Important words and
concepts from Chapter 5, Black, 1999 (3/28/2003):
by Stephen T. Abedon (abedon.1@osu.edu)
for Micro 509
at the Ohio State University
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Course-external links are
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(1)
Chapter Title: Essential Concepts of Metabolism
(2)
Metabolism = Anabolism + Catabolism (anabolism, catabolism)
(a)
Catabolism
is the breakdown of complex things to yield energy
(b)
Anabolism
is the energy-requiring build up of complex things
(c)
Metabolism
is the sum of the biochemical reactions that take place within a living
organism
(d)
See Figure 5.1, Metabolism,
the sum of catabolism and anabolism
(e)
[an
introduction to metabolism (MicroDude)] [index]
(a)
"All
catabolic reactions involve electron
transfer, which allows energy to be captured in high-energy bonds in ATP
and similar molecules. Electron transfer is directly related to oxidation and
reduction"
(b)
[electron transfer reactions
(Google Search)]
[index]
(a)
Oxidation is the removal of an electron from a
molecule or atom
(b)
Oxygen,
by stealing electrons from other atoms (or molecules) oxidizes those molecules
(c)
Oxygen
is an oxidizer
(d)
In
the process of oxidizing other atoms and molecules, oxygen is reduced
(e)
[oxidation (MicroDude)] [index]
(a)
Reduction is the gain of an electron by a molecule or an atom
(b)
[The rusting of metals, the
process involved in photography, the way living systems produce and utilize
energy, and the operation of a car battery, are but a few examples of a very
common and important type of chemical reaction. These chemical changes are all
classified as "electron-transfer" or oxidation-reduction reactions.
The term, oxidation, was derived from the observation that almost all elements
reacted with oxygen to form compounds called, oxides. A typical example is the
corrosion or rusting of iron… Reduction, was the term originally used to
describe the removal of oxygen from metal ores, which "reduced" the
metal ore to pure metal… Based on the two examples above, oxidation can be
defined very simply as, the "addition" of oxygen; and reduction, as
the "removal" of oxygen. But there is a lot more to
"oxidation-reduction"… (Internet Chemistry)]
(c)
[Oxidation-reduction reactions
always involve a change in the oxidation state of the atoms or ions involved.
This change in oxidation state is due to the "loss" or
"gain" of electrons. The loss of electrons from an atom produces a
positive oxidation state, while the gain of electrons results in negative
oxidation states. (Internet Chemistry)]
(d)
[reduction (MicroDude)] [index]
(a)
An
electron acceptor is the substance in a chemical reaction that gains an
electron (that is, is reduced)
(b)
In
catabolism,
ultimately electrons must be donated from one substance (typically containing
carbon) to some other substance (often oxygen)
(c)
The
last substance receiving the electrons before their elimination from the
organism is termed a final electron acceptor (in aerobic organisms the final
electron acceptor is usually molecular oxygen, which is converted to water upon
reception of these electrons)
(d)
Note
that the reception of electrons by an electron acceptor in a biological system
is typically associated with the gain of a bond to a hydrogen atom (H), e.g.,
water is H-O-H which represents a replacement of the O=O bond of molecular
oxygen with H-O bonds
(a)
An
electron donor is the substance in a chemical reaction that loses an electron
(that is, is oxidized)
(b)
The
complex, energy-rich substances broken down during catabolism are
termed electron donors
(c)
Essentially,
electrons are removed from these substances and the energy associated with
those electrons is used to phosphorylate ADP to produce ATP
(d)
For
a carbon-containing electron donor, the donation of elections typically is
associated with the loss of C-H bonds and the gain of C-O bonds
(a)
The
stripping of electrons from biomolecules is performed to a large extent by a
compound that is abbreviated as NAD+
(b)
When
electrons are stripped from a compound by NAD+, the electrons are
stripped off in pairs (i.e., two electrons per NAD+)
(c)
In
addition, when electrons are stripped off of a compound by NAD+, NAD+
additionally removes two protons, a.k.a., hydrogen ions, a.k.a., H+
(d)
This
converts NAD+ into NADH + H+ (i.e., NADH plus one
hydrogen ion)
(e)
Note
that in such reactions NAD+ serves as the electron acceptor (with
NADH + H+ formed upon acceptance of electrons) and the compound from
which the electrons are stripped serves as the electron donor (NAD+
is reduced to form NADH + H+ and the electron-donating molecule is
similarly oxidized)
(f)
[NADH
(MicroDude)]
[index]
(a)
Usually
either physical or chemical sources of energy are converted into ATP
(b)
That
is, the ultimate product of most catabolic pathways within cells is the
generation of ATP
(c)
It
is the stripping of biomolecules of their electrons that, either directly or
indirectly, turns these complex molecules into simpler ones (e.g., ultimately
water and carbon dioxide)
(d)
The
