Transcript Fig. 5-1 - Indiana University Northwest

Metabolism is the sum of all chemical processes carried out by living
organisms. Anabolism = reactions that require energy to synthesize
complex molecules from simpler ones. Needed for growth, reproduction
and repair. Catabolism = reactions that release energy by breaking
complex molecules into simpler ones that can be then reused as building
blocks. Needed for energy for its life processes including movement,
transport, and synthesis of complex molecules (anabolism).
Fig. 5-1
All catabolic reactions involve electron transfer, capturing energy in
high-energy bonds in ATP. Electron transfer is related to oxidation and
reduction (redox reactions).
Oxidation is the loss of electrons, gain of oxygen, loss of hydrogen, and
it is exothermic, exergonic (it gives off heat energy).
Reduction is the
loss of oxygen, gain the electrons, gain of energy (stores energy) and is
endothermic, endergonic (requires energy).
When one substance
gains electrons (is
reduced), another
must lose electrons
(is oxidized).
Think gain electrons =
gains negative = reduction.
Gaining electrons can
mean gaining hydrogen or
losing oxygen.
2H2 + O2  2 H2O
Hydrogen is the reducing agent (electron donor) and
Oxygen is the oxidizing agent. Hydrogen is oxidized.
Fig. 5-1 table
Microorganisms are very versatile in the ways in which they obtain
energy. Microorganisms are categorized by the ways in which obtain
energy and obtain carbon.
Obtain Carbon
Obtain energy
Fig. 5-2
Chemoheterotrophs include all infectious microorganisms. They use
glycolysis, fermentaition, and aerobic respiration to obtain energy.
Glycolysis and fermentation do not require oxygen (anaerobic).
Aerobic respiration does require oxygen as a final electron acceptor
and captures large amounts of energy from a glucose molecule as ATP
as compared to glycolysis and fermentation.
Photosynthetic
microorganisms
and plants use
light energy and
hydrogen from
water to reduce
carbon dioxide
to organic
substances like
glucose.
Fig. 5-3
All chemical processes in living organisms including
photosynthesis, glycolysis, fermentation, and aerobic respiration,
consist of a series of chemical reactions in which the product of
one reaction serves as the substrate (reacting material) for the next,
a metabolic pathway.
Catabolic pathways capture energy
and anabolic pathways make the
complex molecules needed by the
cell, including the enzymes needed
for the metabolic pathways.
Energy captured in catabolic reactions as ATP is used in
anabolic pathways. Do checklist page 111.
Enzymes act as catalysts – substances that remain unchanged while they
speed up reactions 1000s to 1,000,000s of times. Even “spontaneous” or
exothermic reaction require activation energy – the energy to get things
going. Enzymes lower the activation energy required.
Enzymes also allow cells to control when and how much of any
particular molecule is made or broken down.
Fig. 5-4
Enzymes also provide a surface on which reactions can take place. The
enzyme positions the reactants in such a way to enable them to react
easily.
Random movement of
molecules leads the
substrate to bump into
the active site of the
enzyme. Because it
“fits”, it remains there,
forming an enzymesubstrate complex.
This positions the
substrate to allow the
chemical reaction to
take place.
Enzymes are very
specific due to the
shape and the
electrical charges in
the active site. Each
enzyme binds only
one substrate.
Endoenzymes are
intracellular and
exoenzymes, made
inside the cell, work
outside of the cell.
“fits” due to shape and
chemical nature (noncovalent bonds)
Fig. 5-5
Enzymes are usually named by adding –ase to their substrate.
Example: lipases break down lipids
Many enzymes consist of a protein apoenzyme that must combine with
a nonprotein coenzyme (an organic molecule) and/or a cofactor (an
inorganic ion). Many coenzymes are synthesized from vitamins.
Coenzymes are inorganic ions – minerals.
Fig. 5-6
Enzymes are controlled (usually by the cell) in
several ways.
Competitive inhibition
Non-competitive inhibition
Negative (or positive) feedback
In competitive inhibition a
competitive inhibitor binds
reversibly to the active site,
blocking the ability of the
substrate to bind. This inhibition
depends on the concentration of
the substrate and the inhibitor.
Sulfa drugs are competitive
inhibitors. They compete with
PABA, the substrate converted to
folic acid, slowing the production
of folic acid.
Fig. 5-8
Non-competitive (allosteric) inhibition of enzymes.
The inhibitor binds to the enzyme in an area other than the active site.
However, the binding of the inhibitor changes the shape of the enzyme at
the active site and the substrate can not bind while the inhibitor is
present. Some bind reversibly, but others bind irreversibly and
permanently inactivate the enzyme. The allosteric inhibitor does not
compete with the normal substrate for the active site.
Fig. 5-9
• Although not non-competitive inhibitors, lead,
mercury and other heavy metals can bind to other
sites on enzymes and permanently change their
shape. Changing a molecules shape usually
interferes with its function. The enzyme is
inactivated.
