Lecture 2 Topics
Finish discussion of thermodynamics (G, E)
ATP as an universal carrier of chemical energy
Role of enzymes and co-factors
Summary of Lecture 1
Need for metabolism
Provides building blocks for regeneration
Energy conversion compatible with C-based life
Chemical bonds as stores of energy (H)
Rearrangement of bonds release or require H
(- H, exothermic; + H, endothermic)
Free Gibbs Energy (G)
G = H TS
G = Go + RTlnQ
G = nFE
Review
Reduction Potential (E)
yet another way to express G
Metabolic reactions are often redox reactions, involving
transfer of electrons from a donor to an acceptor
1. Direct combination with oxygen (X X + O=O 2O
X)
2. Transfer of the hydride anion (HH, or H- + H+)
3. Transfer of hydrogen (H, or e- + H+)
4. Direct transfer (e-)
Lecture 1
Redox reactions can be written as two half-reactions
(by convention:
convention each is written in the direction of the reduction!)
reduction
Aoxidized + Breduced Areduced + Boxidized
1. Aoxidized + e- Areduced
2. Boxidized + e- Breduced
Electronegativities (Tab. 1) can predict direction of e- transfer
See p. 6
Lecture 1
Question: Which half-reaction has the higher
affinity for electrons at standard conditions ?
Reference
Electrode:
H+ + eH2 half-reaction (1M each)
(Eo= 0.00 V)
Test
Electrode:
A+ + eA
(Eo= ??? V)
half-reaction (1M each)
By convention:
convention
If e- flow from reference to test (test is stronger e- acceptor): Eo > 0 (+V)
If e- flow from test to reference (test is weaker e- acceptor):
See p. 6
Eo < 0 (- V)
Lecture 1
Table 3: Standard Reduction Potentials for Biological Reduction HalfHalf-Reactions
Reactions
Half-Reaction
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
Eo(V)
(written as reduction)
Excited(Chlorophyll)2*
Succinate + CO2 + 2H+ + 2e- -Ketoglutarate + H2O
Acetate + 2H+ + 2e- Acetaldehyde + H2O
SO42- + 2H+ + 2e- SO32- + H2O
Ferredoxin (Fe3+) + e- Ferredoxin (Fe2+)
2H+ + 2e- H2 (at pH 7.0)
CO2 + H+ + 2e- Formate
-Ketoglutarate + CO2 + 2H+ + 2e- Isocitrate
Acetoacetate + 2H+ + 2e- -Hydroxybutyrate
Cystine + 2H+ + 2e- 2 Cysteine
NADP+ + 2H+ + 2e- NADPH + H+
NAD+ + 2H+ + 2e- NADH + H+
Lipoic acid + 2H+ + 2e- Dihydrolipoic acid
1,3-bisPGA + 2H+ + 2e- 3-PGA + Pi
S + 2H+ + 2e- H2S
Glutathione + 2H+ + 2e- 2 Glutathione (reduced)
FAD + 2H+ + 2e- FADH2 (Flavoprotein 0.003-0.091)
FMN + 2H+ + 2e- FMNH2
Acetaldehyde + 2H+ + 2e- Ethanol
Pyruvate + 2H+ + 2e- Lactate
Oxaloacetate + 2H+ + 2e- Malate
Crotonyl-CoA + 2H+ + 2e- Butyryl-CoA
2H+ + 2e- H2 (at standard conditions, 1 M = pH 0)
Fumarate2- + 2H+ + 2e- Succinate2UQ + 2H+ + 2e- UQH2
Cytochrome b (Fe3+)+ e- Cytochrome b (Fe2+)
Cytochrome c1 (Fe3+)+ e- Cytochrome c1 (Fe2+)
Cytochrome c (Fe3+)+ e- Cytochrome c (Fe2+)
Rieske Fe-S (Fe3+)+ e- Rieske Fe-S (Fe2+)
Cytochrome a (Fe3+)+ e- Cytochrome a (Fe2+)
O2 + 2H+ + 2e- H2O2
Cytochrome a3 (Fe3+)+ e- Cytochrome a3 (Fe2+)
Cytochrome f (Fe3+)+ e- Cytochrome f (Fe2+)
NO3- + 2H+ + 2e- NO2- + H20
Photosystem P700
Fe3+ + e- Fe2+
O2 + 4H+ + 4e- 2H20
(Chlorophyll a)2+ + e- (Chlorophyll a)2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
1.0
0.67
0.58
0.57
0.43
0.42
0.42
0.38
0.35
0.34
0.32
0.32
0.29
0.29
0.24
0.23
0.22
0.22
0.20
0.18
0.17
0.02
0.00
0.03
0.06
0.08
0.22
0.25
0.28
0.29
0.30
0.35
0.37
0.42
0.43
0.77
0.82
1.10
Direction of
spontaneous
electron flow.