energy associated with these removed electrons is then extracted to supply the
energy necessary to phosphorylate ADP to make ATP
(e)
Some
of that energy is then liberated to power anabolic reactions as ATP is
converted back to ADP in a dephosphorylation reaction
(a)
Biochemical
pathways, such as those involving ATP and/or NADH, are catalyzed by enzymes
(b)
Enzymes
are proteins with specific amino acid sequences and three dimensional
structures
(c)
Enzymes
tend to be fairly specific in what chemical reactions they are capable of
catalyzing
(d)
The
term catalysis refers to the speeding up of chemical reactions; in this context
it additionally means the allowing of specific chemical reactions to proceed
even at relative low temperatures (low meaning, for example, normal body
temperature rather than, for example, at the boiling point of water)
(e)
The
three-dimensional structures of enzymes are unstable at even modestly high
temperatures, and one reason that heat can be damaging to organisms is that it
serves to denature (inactivate) their enzymes, thus turning off their
biochemical pathways
(f)
Too-low
temperatures can slow or even halt enzyme activity
(g)
Certain
antimicrobials function by inhibiting the activity of specific enzymes
(h)
In
general, enzymes have evolved to display optimal activity within environments
that are similar to those in which the enzymes served during the evolution of
an organism; deviations from these optimal conditions, either in terms of
temperature, pH, or chemical concentrations can and do adversely affect enzyme
functioning
(i)
[enzymes (MicroDude)] [index]
(a)
One,
almost universally common enzyme-catalyzed biochemical pathway is glycolysis
(b)
Glycolysis
is named for the splitting of a sugar (typically taught with glucose as the
starting sugar) into two smaller sugars (actually, the splitting of a
six-carbon sugar into two three-carbon sugars)
(c)
Glycolysis
serves as a catabolic reaction employed to generate ATP
(d)
Additionally,
glycolysis generates compounds that are then employed by cellular respiration (another catabolic
pathway) to generate additional ATP
(e)
In
the course of glycolysis, NAD+ is employed twice, generating
two NADHs (plus two of their associated H+) per glucose molecule
entering this pathway
(f)
In
addition, one ATP is generated (net) per NADH generated
(g)
See Figure 5.11, The
reactions of glycolysis, and note the generation of two NADHs and a net two ATPs (four ATPs are
actually generated per glucose, but two of these are lost in the course of
initiating the reaction)
(h)
[glycolysis (MicroDude)] [index]
(a)
Though
two ATPs are generated by glycolysis (per glucose), this generation comes at
the expense of converting two NAD+ into two NADH
(b)
NADH
is not a substrate for the glycolysis reactions, and cells possess only limited
supplies of NAD+
(c)
Unless
cells additionally possess a means of generating NAD+, they cannot
continue to catalyze the glycolytic pathway and soon run out of ATP (and thus
stop metabolizing)
(d)
Note,
however, that though cells can and do make NAD+ from other
substances in the cell as needed, the majority of NAD+ is produced
via a process of regeneration from NADH
(e)
How
cells regenerate NAD+ from NADH depends on whether they are growing
aerobically (with oxygen, or, at least, with a more or less equivalent final
electron acceptor) or anaerobically (without oxygen or other more or less
equivalent final electron acceptor)
(f)
Cells
growing anaerobically are limited to glycolysis (or analogous catabolic pathways)
to generate their ATP
(g)
[regeneration of NAD+
(Google Search)] [index]
(a)
For
organisms limited to glycolysis (or analogous catabolic pathways)
for their generation of ATP, NAD+ is regenerated via a process
called fermentation
(b)
In
fermentation the electrons (and hydrogen ions) associated with NADH are donated
to an organic molecule
(c)
This
reduces
the electron acceptor (the organic molecule) while NADH is oxidized back to
NAD+, and thus made available to continue glycolysis
(d)
Typically
the electron acceptor is either pyruvate or a product of pyruvate
(e)
Pyruvate
is the organic product of glycolysis
(f)
See Figure 5.11, The
reactions of glycolysis
(g)
The
products of fermentation pathways are varied and depend on the organism doing
the fermenting
(h)
See Figure 5.12,
Fermentation pathways
(i)
The
kind of fermentation pathway employed by an organism, as well as the kinds of
sugars an organism is capable of metabolizing, together are employed as means
of diagnosis (i.e., organism identification) as we will be employing in the
laboratory
(j)
[fermentation (Google Search)]
[fermentation links (including how to make various alcoholic
beverages) (MicroDude)] [index]
(14)
Homolactic-acid fermentation
(a)
Homolactic-acid
fermentation is the fermentation pathway harnessed by lactobacilli
(b)
This
fermentation process is used, for example, to make milk-based sour products
such as yogurt
(c)
Additionally,
homolactic-acid fermentation is employed by our own muscles during anaerobic
exercise
(d)
See Figure 5.13, Homolactic
acid fermentation
(e)
[homolactic fermentation,
