Transcript Metabolism

Metabolism
Oxidation-Reduction
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Two truisms:
– Chemistry is the study of the movement of
electrons between atoms
– Life is applied chemistry
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Oxidation: a molecule loses an electron
– LEO: Lose Electron Oxidation
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Reduction: a molecule gains an electron
– GER: Gain Electron Reduction
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In living cells, there are no free electrons: every
time an electron leaves one molecule, it goes to
another one.
– Thus, all oxidation reactions are coupled with
reduction reactions: one compound is oxidized
while the other is reduced. “Redox” reactions
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Electrons are often accompanied by H+ ions.
Thus, FAD is the oxidized form, and FADH2 is
the reduced form: it has 2 more electrons (and
H’s) than FAD.
– For this reason, enzymes that perform oxidations
are usually called dehydrogenases.
Redox Potential
• Redox potential is a measure of the affinity of compounds for
electrons. The more positive a compound’s redox potential is, the
greater its tendency to acquire electrons.
– Redox potential is measured in millivolts (mV), relative to hydrogen at 1
atm pressure. Compounds are at 1 M concentration.
• H2  2 H+ + 2 e• The idea is, if your compound was mixed with hydrogen gas, would electrons
flow from your compound to the hydrogen (compound has a negative redox
potenitial), or from the hydrogen to your compound (compound has a positive
redox potenital)?
– Redox potential is affected by the concentration of the reactants and also
by the redox potential of the environment
• When electrons in compounds with lower (more negative) redox
potentials are moved to compounds with higher potentials, energy is
released. Organisms capture this energy to live on.
Some Redox Reactions
Used in Bacteria
Some Lithotrophic Reactions
Fermentations
•Fermentation is defined as a process where organic
molecules are both the electron
donor and the electron acceptor.
•Since the complete oxidation of organic molecules
ends at carbon dioxide, fermentations are by
definition incomplete oxidations: there is always
some potential energy left in the products of a
fermentation.
•And thus the fermentation products excreted
by one species are often used as food sources
for another species.
•The best known fermentations involve the products
of glycolysis.
•Glucose is oxidized to pyruvate, but the electrons
from glucose are used to convert NAD+ to NADH.
•To get rid of these electrons, NADH is used to
reduce pyruvate to lactate (as in anaerobic human
muscle) or to ethanol (as in yeast). Both of these
pathways are used in various bacteria.
Other Fermentations
Aerobic Respiration
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The most efficient way of
producing energy is by oxidizing
organic compounds to carbon
dioxide = respiration. This is the
process used by most eukaryotes
and aerobic bacteria.
Energy Generation
• Energy in the cell is generated
and used in the form of ATP.
• Two basic way s of generating
ATP:
– substrate-level
phosphorylation. The simplest
form: transfering a phosphate
group from another molecule
to ADP, creating ATP.
– chemiosmotic: generation of a
proton (H+) gradient across a
membrane. This gradient is
called “proton-motive force”.
Chemiosmotic Theory
•The same basic process in the mitochondria
as in many bacteria.
•High energy electrons from an electron
donor are used to pump H+ ions out of the
cell, into the periplasmic space
•This drains energy from the electrons
•Electron transport
•There are thus more H+ ions outside than
inside: the pH outside is lower than inside.
•The H+ ions are then allowed back into the
cell by passing them through the ATP
synthase protein, which uses the energy of
the H+ ions flowing down the gradient to
attach phosphate (Pi) to ADP, creating ATP.
•the gradient is both chemical: more H+
outside than inside, and electrical: more +
charge outside than inside
Carbon Assimilation
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Heterotrophic organisms obtain
organic carbon compounds from
pre-existing organic molecules.
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often the same molecules they are
using for energy: glucose for
example.
Autotrophs “fix” carbon dioxide into
organic carbon.
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4 pathways:
Calvin cycle (ribulose bis-phosphate
pathway. Used in plants and many
bacteria: the most common pathway
Reductive TCA cycle: run the Krebs
cycle backwards
Reductive acetyl CoA pathway,
which requires hydrogen gas and
produces carbon monoxide as an
intermediate.
3-hydroxypropiuonate cycle. Seems
to mostly be in Archaea
Carbon Assimilation Pathways
Nitrogen Assimilation
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Most of the nitrogen on Earth is
nitrogen gas, N2, which is strongly held
together by a triple bond.