See p. 3
Reduction Potential E for each Half-Reaction (Nernst Equation)
1. Aoxidized +
e-
Areduced
2. Boxidized +
e-
Breduced
E=
Eo
RT [e- Acceptor, Aox]
+ nF ln [e- Donor, Ared]
E=
Eo
RT [e- Acceptor, Box]
+ nF ln [e- Donor, Bred]
E of Redox Reaction (Aox + Bred Ared + Box)
E = EOxidant (A) EReductant (B)
Relationship between E and G
G = nFE
Go = nFEo
E = G/nF
Eo = Go/nF
See p. 6
Table 3: Standard Reduction Potentials
Half-reaction (written as reduction by convention)
Excited (Chlorophyll a)2*
Eo (V)
~ - 1.00
Acetate + 2H+ + 2e- Acetaldehyde + H2O
- 0.58
NAD+ + 2H+ + 2e- NADH + H+
- 0.32
Pyruvate + 2H+ + 2e- Lactate
- 0.18
2H+ + 2e- H2 (at standard conditions, 1M each, pH 0)
0.00
NO3- + 2H+ +2e- NO2- + H2O
+ 0.42
O2 + 4H+ + 4e- 2H2O
+ 0.82
(Chlorophyll a)2.+ + e- (Chlorophyll a)2
+ 1.10
e- flow
See p. 3
Metabolic Life Styles
Chemolithotrophs
Chemoorganotrophs
Fully or partially reduced
inorganic compounds
(e.g., H2, NH3, NO2-,
H2S, S2O32-, S, Fe2+)
Organic compounds
(e.g., sugars, amino or
fatty acids, organic
acids, etc.)
e-
ERed
Initial Electron Donor
E = EOx ERed
Energy Metabolism
E = G/nF
Terminal Electron Acceptor
(e.g., NO3-, NO2-, SO42-, Fe3+,
CO2, partially oxidized
organic compounds)
Anaerobes
O2
e-
EOx
Aerobes
p. 7
Organic
Compound
Eo
Oxidized
Compound
( - 0.60 V)
(+ 0.42 V)
Nitrate (NO3-)
Nitrite (NO2-)
(+ 0.42 V)
(+ 0.82 V)
H 2O
1/2 O2
p. 7
Food
CO2
H 2O
O2
Reduced
Carbon
Respiration
ENERGY
Humans and Animals
Heterotrophic Metabolism
p. 8
Plants and
Photosynthetic Bacteria
Autotrophic Metabolism
LIGHT
Photosynthesis
Fossil Fuels
Day
CO2
H2 O
O2
Reduced
Carbon
Night
Respiration
ENERGY
Food
p. 8
Plants and
Photosynthetic Bacteria
Autotrophic Metabolism
LIGHT
Fossil Fuels
Photosynthesis
Day
CO2
H2O
O2
Reduced
Carbon
Night
Respiration
Food
ENERGY
CO2
H2O
O2
Reduced
Carbon
Respiration
ENERGY
Humans and Animals
Heterotrophic Metabolism
p. 8
JACOB VAN RUYSDAEL (1652)
2H2O
2{H2} + O2
2e- + 2H+
(0.7V)
ATP
O2 (+0.8V)
H2O
Hydrolysis Reactions of Phosphate Esters and Anhydrides
Phosphate esters
O
O
R O
P
O-
O-
H2O
ROH + HO
O-
O-
p. 9
Phosphate anyhydride
O
R O
P
O-
O
O
P
O-
O
O- + H2O
R O
P
O-
OH + HO
O-
O-
p. 9
Acyl phosphate
C O
P
O-
O
O- + H2O
OH + HO
O-
O-
p. 9
ATP (Adenosinetriphosphate), ADP, and Their Mg2+ Complexes
Phosphoester bond
NH2
Phosphoanhydride
bonds
O
-O
P
O-
O
O
P
-
P
O
(Adenine)
(Ribose)
H
OH
H
OH
Mg2+
MgATP
p. 10
NH2
Phosphoanhydride
bond
O
-O
O
O
P
-
OH
OH
H
OH
Mg2+
MgADP
p. 10
The ATP Gun
Spring-loaded phosphate bullets
The gun is safe (kinetically stable),
until you pull the trigger (to overcome activation energy)
Cause for G
of Hydrolysis
o
G
(kJ/mol)
Transfer
Potential
Phosphoenolpyruvate
(Pyruvate + Pi)