homolactic-acid fermentation
(Google
Search)] [index]
(a)
Alcoholic
fermentation is the fermentation pathway employed by yeasts
(b)
Products
include ethyl alcohol and carbon dioxide which are used in bread making and
alcohol beverage fermentation
(c)
See Figure 5.14, Alcoholic
fermentation
(d)
[role of yeast in the
production of alcoholic beverages] [creationism and alcohol fermentation complete with a
wonderful example of how basic knowledge of biochemistry and probability theory
does not a biologist (nor a
theologian) make] [index]
(e)
[alcoholic fermentation,
making beer (Google Search)] [index]
(a)
Mixed-acid
fermentation is the fermentation pathway employed by bacteria such as Escherichia coli
(b)
A
variety of fermentation products are produced
(c)
In
addition to acids, gas is produced by this reaction, which is employed
diagnostically using biochemical tests
(d)
[mixed-acid fermentation,
lambic beers (Google Search)] [lambic beers (which
apparently result from mixed-acid, alcoholic, and lactic-acid fermentations, in
that order) (Peter Van Osta)] [index]
(17)
Aerobic (cellular) respiration
(a)
An
additional means by which NAD+ may be regenerated from NADH is
termed aerobic or, more generally, cellular respiration
(b)
In
aerobic respiration, oxygen serves as a final electron acceptor,
glucose is converted entirely into carbon dioxide and water, and over ten-times
more ATPs are generated than as from glycolysis alone
(c)
More
generally, in cellular respiration an electron transport chain is employed to
oxidize NADH;
in aerobic respiration the final electron acceptor in this electron transport
chain is oxygen, while additionally their exist anaerobic forms of cellular
respiration in which a substance other than oxygen can serve as the final
electron acceptor of the electron transport chain (only a relatively small
subset of bacteria are capable of this anaerobic cellular respiration)
(d)
Thus,
cellular respiration is a means by which many additional ATPs are generated per
glucose while NAD+ is regenerated via the
employment of an electron transport chain; cellular respiration uses the
products of glycolysis and thus requires glycolysis (or analogous pathways) to
proceed
(e)
[cellular respiration overview (MicroDude)]
[index]
(a)
Organisms
must procure carbon, and this carbon comes either from the inorganic
environment or from other organisms
(b)
The
procurement of reduced carbon, or the manufacture of
reduced carbon from not-reduced carbon (e.g., from carbon dioxide), is
essential to life forms since biomolecules (e.g., carbohydrates, proteins,
etc.) are reduced-carbon compounds
(a)
Organisms
termed autotrophs obtain their carbon from the inorganic sources, i.e., carbon
dioxide
(b)
For
example, chloroplasts reduce carbon dioxide into carbohydrate
(c)
Note
that they do this by donating electrons to carbon dioxide (in a complex
biochemical reaction called the Calvin-Benson cycle)
(d)
[autotrophic bacteria
(Google Search)] [autotroph (MicroDude)] [carbon dioxide links (MicroDude)] [photosynthesis
(MicroDude)]
[index]
(a)
Farther
up on the food chain are the heterotrophs which obtain their reduced carbon by
eating other organisms
(b)
Since
organisms are made up of biomolecules, and biomolecules consist of reduced
carbon compounds, organisms are a rich source of reduced carbon compounds
(e.g., this is one aspect of what you obtain from a McDonald's hamburger—you are a heterotroph)
(c)
[heterotrophic bacteria
(Google Search)] [heterotroph (MicroDude)] [catabolism in heterotrophs]
[index]
(a)
Organisms
grow, repair themselves, and reproduce at the expense of energy obtained from
the environment
(b)
Energy
must constantly flow into ecosystems in part to balance the energy lost as
organisms grow, repair themselves, and reproduce
(c)
Energy
may be procured either as chemical energy (e.g., glucose) or as physical energy
(i.e., light)
(d)
[energy
(MicroDude)]
[index]
(a)
An
organism that obtains its carbon from carbon dioxide and its energy from
photons is termed a photoautotroph
(b)
Examples
of photoautotrophs include plants, algae, and cyanobacterial
(c)
[photoautotrophic bacteria
(Google Search)] [photoautotroph (MicroDude)] [index]
(a)
Many
organisms obtain both their energy and their reduced carbon by eating other
organisms, either alive or after the other organism has died, either whole or
in parts
(b)
Such
organisms are termed chemoheterotrophs
(c)
Chemoheterotrophs
are highly relevant to medical microbiology because essentially all cellular
pathogens are chemoheterotrophs
(d)
In
other words, things that cause disease typically live by eating you
(e)
[chemoheterotrophic bacteria
(Google Search)] [chemoheterotroph (MicroDude)] [index]
(a)
Certain
bacteria are capable of obtaining energy from light, but are not similarly
capable of reducing carbon dioxide
(b)
Such
organisms must consume the remains of other organisms to obtain their
reduced-carbon compounds, but can generate energy from light
(c)
Such
organisms are described as photoheterotrophs (and include the purple nonsulfur
bacteria as well as the green nonsulfur bacteria)
(d) <