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Nitrogen’s major use in the cell is as a
component of amino acids, in the
ammonium form: -NH2
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nitrogen fixation, converting nitrogen to
ammonia, is very energy-intensive and
carried out by a small group of bacteria,
including some Clostridium.
some nitrogen is also fixed by lightning.
Many organisms get their nitrogen from
organic nitrogen compounds
some organisms perform
ammonification, which means splitting
the amino group off organic
compounds, releasing ammonium ions.
Nitrogen is also found as nitrate. Most
bacteria can reduce nitrate (NO3-) to
nitrite (NO2-) and then to ammonia:
assimilatory nitrate reduction.
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nitrate is also degraded back into
nitrogen gas by other bacteria:
denitrification.
the reverse process, converting
ammonia into nitrate and nitrite, is used
as an energy source by some
lithotrophs. It is called nitrification.
More Nitrogen Assimilation
• When nitrogen is taken into the
cell in the form of ammonium
ions, it is attached to glutamate,
forming glutamine, using the
enzyme glutamine synthetase.
• Alpha-ketoglutarate, glutamate,
and glutamine can all be
interconverted.
– this is the source of the amino group
of amino acids and amino sugars.
Assimilation of Other Elements
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Cells use several other elements: C,
H, O, and N are the major ones
– also covalently bound: P, S, Se
– ions: Na, K, Mg, Ca, Cl
– trace elements (mostly as enzyme
co-factors): Fe, Mn, Co, Cu, Ni,
Zn, others....
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Sulfur can be incorporated from
organic sources, but it is often
taken into the cell as sulfate (SO42). Getting into the cell requires
attaching it to the ATP derivative
APS, after which it is reduced to
sulfide (S-2) and then attached to
serine, converting it to cysteine.
phosphate (PO4-3) is generally
found in the same form as it is
used. It just needs to be
transported into the cell.
Intermediary Metabolism
• Lots of interconversions.
• it is necessary to make:
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amino acids (proteins)
nucleotides (DNA, RNA, and ATP)
sugars (part of nucleotides, food, structure)
lipids: food storage and membrane
several co-factors for enzymes: biotin, cytochromes, panthothenic
acid, NAD, riboflavin, cobalamin, ubiquinone, etc.
• The central metabolic pathways of glycolysis and the
Krebs cycle have several side branches that feed these
biosynthetic pathways.
Enzyme Nomenclature
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Every chemical interconversion requires an enzyme to catalyze it.
Nearly all enzyme names end in –ase
Enzyme functions: which reactants are converted to which products
– Across many species, the enzymes that perform a specific function are usually
evolutionarily related. However, this isn’t necessarily true. There are cases of two entirely
different enzymes evolving similar functions.
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Enzyme functions are given unique numbers by the Enzyme Commission.
– E.C. numbers are four integers separated by dots. The left-most number is the least
specific
– For example, the tripeptide aminopeptidases have the code "EC 3.4.11.4", whose
components indicate the following groups of enzymes:
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EC 3 enzymes are hydrolases (enzymes that use water to break up some other molecule)
EC 3.4 are hydrolases that act on peptide bonds
EC 3.4.11 are those hydrolases that cleave off the amino-terminal amino acid from a polypeptide
EC 3.4.11.4 are those that cleave off the amino-terminal end from a tripeptide
Top level E.C. numbers:
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E.C. 1: oxidoreductases (often dehydrogenases): electron transfer
E.C. 2: transferases: transfer of functional groups (e.g. phosphate) between molecules.
E.C. 3: hydrolases: splitting a molecule by adding water to a bond.
E.C. 4: lyases: non-hydrolytic addition or removal of groups from a molecule
E.C. 5: isomerases: rearrangements of atoms within a molecule
E.C. 6: ligases: joining two molecules using energy from ATP
Detailed Pathways
• For many compounds, there can be more than one way to
produce it. Some organisms have more than one pathway
to a given compound, and sometimes different organisms
produce it by different mechanisms.
• KEGG (Kyoto Encyclopedia of Genes and Genomes) has a
comprehensive set of pathway maps, with individual
species differences noted.
– KEGG also has information about individual enzymes and ligands.
You can get there by clicking the elements of the map.
– http://www.genome.ad.jp/kegg/pathway.html