Transcript lecture 02b

Bacteria need to maintain
themselves, and they try to
reproduce.
To build more copies of
themselves, they require 2 THINGS:
A source of raw materials, and a
source of energy. Without both of
these, life cannot exist.
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Metabolism
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• The chemical reactions used by living cells to obtain
energy from their environment and to use that
energy to make cell material are called metabolism.
• Metabolic reactions are classified as either
– Catabolism: reactions that break molecules down into
simpler forms to get smaller molecules or TO RELEASE
THE ENERGY IN THOSE MOLECULES.
– Anabolism: reactions that USE energy to put molecules
together to make bigger molecules. (building up)
• E.g. reactions that assemble amino acids into proteins
Availability of energy is related to control
• Bacteria require raw materials and energy to grow
– If either one is missing, bacteria cannot reproduce!
– If both are readily available, bacteria will likely multiply
quickly.
– Many bacteria can survive a while without growing, and
can be transported from place to place.
– Bacteria in a nutrient rich environment can grow rapidly
• Infected person
• Hamburger left out at room temperature
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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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Bacteria obtain energy through
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).
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Redox reactions release energy for use
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• 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
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
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ATP is hydrolyzed to
ADP to release
energy.
Energy is used to
reattach the
phosphate to ADP to
regenerate ATP.
www.cat.cc.md.us/.../ metabolism/energy/fg1.html
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Important molecules: the electron carriers -1
• 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, energy has been saved in that reduced
molecule.
• Certain molecules have the job of getting reduced
and carrying electrons to save that energy: NAD
Important molecules: the electron carriers -2
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• The most common electron carrier in biological
redox reactions 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).
An overview of bacterial catabolism
• Model compound: glucose, C6H12O6
• Aerobic metabolism
– With oxygen gas (O2)
– Fermentation and anaerobic respiration – later
• Four major pathways
– Glycolysis, Krebs cycle, electron transport, and
chemiosmosis
• The Goal: gradually release the energy in the
glucose molecule and use it to make ATP.
– The carbons of glucose will be oxidized to CO2.
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Glycolysis: glucose is broken
Glucose is activated
Glucose Glu-6-P
2 ATPs are “invested”
Glu (6 C’s) broken into two 3-C
pieces
2 oxidations steps
NAD
NADH
4 ATPs are produced, net gain:
2 ATPs
2 molecules of pyruvic acid are
produced.
http://members.tripod.com/beckysroom/glycolysis.jpg
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3 ways bacteria use glucose
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EMP = EmbdenMeyerhof-Parnas pathway
Traditional glycolysis, yields 2 ATP
plus 2 pyruvic acids.
Pentose Phosphate
Complicated pathway, produces 5
carbon sugars and NADPH for use
in biosynthesis.
Entner-Doudoroff
Yields only 1 ATP per glucose, but only used by aerobes such
as Pseudomonas which make many ATP through aerobic
respiration.
Krebs Cycle
detailed
http://www.personal.kent.edu/~cearley/PChem/Krebs1.gif
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What happens: carbons of
glucose oxidized completely
to CO2
Preliminary step: pyruvic
acid oxidized to acetyl-CoA.
Things to note: several
redox steps make NADH,
FADH2
One ATP made
OAA remade, allowing
cycle to go around again.
http://www.sp.uconn.edu/~bi107vc/images/mol/krebs_cycle.gi
f
Electron transport
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• Metabolism to this point, per molecule of glucose:
– 2 NADH made during glycolysis, 8 more through the end of Krebs
Cycle (plus 2 FADH2)
• What next?
– If reduced NAD molecules are “poker chips”, they contain energy
which needs to be “cashed in” to make ATP.
– In order for glycolysis and Krebs Cycle to continue, NAD that gets
reduced to NADH must get re-oxidized to NAD.
– What is the greediest electron hog we know? Molecular oxygen.
– In Electron transport, electrons are passed to oxygen so that these
metabolic processes can continue with more glucose.
– Electron carriers in membrane are reversibly reduced, then reoxidized as they pass electrons (or Hs) to the next carrier.
About Hydrogens
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• A hydrogen atom is one proton and one electron.
• In biological redox reactions, electrons are often
accompanied by protons (e.g. dehydrogenations)
• In understanding metabolism, we are not only
concerned with electrons but also protons.
– Also called hydrogen ions or H+
– H+ (hydrogen ions) and electrons are opposites!! Don’t
get them confused!
Electron transport
All occurs at the cell membrane
NADH is oxidized to NAD
H’s are passed to next electron
carrier; NAD goes, picks up more
H.
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Electrons are
passed carrier to
carrier, releasing
energy.
Process can’t continue
without an electron
acceptor at the end. In
aerobic metabolism,
the acceptor is
molecular oxygen.
http://employees.csbsju.edu/hjakubowski/classes/ch331/oxphos/oxphos.gif
Chemiosmosis: electron transport used to make ATP
The membrane acts as an insulator;
protons can only pass through via
the ATPase enzyme; the energy
released is used to power synthesis
of ATP from ADP and Pi.
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Energy
released during
electron
transport used
to “pump”
protons
(against the
gradient) to the
outside of the
membrane.
Creates a proton current (pmf)
much like the current of
electrons that runs a battery.
Proton motive force
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Electrochemical gradient establishes a voltage across the
membrane. Flow of protons (instead of electrons) does work
(the synthesis of ATP).
http://www.energyquest.ca.gov/story/images/chap04_
simple_circuit_light.gif
Overview of aerobic metabolism
• Energy is in the C-H bonds of glucose.
• Oxidation of glucose (stripping of H from C atoms)
produces CO2 and reduced NAD (NADH)
– Energy now in the form of NADH (“poker chips”)
• Electrons (H atoms) given up by NADH at the membrane,
energy released slowly during e- transport and used to
establish a proton (H+) gradient across the membrane
– Energy now in the form of a proton gradient which can do work.
– Electrons combine with oxygen to produce water, take e- away.
• Proton gradient used to make ATP
– Energy now in the form of ATP. Task is completed!
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Central Metabolism:
Funneling all nutrients into central pathways
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•Many other
molecules
besides glucose
can serve as a
source of carbon.
Central Metabolism:
A source of building blocks for biosynthesis
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BUT, these
molecules can’t be
broken down to CO2
for energy AND used
for biosynthesis