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design of metabolism
design of metabolism
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Bil 255 – CMB
the design of metabolism
design of metabolism
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The Design of Metabolism...
Biological Order and Cell Energy Transformations
CELLS Do OBEY LAWS of CHEMISTRY & PHYSICS…
cells possess Potential Energy by having different bonds
2 kinds of traditional energy:
Potential Energy
... stored energy, due to mass in position
Kinetic Energy
(energy of movement)
ex:
heat
(thermal) energy which flows from higher heator greater molecular motion to lower heat content;
radiant energy
kinetic energy of photons (light);
when molecules absorb light radiant --> thermal
chlorophyll --light--> ATP in photosynthesis
mechanical energy
- push/pull of cytoskeletal filaments
electrical energy
- energy of moving electrons
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ENERGY in cells is housed
in a molecules CHEMICAL BONDS
cells possess Chemical Potential Energy^ occurs in such forms as:
chemical concentrations gradients
across membranescan diffuse from [higher] to [lower]
electrical gradients
(potential differences)
across membranesa separation of chargeas much as 200,000 volts per cm
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THERMODYNAMICS:
SCIENCE of ENERGY TRANSFORMATIONS
1st Law of Thermodynamics... Energy can neither be created nordestroyed, but is convertible
[nuclear blast - mass of U
--> heat/light]
all forms of energy are inter-convertible
& thus all are expressed in same units of measure
Joule, but biologists use more common calorie
calorie is heat
1gm 1oC
1 Kcal = 1,000 cal = 4,184 Joule
[1 cal = 4.184 J]
2nd Law of Thermodynamics…
ENTROPY
is commonly referred to as a measure of degree of order of the Universe,& thus its randomness (Entropy - disorder) can only increase
Entropy is maximum disorder..... "heat“Events in the Universe have a direction --> max entropy
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The Rules of the Universe are simple:Cities crumble, Stars go Supernova, & we are all equlibrium...izing (dying) Yet, WOW! …
Cells are highly ordered...
wings of a bird, human eye, spider’s weband all cells - feed, grow, and differentiate
HOW...
in light of the 2nd law of thermodynamics?
FOOD
(light energy & covalent bond energy)
HEAT
= overall increased entropy
Entropy must increase (heat); yet disorder within one part of Universe
can decrease at the greater expense of the Total Surroundings.
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ENERGY IN --> CELL STRUCTURE --> ENERGY OUTWhat we need to be able to do is measure Energy in systems,
esp. energy able to do work
Willard Gibbs
(1839-1903)
applied the principles of Thermodynamics
to chemical systems to determine the energy content and changeswithin a chemical reaction and derived the...
FREE ENERGY EQUATIONS
G
H
- T
S
free energy
enthalpy
entropy
Δ G is a numerical measure of how far a reaction is from equilibrium Δ G is measure amount energy in system able to do work
(to stay away from equilibrium)... Disorder increases (thus entropy increases) when useful energy,that which could be used to do work, is dissipated as heat...biological systems are are ISOTHERMAL,
e.g., held at constant temp/pressure
o^ to
^45
o^
)^
and
thus
H = 0
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What Gibbs showed was that "cell chemical systems change so that FreeEnergy is minimized“
thus, DG can PREDICT..... the Direction of Cellular Reactions......
TOWARD EQUILIBRIUM and to Maximum ENTROPY
Any natural process occurs spontaneously, if and only if,
the associated change in G for the system is negative (
G
when -
D
G is negative a reaction is spontaneous, R --> P, & there is a
decrease in entropy Likewise, a system reaches equilibrium when the associated change in G
for the system is zero (
Δ G
= zero),
& no spontaneous process will occur, if the change in G is positive (
G
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CHEMICAL REACTION
A <---> B
Which Way?
