Lecture 1- Metabolism: Basic
Concepts and Design
Chem 454: Regulatory Mechanisms in Biochemistry
University of Wisconsin-Eau Claire
1
Introduction
Questions we will focus on this
semester:
How does a cell extract energy and reducing
power from its environment?
How does a cell synthesize the building blocks
of its macromolecules and the then the
macromolecules themselves?
How are these processes integrated and
regulated?
2
2
Introduction
Living organisms require an input of
free energy to meet various needs:
For mechanical work
For active transport of molecules and ions
For synthesis of biomolecules
3
3
Introduction
Living organisms require an input of
free energy
Phototrophs
Use energy from the sun to convert energy-poor molecules
into energy rich molecules
Chemotrophs
Obtain energy by oxidizing the energy-rich molecules made
by the phototrophs
4
4
Introduction
Reduced molecules are energy-rich
Oxidized molecules are energy-poor
5
5
Introduction
Energy from photosynthesis or the
oxidation of fuels can be transformed
into an unequal distribution of ions
across a biological membrane.
The ion gradient can be used for
Oxidative phosphorylation to make ATP
Active transport across membranes
Nerve transmission
6
6
Introductions
Ion gradients:
See Chapter 2.3.3
7
7
Metabolism
Metabolism is composed of many
coupled interconnecting reactions
8
8
Metabolism
9
9
Metabolism
Classes of metabolic pathways:
Catabolic pathways
Those that convert energy into biologically useful forms
Fuels (carbohydrates, fats)
CO2
+ H2O
+
useful energy
Anabolic pathways
Those that require an input of energy
Useful energy
+ small molecules
complex molecules
10
10
Metabolism
Basic concepts of metabolism include:
Thermodynamically unfavorable reactions can be
driven by favorable reactions.
ATP is the universal currency of free energy.
ATP hydrolysis drives metabolism by shifting the
equilibrium constant of coupled reactions.
There is a structural basis for the high phosphoryl
transfer potential of ATP.
The phosphoryl transfer potential is an important
form of cellular energy transformation.
11
11
Thermodynamics
Thermodynamically unfavorable
reactions can be driven by favorable
reactions.
Free energy change for a reactions:
A+ BÆC+ D
Ê [C ][ D] ˆ
DG = DG 0' + RT lnÁ
˜
†
Ë [ A][ B] ¯
12
†
12
Thermodyamics
Coupling unfavorable reactions with
favorable ones
A¨ B+C
DG o' = +5 kcal mol-1
BÆD
AÆC+ D
DG o' = -8 kcal mol-1
DG o' = -3 kcal mol-1
†
13
13
ATP
ATP is the universal currency of free
energy
14
14
ATP
Hydrolysis of ATP:
ATP
+
H2O
ADP
+
Pi
DGo' = -7.3 kcal mol -1
ATP
+
H2O
AMP
+
PPi
DGo' = -10.9 kcal mol -1
15
15
ATP Hydrolysis
ATP hydrolysis drives metabolism by
shifting the equilibrium of coupled
reactions
16
16
ATP Hydrolysis
Problem:
Under standard conditions, the free energy for
the hydrolysis of L-glycerol phosphate to form
glycerol and inorganic phosphate is -2.2 kcal/
mol. Calculate the factor by which the
equilibrium ratio for the concentration of Lglycerol phosphate to glycerol is increased when
ATP is used as the phosphoryl donor for the
formation L-glycerol phosphate in place of
inorganic phosphate.
Do this calculation for liver where the
concentrations for ATP, ADP and Pi are 3.5
mM, 1.8 mM and 5.0 mM, respectively.
