweight, 30.4% were obese, and 4.9% were classified as extremely obese
- in 1999-2002, 31.0% of children aged 6 through 19 years, were at risk for overweight or
overweight and 16.0% were measured to be overweight
- Due to the connection of prolonged overweight and obesity with several health
problems, the high levels of overweight among children and obesity among adults
remain a major public health concern
Source: National Health and Nutrition Examination Survey (NHANES)

Today we know, that the onset of overweight and obesity is influenced by many
factors, including eating habits, genetic back ground and hormonal control, but the
single most important critical factor leading to overweight and obesity in humans is
the prolonged disturbance of the energy balance within the body (see Graphic
below) due to our modern life style habits

Overweight and obesity develops in humans whenever the chemical energy taken
up by the nutrition exceeds the energy given off by the body in form of (physical)
work, heat and metabolic waste products
Overweight arises when the daily input of energy exceeds the daily demand of
energy or energy consumption even for little amounts

Excess, unbalanced energy uptake in humans over long periods of time
unavoidably leads to fat build-up and storage, weight gain, overweight and obesity
For every 3,500 “unbalanced” kcal of food energy, the human body gains one
pound of body weight (mostly in form of fat)!
The average 8 year weight gain in the U.S. is between 14 – 16 pounds (Source:
CARDA study)
39
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

On the cellular level, the excess, unbalanced nutritional energy after complete
catabolism by cellular respiration leads to a build-up of high levels of the desired
metabolic end product molecule ATP

since ATP cannot be stored by cells (as this is the case with excess amino acids or
glucose, which are converted into the macromolecules proteins and glycogen), the
cells are “forced” to get rid of the high amounts of intracellular ATP by using it up in
ATP consuming chemical pathways; one of the most important ATP-dependent and
consuming chemical pathways is called fatty acid and fat synthesis (see Graphic
below)
Metabolism, Overweight & Obesity
FOOD
INTAKE
PHYSICAL
ACTIVITY
Carbohydrates
Proteins
Fats
the intricate
energy balance
ATP
ATP
ATP
Cellular
Respiration
Muscle
Contractions
(all cells)
(skeletal muscle cells)
Fatty acid
synthesis
(adipocytes)
Graphics©E.Schmid/2003
FAT
An energy excess of 1% leads to a weight gain of 1.5 kg over a one year period
mostly in form of fat

fatty acid synthesis is an ATP-consuming chemical reaction pathway predominantly
performed by a unique cell type called adipocyte
(for more information about the individual steps of fatty acid synthesis I refer to my
Molecular & Cell Biology (Bio211) section of this website)

the gradual build-up of fat within the body as a consequence of a continuously
unbalanced energy household leads to an overweight body and over longer
unbalanced periods of time to obesity
40
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

The degree of overweight or obesity by a human person can be defined by
several parameters, but the most commonly used measure is via calculation of the
Body Mass Index or for short BMI

The BMI is calculated by dividing the measured body weight of a person (in kilo
grams) by the square of the height of that individual (measured in meters) (see
Formula below)
- if the calculated BMI is larger than 25 kg/m2 then the person is considered to be
overweight
- if the calculated BMI turns out to be larger than 30 kg/m2 then the person is
considered to be obese
Calculation of the Body Mass Index (BMI)
BMI =
Body weight [ kg ]
(Body height)2 [ m2 ]
BMI > 25 kg/m2  overweight
BMI > 30 kg/m2  obese

the long-term monitoring of body weight and the BMI is advised to the fact that
obesity has been shown to be connected to a series of health problems and
disorders in the human population

obesity is a major health risk factor for:
1. developing Diabetes 2
- people often observe previous glucose intolerance and cellular
unresponsiveness to the hormone insulin (= insulin resistance)
- as a consequence affected human individuals have elevated levels of
glucose in their blood stream since their cells are incapable to take up the
nutritional glucose
2. developing coronary heart disease
- people often suffer from arteriosclerosis which can lead to heart attacks
and stroke
- this observation is connected to the high cholesterol and triglyceride
levels which are frequently observed in obese people
3. developing gestational diabetes and miscarriages
4. developing degenerative joint disease and arthritis
- this health disorder is connected to the larger mechanical stress on the
lower skeletal part due to the overweight
41
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
5. developing psychological disorders, e.g. depression
In the U.S., approx. 300,000 people die of obesity-related diseases every year

even though obesity is primarily triggered by excessive food intake in relation to
physical activity (“Sitting society syndrome”), it can also be the cause of:
1. Hormonal dysbalance of the body’s weight control system
- involving appetite and sugar level controlling hormones such as
Ghrelin,PYY, Leptin, Insulin
2. Peripheral nervous system irritations
3. Genetic defects/Mutations
 “Prader- Willi – syndrome”
 patients have high Ghrelin levels

