Download Metabolism: the chemical reactions of a cell

Metabolism: the chemical reactions of a cell
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• All organisms need two things with which to grow:
– Raw materials (especially carbon atoms)
– Energy.
• Types of metabolic reactions:
– Anabolism: biosynthesis; reactions that create
large/complex molecules from smaller, simpler ones. Use
raw materials and energy.
– Catabolism: degradation; reactions that break down
large/complex molecules, used to generate energy for use
and to produce smaller, building block molecules.
Energy: where from? What for?
• Chemotrophs vs. phototrophs
– Chemotrophs get energy from molecules
• Chemolithotrophs get energy from oxidation of
inorganic substances.
• Chemoorganotrophs get energy from oxidation of
organic compounds (like we do).
– Phototrophs get energy from sunlight
• Energy is needed to power the cell
– Biosynthesis to respond to environment, to grow
– Active transport, motility, etc.
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Bacteria obtain energy through
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oxidation/reduction reactions
Oxidation: molecule gives up electrons
Reduction: molecule accepts electrons
Oxidation/reduction (redox) reactions always occur
in pairs; if electrons are removed, they must go
somewhere!
Biological redox reactions usually involve PAIRS of
electrons.
Biological redox reactions often involve entire
hydrogen atoms, not just the electrons (so called
dehydrogenation reactions).
Redox reactions release energy for use
• Depends on concentration, redox potential, etc.
• XH2 + Y
X + YH2 shows oxidation of X, reduction of Y
• Note that 2 H atoms are transferred, not just electrons
• Familiar redox reaction that releases energy:
• CH4 + 2O2
CO2 + 2H2O natural gas burning.
• Biological reactions release energy gradually, trap it as
ATP
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Is it good to eat?
• Reduced molecules have
lots of energy.
• Have lots of H, few O
• Oxidized molecules have
little energy;
• lots of O or few H.
Carbon dioxide
glucose
Redox Calculations
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• One can assign an oxidation number to the carbon
atoms in a molecule to determine how much energy
an organic molecule has.
• Oxidation numbers:
H = +1
O = -2
Oxidation state of carbon in methane (CH4):
Not charged, so numbers add up to 0. So if all the
H = 4 x 1 = +4, then C must be -4.
For CO2, 2 x -2 = -4; no net charge, then C must be = +4.
Observe the origin of the term “reduced”: If carbon
dioxide is ‘reduced” to methane (carbon accepts
electrons), then the oxidation number of the carbon gets
reduced (number gets lower) from +4 to -4.
Metabolic reactions require enzymes
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• Reactions operate in pathways:
A B C D
Where A-D are different molecules
Each step is catalyzed by a different enzyme.
A Catalyst is something that speeds up a chemical reaction and
is not consumed in the reaction, but can be re-used.
Enzymes are biological catalysts; 99.99% of them are proteins.
Enzymes are very specific; a different one is required for
each type of chemical reaction.
Because the 3-D shape of an enzyme is critical for its
function, anything that alters that (heat, high salt, extreme
pH) will affect how fast or whether it works.
Importance of 3D shape
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• Every enzyme has an active site, a location where
the substrate (the molecule to be acted on) fits into
the enzyme.
• The enzyme then performs chemistry on the
substrate, producing a product(s) which then
diffuses away, leaving the enzyme free to act on the
next substrate.
• Every metabolic reaction we will look at happens in
this way.
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Enzyme function depends on shape
Product
Substrates
Enzyme brings substrates together in active site, increasing
the rate at which they react.
http://www.columbia.edu/cu/biology/courses/c2005/images/substratesarelig.6.gif
More about Enzymes
• Sometimes an enzyme needs help
– Protein alone = apoenzyme
– Helper molecule: cofactor
• Could be inorganic like a metal ion (Fe+2)
• Could be organic coenzyme (like CoA, NAD)
– Apoenzyme + cofactor = holoenzyme.
– Cofactors have an effect on nutrition
• Bacteria have certain mineral requirements.
• Vitamins are cofactors that are needed in the “diet”.
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Enzymes can be stopped
• Conditions that disrupt the 3D shape
– Acidic, alkaline, high salt, high temperature, etc.
– These conditions thus affect growth of cell also.
• Inhibitory molecules affect enzymes
– Competitive inhibitors
• Fit in active site but are not changed; prevent normal
substrate from binding, prevent reaction.
– Non-competitive inhibitors
• Bind permanently to active site or other site which
changes molecular shape; prevents reaction.
– Allosteric inhibitor: temporary binding, regulates.
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Competitive Inhibition
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Both the substrate and the
inhibitor fit into the active
site, but the inhibitor isn’t
altered by the enzyme. As
long as the inhibitor is in
the active site, the substrate
cannot enter the active site
and react. The more
inhibitor molecules that are
present, the more often one
of them occupies the active
site.
ghs.gresham.k12.or.us/.../ competitiveinhib.htm
Allosteric sites
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In allosteric site, inhibitor is not reacted, but causes a shape
change in the protein. The substrate no longer fits in the active
site, so it is not chemically changed either.
ghs.gresham.k12.or.us/.../ noncompetitive.htm
Introduction to important molecules in
metabolism
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• Biological reactions release energy from redox reactions
gradually, trap it as ATP
• ATP is the energy molecule that cells use to power
most of their activities. “energy currency”
• ATP is a molecule under stress:
– too many negative charges in one place. Release of 1
phosphate: ATP → ADP + Pi relieves that stress,
releases energy which can be used for:
– cellular activities such as transport, motility,
biosynthesis, etc.
Structure of ATP
http://www.ustboniface.mb.ca/cusb/abernier/Biologie/Module1/Image
s/atp.jpg
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The ATP cycle
ATP is hydrolyzed to
ADP to release
energy.
Energy is used to
reattach the
phosphate to ADP to
regenerate ATP.
Other molecules used for energy
include GTP and PEP.
www.cat.cc.md.us/.../ metabolism/energy/fg1.html
Important molecules: the electron carriers
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• The energy released in redox reactions is often thought of as
the energy in the bonds between the H and the C; when a
molecule is reduced by transfer of the H, the energy is
conserved in that reduced molecule.
• The most common electron carrier is NAD:
• NAD + XH2
X + NADH + H+
– where NAD carries 2 e-, 1 H+
– Reduced NAD (NADH) is like poker chips, energy that
can’t be spent, but can be “cashed in” later to make ATP
(which can be “spent”, i.e. used as an energy source for
cell activities).
Other electron carriers
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• NADP
– Reduced during some reactions such as those in the
Pentose Phosphate pathway, Photosynthesis
– NADPH used to donate H for biosynthesis reactions such
as the Calvin Cycle, amino acid biosynthesis.
• FAD
– Reduced to FADH2
– Used in the Krebs Cycle, other reactions
Oxidations for energy
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If this reaction is reversible, and every oxidation is coupled to
a reduction, how can the oxidation of XH2 yield energy?
Describes the tendency of a reaction to occur spontaneously, to
release energy. Two major factors are the tendencies of X and
Y to give up or accept electrons and their concentrations.
In this example, we expect that YH2 will subsequently be
oxidized, driving the reaction to the right and that XH2 has a
greater tendency to give up electrons than YH2 .