Bot 130 Lecture 10

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RNA processing in eukaryotes
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• Flow of Energy
• Bot 130
• Lecture 10

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The sun is the source of energy for life
This was not always so. At first, life used
preexisting compounds in the prebiotic soup.
Then, some bacteria gained the ability to use
chemical reactions, especially involving sulfur
and iron. These organisms were chemoautotrophs.
They made their food from chemical power
preexisting in the environment.
As more and more of the preexisting chemical
gradients were used up, organisms that could
make their own food using sunlight were at a
distinct advantage. These are the photoautotrophs.
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Autotrophy ? Photosynthesis Heterotrophy ?
Respiration
All organisms respire
Autotrophs can carry out photosynthesis or
chemosynthesis
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The sun is the source of energy for life
Thermodynamics is a branch of chemistry developed
to understand steam engines. It also tells us
about energy flow in living systems.
In thermodynamics, things that are accepted by
everyone is called a law, just as in physics. In
biology we would call these theories. Examples
include the theory of evolution and cell theory.
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The first two laws of thermodynamics can be
understood intuitively
The first law Conservation of energy and
mass The best you can do is break even There
is no free lunch Perpetual motion machines
dont work If it sounds too good to be true, it
probably is
The second law Entropy (disorder) always
increases You cant even break even
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Redox reactions
Metallurgists recognized long ago that if you
heat iron ore, you could convert rocks (iron ore)
to iron, but the amount of iron was less than
the starting iron ore. Thus, the ore is
reduced to iron. Fe2O3 ? Fe O Fe2?
Fe0 Iron is said to gain electrons when iron ore
is reduced to metallic iron by heating
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Redox reactions
Now, chemists use the term reduction whenever
electrons are added to an atom during a
reaction The opposite reaction is oxidation, but
it does not have to include oxygen in the
reaction. When one thing is reduced, something
else is oxidized. BUT, it is not always easy to
see where electrons go during a reaction (at
least for me)
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Intuitive redox reaction
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Less intuitive redox reaction important in biology
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Redox - keep your eye on the electron

• If an electron moves from one molecule to
  another, that is a redox reaction
• If a hydrogen atom moves, that is a redox
  reaction
• If a hydrogen ion (H) moves, that is not a redox
  reaction

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Redox reactions
Consider the following reaction 2Fe(OH)2 O2
? Fe2O3? 2H2O ½ O2 You can guess this is an
oxidation of iron, but it takes a bit of work to
see that Fe goes from oxidation state 2 to
3. This is what happened on Earth when
photosynthesis evolved. It has been said that the
oceans rusted. This caused the deposit of most
of the worlds iron ore in red beds. These are
particularly striking near the Grand Canyon.
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The oxidation states of carbon
Reduced
CH4 Methane Alkane (fats) H3COH
Methanol Alcohol (sugars) H2CO
Formaldehyde Aldehyde HCOOH Formic
acid Carboxylic acid CO2 Carbon dioxide
Oxidized
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The oxidation states of carbon
Reduced
CH4 Methane Alkane (fats) H3COH
Methanol Alcohol (sugars) H2CO
Formaldehyde Aldehyde HCOOH Formic
acid Carboxylic acid CO2 Carbon dioxide
Photosynthesis
Oxidized
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The oxidation states of carbon
Reduced
CH4 Methane Alkane (fats) H3COH
Methanol Alcohol (sugars) H2CO
Formaldehyde Aldehyde HCOOH Formic
acid Carboxylic acid CO2 Carbon dioxide
Respiration
Oxidized
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The oxidation states of carbon
Anabolic metabolism
Catabolic metabolism
Reduced
Fats Sugars Acids CO2 Carbon dioxide
Oxidized
Respiration
Photosynthesis
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Enzymes often work with cofactors
Formal presentation of the reaction NAD(P) 2H
? NAD(P)H H
Notice that it carries two electrons
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Enzymes

• The products of enzyme-catalyzed reactions always
  have less energy than the starting materials.
• Then how can animals make fats from sugars?
• By linking an energy-losing reaction (exergonic)
  to an energy-gaining reaction (endergonic).

Glucose phosphate ? Glucose 6-phosphate
Glucose 6-phosphate has more energy than glucose
and so this reaction normally goes right to left.
This is a phosphatase reaction.
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Enzymes

• The products of enzyme-catalyzed reactions always
  have less energy than the starting materials.
• Then how can animals make fats from sugars?
• By linking an energy-losing reaction (exergonic)
  to an energy-gaining reaction (endergonic).

Glucose phosphate ? Glucose 6-phosphate
Glucose 6-phosphate has more energy than glucose
and so this reaction normally goes right to left.
This is a phosphatase reaction.
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Linking reactions
Glucose ATP ? Glucose 6-phosphate ADP
This reaction normally goes left to right and is
called a kinase reaction. It can be thought of
as the sum of two reactions.
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Metabolic pathways

• When compounds often undergo the same series of
  reactions we group those reactions together and
  describe a metabolic pathway.
• Two major types linear pathway and cycle
• Linear pathway glycolysis in respiration
• Cycles Krebs Cycle in respiration and Calvin
  Cycle in photosynthesis

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Metabolic pathways
A ? B ? C ? D ? E A linear metabolic
pathway
A very common type of regulation of linear
pathways is feedback regulation. When there is
enough E, E will reduce the rate of conversion
from A to B.
A ? B ? C ? D ? E
There are many other types of regulation of
metabolism. (For me as a biochemist, this is
where the fun begins. Unfortunately, this is
where introductory biology stops.)
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Reversibility
Most reactions are reversible
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Reversibility
Most reactions are reversible
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Apparently irreversible reactions can be made
reversible by coupling them. Relatively few
reactions are mechan- istically irreversible.
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Enzymes are catalysts and are not changed by the
reaction.
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Enzymes often move after binding their substrate
(induced fit).
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