• Feedback inhibition is the most common way in
which a cell controls enzymes. When a synthetic
pathway has made enough of the product, the
product itself will inhibit one of the 1st enzymes in
the pathway – reversible non-competitive
inhibition.
See checklist on page 114 and
How to Ruin an Enzyme
Factors That Affect Enzyme Reactions
Temperature
pH
Concentrations of substrate, product and enzyme
Substrate and enzyme
move around more as temp
increases so they bump
into each other more often
Acidic or alkaline
conditions also denature
enzymes – used to kill
microbes
Fig. 5-10
• Chemical reactions, including enzyme- catalyzed
reactions are reversible given the right
circumstances.
• A + B  AB or AB  A + B
• Chemical equilibrium is reached when there is no
net change in the concentrations of AB, A, or B.
• The concentrations of the substrates and products
influence the direction and the speed (rate) of the
reaction.
– Lots of AB will “push” the reaction toward producing A
and B
– If A and B are used up in other reactions as soon as they
are made, this will keep their concentration low and
“push” the reaction in the same direction – toward A +
B production
Anaerobic metabolism: Glycolysis and Fermentation
Glycolysis: Does not require oxygen
Fig. 5-11
Four major events
1.Phosphorylation
Increased energy
Uses 2
ATP
Incapable of leaving
the cell
2.Breaking sixcarbon sugar  2 3carbon
3.Transfer of
electrons to NAD
4.Capture of energy
in ATP
NADH
2 ATP
made
2 ATP
made
Glycolysis provides relatively small amount of energy (ATP & NADH).
Uses 2 ATP to produce 4 ATP. Electrons are removed from NADH during
fermentation, producing NAD+ which is needed to keep glycolysis going.
Fermentation = metabolism of pyruvate in the absence of oxygen.
Very important because NAD+ must be recycled for glycolysis.
What happens if pyruvic
acid just accumulated in
the cell?
What happens if
there is no NAD+?
Fig. 5-12
Many kinds of
fermentation are
performed by a great
variety of microbes
including pathogens.
The products are
used in diagnosis.
Butyric-butylic
fermentation occurs
in Clostridium
species that cause
tetanus and botulism.
The production of
butyric acid by
Clostridium
perfringens causes
severe the tissue
damage of gangrene
Homolactic Acid fermentation occurs in some types of bacteria called
lactobacilli, in streptococci, and in mammalian muscle cells. This
pathway in lactobacilli is used in making some cheeses.
NADH from step 6 of
glycolysis
NAD+ can now be
reused in glycolysis,
step 6.
Fig. 5-13
Alcoholic fermentation is common in yeasts and is used in making bread
and wine.
NADH from step 6 of
glycolysis
NAD+ can now be
reused in glycolysis,
step 6.
Fig. 5-14
• The ability to ferment sugars other than
glucose forms the basis of other diagnostic
tests. For example, the pathogenic
bacterium Staphylococcus aureus ferments
mannitol (a simple sugar) and produces
acid, which causes phenol red in the
medium to turn yellow (see Figure 5.15).
The nonpathogenic bacterium
Staphylococcus epidermidis fails to ferment
mannitol and does not change the color of
the medium.
Aerobic Respiration
Both anaerobes and aerobes carry out glycolysis. Anaerobes do not use
oxygen, some are killed by exposure to oxygen. Aerobes do use oxygen,
some must use oxygen to survive. Microbes that can use oxygen if it is
available but do not need it are facultative anaerobes. Aerobes do
produce some energy during glycolysis, however, aerobes use glycolysis
as a prelude to aerobic respiration – a much more productive process
which requires oxygen.
In prokaryotes, these reactions occur
in the cytoplasm, in eukaryotes, in the
matris of the mitochondria
Fig. 5-16
The Krebs Cycle (tricarboxylic acid [TCA]
cycle / citric acid cycle) is a sequence of
reactions in which acetyl groups (2 carbon
group) are oxidized to carbon dioxide.
Hydrogen atoms are also removed by NAD+
or FAD and their electrons are transferred to
coenzymes in the electron transport system
which pumps the protons across a membrane
creating a steep gradient.
Each reaction in the cycle is controlled by a
specific enzyme.
The reactions (metabolic pathway) forms a
cycle because oxaloacetic acid, the 1st
reactant, is regenerated.
Three main events:
1. The oxidation of carbon to CO2
2. The transfer of electrons to coenzymes
NADH and FADH2
3. Energy is captured in GTP
During glycolysis H atoms are transferred to NAD or FAD. These transfer the H atoms
to electron carriers embedded in the cell membrane of bacteria or in the inner
membrane of the mitochondria.
Eventually these electrons combine with
the final electron acceptor,
oxygen, to form water.