- 62.2
62.2
Enolic
phosphate
Tautomerization of product (Pyr);
Resonance stability of Pi
1,3-Bisphosphoglycerate
(3-PGA + Pi)
- 49.6
49.6
Acyl
phosphate
Ionization of product (3-PGA);
Resonance stability (Pi, 3-PGA)
Phosphocreatine
(Creatine + Pi)
- 43.3
43.3
Guanidine
phosphate
Resonance stability of product
(creatine)
Pyrophosphate (PPi)
(Pi + Pi)
- 33.6
33.6
Phosphoric acid
anhydride
Electrostatic bond strain in PPi
substrate; Ionization and
resonance stability of Pi group
ATP (ADP + Pi)
- 30.5
30.5
Same as PPi
Same as PPi
ADP (AMP + Pi)
- 30.5
30.5
Same as PPi
Same as PPi
Acetyl-CoA
(and other thioesters)
- 31.5
31.5
Thioester
No resonance stabilization of
Acetyl-CoA;
Ionization and resonance
stabilization of acetate
Glucose-1-P (Glucose + Pi)
- 20.7
20.7
Phosphate
semiacetal
Bonds in glucose-1-P not
that strained
Glucose-6-P (Glucose + Pi)
- 13.9
13.9
Phosphate
ester
Bonds in glucose-6-P not
strained
AMP (Adenosine + Pi)
- 9.2
9.2
Phosphate
ester
Bonds in AMP not strained;
Adenosine does not ionize
0.0
0.0
Phosphate
Compound
(hydrolyzed to)
Type of
Compound
(Acetate + CoA-SH)
Phosphate (Pi)
Table 4: Standard Free
Energies of Hydrolysis
Compounds with
decreasing Go of hydrolysis
p. 4
Cause for G
of Hydrolysis
o
G
(kJ/mol)
Transfer
Potential
Phosphoenolpyruvate
(Pyruvate + Pi)
- 62.2
62.2
Enolic
phosphate
Tautomerization of product (Pyr);
Resonance stability of Pi
1,3-Bisphosphoglycerate
(3-PGA + Pi)
- 49.6
49.6
Acyl
phosphate
Ionization of product (3-PGA);
Resonance stability (Pi, 3-PGA)
Phosphocreatine
(Creatine + Pi)
- 43.3
43.3
Guanidine
phosphate
Resonance stability of product
(creatine)
Pyrophosphate (PPi)
(Pi + Pi)
- 33.6
33.6
Phosphoric acid
anhydride
Electrostatic bond strain in PPi
substrate; Ionization and
resonance stability of Pi group
ATP (ADP + Pi)
- 30.5
30.5
Same as PPi
Same as PPi
ADP (AMP + Pi)
- 30.5
30.5
Same as PPi
Same as PPi
Acetyl-CoA
(and other thioesters)
- 31.5
31.5
Thioester
No resonance stabilization of
Acetyl-CoA;
Ionization and resonance
stabilization of acetate
Glucose-1-P (Glucose + Pi)
- 20.7
20.7
Phosphate
semiacetal
Bonds in glucose-1-P not
that strained
Glucose-6-P (Glucose + Pi)
- 13.9
13.9
Phosphate
ester
Bonds in glucose-6-P not
strained
AMP (Adenosine + Pi)
- 9.2
9.2
Phosphate
ester
Bonds in AMP not strained;
Adenosine does not ionize
0.0
0.0
Phosphate
Compound
(hydrolyzed to)
Type of
Compound
(Acetate + CoA-SH)
Phosphate (Pi)
Phosphoryl-group
transfer potentials
Receive P~group
Donate P~group
p. 4
High Energy
Substrates
Cellular
Macromolecules
ATP + H2O
G
+G
+G
ADP + Pi
Intermediates
of Metabolism
Low Energy
Products
Enzymes (biological catalysts)
do NOT change G of chemical reactions !!!