J. Willard Gibbs (1839-1903)
G =
G0’ +
R T
ln [
p
]/[
r
]
change in free energy content of a reaction...depends upon:
- energy is stored in molecule's covalent bonds2. remember, temperature is negligible... cells are isothermal, i.e.,
G
=^
actual free energy
Go'
=^
standard free energy [change under std conditions]
R
gas constant ( 2 x 10
Kc/mol)
T^
=^
absolute temp (-
o K)
ln
=^
natural log (conversion log
at equilibrium
G = 0
and
[p]/[r] = Keq
if we solve above equation for
Go' we can see relationship* of Keq to
G0’
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CHEMICAL REACTIONS
A <----> B
Which way & Why?
EXERGONIC REACTION
- is one which releases free energy
Product
[B]
<<< energy
Reactant
[A]
[stored in covalent bonds]
ex:
burning wood (cellulose)
glucose monomers = potential energybreaks bonds, release heat & light ---> CO
& H
2 O
cell respiration - (heterotrophy) - cellular burning of glucose
slower,
multi-step process to capture & releaseenergy.... as ATP
ENDERGONIC REACTION
-^
requires input of energy for
A --> B
Product
[B]
>>>energy
Reactant
[A]
ex:
photosynthesis - (autotrophy)
glucose made from CO
2
+ H
O --light---> 2
C
H 6
12
O
6
energy poor
vs.
energy rich
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How does Metabolism create more order in chemical reactions?COUPLED REACTION via ATP hydrolysis:
if
G for the reaction B + C --> D is +,but less than the DG of ATP hydrolysis,then the reaction can be driven to completion by coupling.
ATP hydrolysis energy can be coupled to:conformational changes in enzyme,as kinases, which phosphorylateproteins converting then from inactive to active (& vice versa);energy gained in the stressed conformation is released,
when the protein relaxes.
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Design of Metabolism:
2 Categories of metabolic reactions
[ enzyme catalyzed metabolic pathways ]
fig 3.
Anabolic
biosynthesis in
autotrophs
coupling reactions that are energetically unfavorablewith reactions that are energetically favored
done by linking hydrolysis of ATP (favored) to reactionslinking atoms together (not favored), creating new biological order
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Design of Metabolism:Catabolic
- cell respiration in heterotrophs
fig 3.
oxidation (removal) of e-’s from foodstuffs
3 steps:
1. Digestion of polymers (foods) into monomers2. GLYCO-LYSIS ---> AcoA
splits sugar monomers
3. Oxidation of AcoA ---> CO 2 + NADH ---> H 2O
ADP + P ---> ATP
FREE ENERGY EQUATIONS
Δ G =
H - T
S
a numerical measure of how far a reaction is from equilibrium
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Design of Metabolism...
or how biological order comes about
Organisms are classified by the nutritional habits...
Autotrophs:
light energy...
is converted into covalent chemical bond energy
e-
CO
2
oxidized form
H
O 2
NADPH + ATP
H
+^
▼ CH
O 2
reduced form
Heterotrophs:
food stuffs
more energetically stable
[CH
O]n 2
+^
NAD
+^
CO
+^
H
O + 2
ATP
+^
NADH
Key Cell energy intermediates - NADH & NADPH, FAD, & ATP*
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Design of metabolism…
OXIDATION / REDUCTION
e- &/or H+
transferred between oxidized & reduced forms
AH
A
+^
- e
H
+
oxidation
-^
removal of e- from substrate
reduction
-^
gaining of e- (& often a proton, H
fig 3.
NAD+
respiration
NADH
6O
2
+ C
H 6
12
O
6
6CO
2
+ 6H
O 2
NADP+
photosynthesis
NADPH
fig 3.
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KEY METABOLIC REACTIONS: 6 major categories of bio-chemical reactivity
Bio-chemical reactivity is bond breaking & reformingthese are violent events inside cells, carefully controlled by ENZYMES
1. functional group transfers
glu + ATP <--> G6P + ADP
2. redox reaction (oxid/reduction)
PGAld + NAD+ <--> 1,3di-PGA + NADH
3. rearrangement (isomerizations) glucose-6P <--> fructose-6P4. C-C breaking or re-formation
fruc1-6bP
DHAP + 3PGAld
5. Condensations
protein(n) + aa1 <--> protein(n+1) + H
O 2
6. Hydrolysis
glu-glu(n)
+^
H
O <--> 2
glu-glu(n-1)