Even though scientists unraveled many factors that determine the energy
consumption or energy demand of the human body, it is well understood that the
single most important factor counteracting the taken up nutritional chemical energy
is the degree and intensity of mechanical work of the skeletal muscles triggered by
different forms of physical activities (see activity demand in the Figure below)

The total daily energy demand of the human body is comprised of the basic
demand (or basal metabolism) and the activity demand
- the basic caloric demand of the human body is primarily due to the primary
metabolic activities of the body’s major tissues and organs, such as the skin,
brain, kidney, liver and lungs
- major caloric demand is also due to the permanent contractile activity of the
muscles of the diaphragm which is important for breathing and gas exchange in
our lungs
- the average basic caloric demand for a 50kg weighing human female is about
1,200 kcal/day and for a human male with a body weight of 70kg around 1,700
kcal/d (also see Figure below)

important factors that modulate (increase or decrease) the basic energy
demand or basal metabolic rate of the human body are:
1.
2.
3.
4.
5.
6.

Age
Gender
Body surface
Day time
Endocrine activity and hormonal function
Genetic factors
The activity energy demand of the human body is strongly dependent on the kind,
intensity and duration of physical activity and consequently use of different skeletal
muscles during the activity (see Figure below and Table II)
42
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Energy Demand in Humans
Age
Gender
- primary metabolic
activities
- brain, organ function
- breathing
e.g. 1,680
kcal/d
(70 kg person)
Body Surface
Basic Demand
1 kcal / kgbw x h
e.g. 210 kcal
after 1 hour jogging
(70 kg person)
Thyroidal function
Genetic
Factors
+
- metabolic activities
due to workplace or
life style activities
- growth
- pregnancy
- disease or injury
Day Time
(Basal Metabolism)
Activity Demand
Activity
Sleeping
Standing
Sitting
Office Work
Car Driving
Walking
Exercise
- Moderate
- Fast
Jogging
Swimming
Biking
Stair climbing
Rowing
kcal / kgbw x h
0.9
1.3
1.4
1.5 – 1.7
1.9
3.0
4.1
6.4
3.0
8.9
3.5
15.7
17.0
Total Energy Demand [ kcal / kgbw x h ]
bw = body weight (in kilograms)
43
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Due to the in average much lower activity demand of humans in our modern
societies, characterized by professions and life style habits which demand less and
less physical activities, e.g. office jobs, car driving, TV watching, together with the
plentiful and high calorie supply of foods, more and more people are struggling to
keep their energy household in balance

In industrialized nations more and more people end their days with an excess
unbalanced energy uptake; in the U.S. the average daily adult energy consumption
is between 3,800 – 4,500 kcal, which is in excess of 1,600 -1,800 kcal regarding the
recommended energy uptake (see Graphic below)
Recommended Nutritional Energy Uptake & Energy Demand in Humans
Average Adult
Excess,
E
n
e
r
g
y
Consumption (U.S.)
M a le
Unbalanced
Female
70kg
Energy uptake
50kg
2,200
kcal/d *
1,000
1,200
1,000
1,680
• = 2,600 kcal/d
2,680
kcal/d
3,800 – 4,500
kcal/d
Recommended
Energy Uptake
during
pregnancy
Basic Energy
Demand
(1 kcal/kg x h)

To prevent the unavoidable conversion of the excess unbalanced energy uptake
into fat storage (which ultimately will lead to overweight), one of the most effective
means to counteract this process is to “burn” the extra calories with the help of
ATP-consuming physical activities
- different forms of physical activities, due to the fact that different skeletal
muscles will be used, have different caloric demands
- the Table II below shows the caloric demand for different physical activities
44
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Table II: Approximate Caloric Conversions for Different Human Activities
A
Accttiivviittyy
E
Enneerrggyy C
Coonnssuum
mppttiioonn
[ Cal / h x kgbw ]
Sleeping
0.9
Sitting
1.4
Standing, Reading, Writing
1.5
Driving a Car
1.9
Light Exercise
2.4
Walking (3 miles per hour)
3.0
Bicycling (moderate speed)
3.5
Moderate Aerobic Exercise
4.1
Dancing
5.0
Fast Aerobic Exercise
6.4
Hiking (mountain up)
6.3
Slow Running (5 miles per hour)
8.1
Swimming
8.9
Speed Walking (7 miles per hour)
9.6
Walking Upstairs
15.7
Competitive Rowing
17.0
Basic Caloric Demand (Human): 1 Cal (kcal)/kgbw x h
 the basic caloric demand of humans is higher during:
1. sickness, fever
2. stress
3. pregnancy
4. high or low temperature

summarized, good nutritional habits and the integration of an adequate regimen
of physical activity into our daily lives will effectively help us to keep our energy
household in balance and to prevent us from eventually suffer from the detrimental
long term effects of overweight and obesity on our health status
45
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Good nutritional habits involves:
1. the regular eating of a varied and balanced diet that considers our personal life
style habits and includes every kind of macro- and micro-nutrients, such as
proteins, polysaccharides, unsaturated fats, minerals, trace elements and
vitamins
2. the regular take up of foods that are high in dietary fibers, consisting of cellulose
and other complex carbohydrates and pectins, such as fruits and vegetables
3. limitation of foods that are rich in saturated fats and cholesterols
6.8. Anaerobic respiration & Fermentation