but decrease their activation energies
inrease the rate (107 to 1019-fold) of attaining
equilibrium (G is not a kinetic constant!)
reaction rates (flux) can be regulated
provide specificity and couple reactions
coordinate many reactions into metabolic
networks (pathways) via shared intermediates
A
Large -G
F
Small -G
OOC
NH3
The 20 Protein Amino Acids
H
L-Amino Acid
(constituents of enzymes)
A. Nonpolar, Aliphatic R-Groups
O
H2N
CH C
O
OH
H2N
CH C
OH
H2N
CH CH3
CH3
H2N
CH C
CH3
Valine
Val, V
O
OH
Leucine
Leu, L
O
OH
CH2
CH2
OH
CH2
CH CH3
Glycine
Gly, G
CH C
HN
H2N
CH
OH
CH
CH3
CH2
S
CH3
Methionine
Met, M
Proline
Pro, P
CH3
Isoleucine
Iso, I
p. 12
B. Aromatic R-Groups
O
H2N
CH C
O
OH
H2N
CH C
O
OH
CH2
CH2
H2N
CH C
OH
CH2
HN
Tryptophan
Trp, W
OH
Tyrosine
Tyr, Y
Phenylalanine
Phe, F
p. 12
C. Polar, Uncharged R-Groups
O
H 2N
CH C
OH
H2 N
CH C
CH 2
CH OH
SH
CH 3
OH
CH C
OH
CH2
O
NH2
Threonine
Thr, T
H 2N
Cysteine
Cys,C
H 2N
Asparagine
Asn, N
CH C OH
H 2N
CH C
OH
CH2
CH 2
CH2
OH
NH2
Serine
Ser, S
Glutamine
Gln, Q
p. 13
D. Positively Charged R-Groups
O
H2N
CH
O
H2N
OH
CH C
OH
H2N
CH2
CH2
CH2
CH2
CH2
NH
NH
Histidine
His, H
OH
CH2
CH2
CH C
NH
NH2
CH2
Arginine
Arg R
NH2
Lysine
Lys, K
E. Negatively Charged R-Groups
O
H2N
CH C
O
OH
CH2
CH2
C
H2N CH C OH
CH2
C O
OH
Aspartate
Asp, D
OH
Glutamate
Glu, E
p. 13
F. Peptide Bond
R1
H 3N
R2
G. Isopeptide Bond
R1
COO-
H3N
NH 3
(CH 2)4
COO-
Lysine
H
H3N
O
CH 2
CH 2
COO-
R2
N
COO-
Glutamate
p. 14
Polar and charged side-chain terminal groups and
carboxylate-arginine and carboxylate-carboxylate dyads
Gutteridge and Thornton (2005) Understanding natures catalytic toolkit.
Trends Biochem Sci 30:622-629
pKa values of polar and charged amino acids
Gutteridge and Thornton (2005) Understanding natures catalytic toolkit.
Trends Biochem Sci 30:622-629
Gutteridge and Thornton (2005) Understanding natures catalytic toolkit.
Trends Biochem Sci 30:622-629
CO-FACTORS
(Non-protein moieties required for catalytic activity)
1. Metals
Structural role (e.g., Mg2+)
Catalytic role (e.g., Fe2+)
2. Co-enzymes
Organic molecules (catalytic)
Co-substrates
- If transiently bound (e.g., ATP)
Prosthetic group - If covalently bound (e.g., FAD)
Must be regenerated if altered in reaction (by same or different enzyme)
Most water-soluble vitamins are precursors of co-enzymes
see p. 14/15