17
17
ATP Hydrolysis
Phosphoryl transfer is a common
means of energy coupling
Molecular motors
Muscle contraction
Ion pumps
18
18
Phosphoryl Transfer
Structural basis for high transfer
potential
Compare:
ATP
+
H2O
ADP
Glycerol 3-phosphate
+
DGo' = -7.3 kcal mol -1
Pi
+ H2O
Glycerol
+
DGo' = -2.2 kcal mol -1
Pi
19
19
Phosphoryl Transfer
Phosphate ester vs Phosphate
anhydride
CH2 OH
CH
OH
O
Adenosine
O
CH2 O
P
O
O
O
Phosphate ester
20
O
O
P
O
O
O
P
O
O
Adenosine triphosphate (ATP
O
P
P
O
O
O
Glycerol 3-phosphate
CH2 O
O
O
P
O
O
O
P
Y
O
O
Phosphate anhydryde
X
O
O
P
O
O
20
Phosphoryl Transfer
Stabilization of orthophosphate
resonance stabilization
electrostatic repulsion
hydration
21
21
Stabilization of Orthophosphate
Resonance stabilization
Orthophosphate
Pyrophosphate
22
22
Phosphoryl Transfer and
Energy Transfer
There are other
molelcules with
favorable
phosphoryl
transferase
energies
23
23
Phosphoryl Transfer
In terms of energy for phosphoryl
transfer, ATP is intermediate:
24
24
Phosphoryl Transfer
Question:
What information do the ∆Go’ data given in
Table 14.1 provide about the relative rates of
hydrolysis of pyrophospate and acetyl
phosphate?
25
25
Phosphoryl Transfer
Creatine phosphate is used to
generate ATP in the short term:
26
26
Cellular Energy
The oxidation of Carbon fuels is an
important source of cellular energy
27
27
Cellular Energy
The oxidation of Carbon fuels is an
important source of cellular energy
28
28
Cellular Energy
High phosphoryl transfer potential
compounds can couple carbon
oxidation to ATP synthesis.
Ion gradients across membranes
provide an important form of
cellular energy
The extraction of energy from
foodstuffs occurs in stages.
29
29
Coupling oxidation to ATP synthesis
High phosphoryl transfer potential
compounds can couple carbon
oxidation to ATP synthesis.
Example from glycolysis:
O
O
O
C
H
C
O
CH
OH
O
CH
+
OH
NAD+ + HO
O
CH2 O
P
P
P
O
O
O
+
NADH
+ H+
O
O
O
CH2 O
O
Glyceraldehyde 3-phosphate
P
O
O
1,3-Bisphosphoglycerate
30
30
Coupling oxidation to ATP synthesis
In the next step ATP is harvested
from the high energy phosphate
intermediate.
O
O
C
O
P
O
O
C
O
CH
OH
H
O
CH
+
OH
ADP
P
+
ATP
O
O
CH2 O
O
O
1,3-Bisphosphoglycerate
CH2 O
P
O
O
3-Phosphoglycerate
31
31
Ion Gradients
Ion gradients across membranes
provide an important form of cellular
energy
32
32
Cellular Energy
Ion gradients across membranes can
be used to synthesize ATP
33
33
Cellular Energy
Extraction of energy from foodstuffs
is carried out in stages:
34
34
Recurring Motifs in Metabolism
Activated carriers exemplify the
modular design and economy of
metabolism.
Key reactions are reiterated
throughout metabolism.
Metabolic processes are regulated in
three principle way.
35
35
Activated Carriers
ATP is an activated carrier of
phosphate groups
Other examples include:
Activated carriers of electrons in oxidation
reactions
Activated carriers of electrons in reductive
biosynthesis
Activated carriers of two-carbon fragments
36
36
Activated carriers of electrons in
catabolism
NAD+
(Nicotinamide
Adenine
Dinucleotide)
37
37
Activated carriers of electrons in
catabolism
FAD
(Flavin
Adenine
Dinucleotide)
38
38
Activated carriers of electrons in
catabolism
Reduction of isoalloxazine ring of FAD
39
39
Activated carriers of electrons in
biosynthesis
NADPH
(Nicotinamide
Adenine
Dinucleotide)
40
40
Activated carriers of acyl groups
Coenzyme A is a carrier of Acyl
groups
41
41
Activated Carriers
Other common activated carriers:
42
42
Key Reactions
There are six basic reactions in
metabolism:
43
43
Key Reactions
Metabolic motifs
44
44
Metabolic Regulation
Metabolic processes are regulated in
different ways:
Enzyme levels (Genetic control)
Enzyme activity (Allosteric control)
Accessiblity of substrates to the enzyme
(Competitive inhibition)
45
45
Metabolic Regulation
Degradative and biosynthesis
pathways are usually distinct
Compartmentalization
Allosteric control
46
46
Metabolic Regulation
The energy charge
Energy Charge =
[ATP] + 12 [ADP]
[ ATP] + [ADP] + [ AMP]
†
47
47