Since adequate availability of oxygen and oxygen supply to the cell is not always
the case, cells developed other metabolic mechanisms to survive under lacking
oxygen conditions or so-called anaerobic conditions
- some organisms, such as anaerobic bacteria, thrive best and will only grow
under complete absence of oxygen
- they completely rely on anaerobic respiration for survival and will die in the
presence of oxygen

metabolism in the absence of oxygen is called anaerobic respiration

In principle, anaerobic respiration is the same as aerobic respiration, but under
anaerobic conditions cells use oxidizing agents other than oxygen, such as nitrate,
sulfate or fumarate, to take care of the electrons in the terminal reaction at the end
of the electron transport chain
- a proton gradient and pmf is generated with the help of an anaerobic electron
transport chain
- e.g. sulphate and sulphur-reducing bacteria, such as Desulfovibrio and
Desulfuromonas, use sulphate and sulphur as terminal electron acceptor
molecules
Anaerobic respiration & Environment:
The sulphate- and sulphur-reducing anaerobic bacteria Desulfovibrio and
Desulfuromonas thrive in oxygen-poor or depleted mud or soil where
they are responsible for much of the rotten eggs-smelling hydrogen
sulphide (H2S); H2S is responsible for the typical, unpleasant smell of
stagnant and polluted waters
46
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Fermentation is a type of energy-converting metabolism in which the substrate is
metabolized without the involvement of an outside (= exogenous) oxidizing agent
(in the most common case oxygen)
Note: Fermentation typically – but not necessarily – occurs anaerobically, i.e. in the
absence of oxygen, but this is NOT the distinguishing feature of fermentation

In fermentation, the “metabolically collected” electrons are taken up by (a) cell
internal (= endogenous) molecule(s), i.e. most importantly (as you will see further
below) by pyruvate

During fermentation and under anaerobic conditions a cell uses solely the glycolytic
pathway (= Glycolysis) of cellular respiration to run its energy household
 after fermentation of glucose only 2 ATP are retrieved by this truncated cellular
Respiration
 in order to keep the fermentive, ATP-generating pathway running, the
resulting NADH + H+ molecules are regenerated by converting the end product
pyruvate into either:
1. Ethanol
 yeast and bacteria switch to this process called ‘alcoholic fermentation’
(see Graphic below)
2 Pyruvate (C3) + 2 NADH + H+  2 Ethanol (C2) + 2 CO2 + 2 NAD+
 CO2 and ethanol, as a still energy-rich molecule, are produced and the latter
molecule accumulates as a (toxic) waste product during this reaction
 anaerobic fermentation is of great importance in the industrial production of
alcoholic beverages e.g. beer, wine and cider
another way of regenerating (=recycling) NADH + H+ is by formation of
2. Lactic Acid
 is formed in various cells under lack of oxygen supply in a process called
‘lactic acid fermentation’ (see Graphic below)
 only 2 ATP are gained pro molecule of glucose (same as in alcoholic
fermentation) but no CO2 is released and the acidic 3-carbon molecule
lactate is the end product
 lactate fermentation plays a fundamental role in the industrial production of
dairy products, e.g. cheese and yoghurt, or fermented foods, such as
sour cabbage (“Sauerkraut”)
 Lactic acid is also formed in the skeletal muscle under strenuous exercise
conditions when the oxygen supply usually becomes limited; there lactate
contributes to the aching body symptoms commonly called ‘sour muscles’
47
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
1) Alcoholic fermentation



metabolic dead-end product
ethanol is toxic
carbon-loss for the cell
2) Lactic acid fermentation



end product can be recycled back to pyruvate
(in the presence of oxygen!)
lactate changes the intracellular pH
no carbon loss for the cell!
 e.g. red muscle cells after heavy exercise, lactobacilli
48
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Many bacteria which live in scarcely oxygenated environments, e.g. deep soil or
teeth cavities are so-called strict anaerobes
 that means, they need anaerobic conditions to grow and are poisoned in the
presence of oxygen
Anaerobic respiration & Disease
Anaerobic bacteria living in the oxygen-poor crevices of our teeth, such as
Porphyromonas gingivalis or Bacteroides forsythus, are majorly
responsible for the development of tooth decay (cavities) and periondontal
disease

Other bacteria which switch between ATP-formation by fermentation or with the
help of chemio-osmosis and the pmf are called facultative anaerobes
 one example is a bacterium called Escherichia coli (or E.coli) which thrives as
an important so-called symbiotic organism in our intestine
 modified strains of the same bacterium play a tremendously important role in the
modern techniques of Molecular Biology and Biotechnology (see UNIT 7)
49