The arrangement of the
various carriers in the
membrane result in
the protons being
pushed from the bacterial
cytoplasm to outside the cell.
The proton gradient created
in this way is used to make ATP
(oxidative phosphorylation). The electrons and
protons carried by each NADH result in enough energy
via the proton gradient to produce 3 ATP, while
each
FADH2 results in only 2 ATP.
The Electron Transport Chain
Oxidation/reduction
Fig. 5-19
Eukaryotic cells
make ATP via
aerobic
respiration in the
mitochondria
The proton gradient created by the electron transport chain “powers” ATP
synthase, which makes ATP. Like a waterfall, the protons move from high
concentration to low through ATP synthase.
• All electron transport chains are not alike, they
differ from organism to organism. However all
have carriers which accept only hydrogen atoms
and carriers that accept only electrons – resulting
in the pumping of H atoms.
• From the metabolism of a single glucose
molecule, 10 pairs of electrons are transported by
NAD (2 pairs from glycolysis, 2 pairs from
pyruvic acid conversion and 6 pairs from Krebs).
Two pairs are transported by FAD
– 10 X 3=30, 2 X 2=4, total = 34 ATP, plus 2 ATP
molecules from glycolysis and 2 GTP from Krebs
= 38 ATPs per glucose molecule.
– Compare to glycolysis and fermentation alone!
Chemiosmosis occurs in and around the cell membrane in bacteria
and the inner membrane of mitochondria in eukaryotic cells.
Electrons are transferred along the electron transport chain, protons
are pumped outside the membrane, so the ions’ concentration is
higher outside. This produces a force that drives the protons back
into the cell or mitochondrial matrix. In addition, there is an
electrochemical gradient, with outside more positively charged
(more H+ ions).
The protons flow through
special channels in
ATP synthase, energy
released is used
to produce ATP.
Fig. 5-20
Anaerobic Respiration
Some bacteria use only parts of the Krebs’ Cycle and the electron
transport chain. These anaerobes do not use free oxygen as their final
electron acceptor. Instead they use inorganic oxygen-containing
molecules. However, this produces
fewer ATP molecules.
Urinalysis can be done to test for removal
of one oxygen atom from nitrate to form
nitrite. A positive test indicates the
presence of bacteria like E. coli.
Checklist page 125
See table 5.2 & 5.3
Fig. 5-21
Catabolism of fats
Beta oxidation (oxidation of
the beta carbon)
Fatty acids are broken
apart 2 carbons at a time
to acetyl-CoA.
Fig. 5-22
Fig. 5-24
Amino acids, nucleic acid bases, and ribose are made (anabolic)
from intermediates in glycolysis and from the Krebs cycle
(catabolic). Therefore, these pathways are actually amphibolic.
All organisms
share many
biochemical
characteristics
and require the
same building
blocks to make
proteins and
nucleic acids.
Fig. 5-27
Many biosynthetic pathways are complex, often requiring many
reactions, each with a specific enzyme requirement. Tryptophan
synthesis needs at least 13 different enzymes. Absence of a single
enzyme means the microbe must take up tryptophan from the
environment or die. Microbes also synthesize many carbohydrates and
lipids of course - petidoglycan, etc.
Microorganisms also use
energy for transporting
substances across membranes
and for their own movement.
Fig. 5-28
Active transport requires energy (usually ATP). Active transport uses energy to move
molecules or ion against their concentration gradient. This is like moving something up
a hill, it requires energy.
Active transport is important for
microorganisms to move nutrients that are
present in low concentrations in their
environment. In Gram negative bacteria
porins in the outer membrane form
channels for ions and small hydrophilic
metabolites (facilitated diffusion). After
entering the periplasmic space, a specific
periplasmic protein binds to the
metabolite and allows it to be moved into
the cytoplasm via cell membrane proteins
then act as carriers and enzymes. They
are specific for a single or a few
molecules or ions, and require energy to
move these molecules against their
concentration gradient.
Fig. 4-32
• Group translocation reactions move a substance from
outside to inside a cell while modifying it at the same time.
Ex. Glucose is phosphorylated and can not leave the cell.
– Phosphotransferase system (PTS) consists of
sugar-specific enzyme complexes called
permeases which form a transport system
through the cell membrane. PTS uses energy
from the high-energy phosphate molecule
phosphoenolpyruvate (PEP). PEP provides
energy and a phosphate group. The enzyme
transfers the phosphate to a sugar and at the
same time moves the sugar across the
membrane.
Cell movement requires energy
• Most motile bacteria move by means of
flagella
– Flagellated bacteria move by rotating their
flagella. The energy for this appears to be
provided by a proton gradient much like
chemiosmosis (electron transport chain).
• Some glide etc.
– Myxococcus secrete a substance called a
surfactant which lowers surface tension at one
end of the bacteria. The difference in surface
tension front to back causes the bacterium to
glide.