Biochemistry I
Introduction to Metabolism:
Bioenergetics and Carbohydrate
Catabolism
Why is ATP the Universal Currency of Energy
and How is it Made?
?
Carbohydrate Oxidation and
Phosphoryl Group Transfer Reactions
Chapter 15 – part 1
1
Dr. Ray
Metabolism: Basic Concepts and Design
Two fundamental questions in Biochemistry:
1. How do cells extract energy and reducing power from the
environment?
2. How do cells synthesize the building blocks for their
macromolecules?
Metabolism:
A highly integrated network
of chemical reactions
• More than 1,000 reactions in E. coli
• Coherent design containing many
common motifs
• Relatively small number of kinds (types)
of reactions
2
Catabolic and Anabolic Pathways
We can divide metabolic pathways into two broad classes:
(1) Those that convert energy into biologically useful forms. Reactions that
transform fuels into cellular energy are called catabolic reactions or,
more generally, catabolism.
(2) Those that require input of energy to proceed. Those reactions that
require energy such as the synthesis of glucose, fats, or DNA are called
anabolic reactions or anabolism.
• The useful forms of energy that are produced in catabolism are employed:
(1) in anabolism to generate complex structures from simple ones, or
(2) to form energy-rich states from energy-poor ones.
• Some pathways can be either anabolic or catabolic, depending on the
energy conditions in the cell. They are referred to as amphibolic pathways,
3
such as the citric acid cycle.
Metabolism
Metabolism is a highly integrated ensemble of linked
chemical reactions that begins with a particular
molecule and converts it to some other molecule
(metabolite) in a carefully defined fashion.
2 ATPs
formed
• For example, glucose is
metabolized to pyruvate in
10 linked reactions, known
as glycolysis
• Under anaerobic
conditions, pyruvate is
metabolized to lactate and,
under aerobic conditions,
to acetyl CoA.
• The glucose-derived carbons are
subsequently oxidized to CO2.
1. Where is most of the energy in
food, used to generate ATP?
Oxidative phosphorylation using energy released
by electron transfer from NADH to O2
http://www.wiley.com/college/fob/quiz/quiz16/16-1.html
energy
extracted
& 2 GTP
formed
4
McMurry – Chapter 29 – Organic Chem of Metabolism
Fig. 29-1, p. 1155
Overview of Carbohydrate Catabolism
• Energy yielding degradation of
nutrient molecules.
• Complex metabolites (carbohydrates)
are broken into their monomeric units
(glucose) by _________________ .
1. Is catabolism an oxidative or
reductive process?
_________________________________
which eventually results in ATP
synthesis
• Glucose is broken down into 2C units
of acetyl CoA, which is completely
oxidized to CO2, via a series of
oxidative enzyme-catalyzed reactions.
• Electrons flow through NADH and
FADH2 cofactors to O2 (the final
electron acceptor) which is reduced to
H2O, and coupled to ATP synthesis.
• Convert energy released by electron
transfer into chemical energy (ATP).
6
Overview of Carbohydrate Catabolism
H
O
C
H
HO
H
OH
H
OH
H
OH
CH2OH
1. Draw Structures
2. Label Pathways
2 x pyruvate
(3C)
2 x CO2
CO2O
CO2
CoAS
2 x Acetyl CoA
(2C)
O
CH3
CH3
4C oxaloacetate
6C citrate
D-glucose
(6C)
2 CO2
4 x CO2
(1C)
PDHC =
Free Energy of Oxidation of Carbon Compounds
In aerobic organisms, the ultimate electron acceptor in the oxidation of
carbon is O2 and the oxidation product is CO2 . So, the more reduced a
carbon is to begin with, the more exergonic its oxidation will be.
most reduced
 increase number of C-O bonds 
most oxidized
• Although fuel molecules are more complex than the single-carbon
compounds, when a fuel is oxidized during catabolism, the oxidation
takes place one carbon at a time.
Some of the carbon oxidation energy is used to directly create a
compound with high phosphoryl transfer potential, and the rest is
used to create an ion gradient which results in formation of ATP. 8
Free Energy of Oxidation of Carbon Compounds
1. Why are fats a more efficient fuel source than carbohydrates such
as glucose?
because the carbons in fats are ______________
1
2
2. The structure of the glycolytic intermediate
3
glyceraldehyde-3-phosphate (GAP) is shown:
(a) Which C is most oxidized and which is the least
oxidized (most reduced)?
(b) Can the most oxidized carbon be oxidized any further?
If so, draw the structure of the product, and name it.
(c) Oxidation of which carbon will release the most energy?
Most Ox =
3-phosphoglycerate
(3PG)
Least Ox =
9
 Oxidation of ___________ will release the most energy (since most reduced)
Flow of Energy and Raw Materials in the Biosphere
1) Write a reaction for the combustion
of GLUCOSE C6H12O6
• balance the reaction
• is the reaction endergonic or exergonic ?
2) Does glucose catabolism involve the
same or different overall reaction as (1)?
_____, alot of released energy is trapped in ATP
3) Is glucose oxidized or reduced during
catabolism?
4) Which species is reduced?
C6H12O6 + 6 O2  6 CO2 + 6 H2O
Have sense of the magnitude
(size) of the energy cost of
interactions or reactions:
Covalent bonds:
• C-C bond cleavage ~ 350 kJ/mol
• ATP hydrolysis ~ 30 kJ/mol
Non-covalent interactions:
• H-bond ~ 4 to 20 kJ/mol
Energy
Oxidation of organic
compounds produces
Very exergonic , DG negative (heat produced) energy. Draw an energy
level diagram for rxn:
Reaction coordinate
Free Energy is a Useful Thermodynamic
Function for Understanding Enzymes
Text 8.2 (p. 208-210)
The laws of thermodynamics allow us to determine the conditions under
which a particular reaction can or cannot occur, and govern the behavior
of biochemical systems.
DG = DH –T DS
Free Energy Enthalpy Entropy
D Free Energy = D Enthalpy (heat of reaction) – Temp x D Entropy
• First Law: The total energy of a system and its surroundings is constant.
Energy cannot be created or destroyed.
Energy is converted from one form to another.
• Second Law: The total entropy (disorder) of a system plus that
of its surroundings always increases.
Thus, processes tend towards an increase in disorder: + DS
Reactions can be driven by: enthalpy (heat of reaction, DH)
or entropy (disorder, DS) changes, or both.
11
Concentrations are
1M, when mixed
o
Physical Chemistry Standard State: DG
together, BEFORE
reaction occurs!
• Temp = 298 K = 25 oC
• Pressure = 1 atm
If DG is negative:
• Concentration of all Reactants and Products = 1 M (molar) conc of products get
But [H+] = 1M means pH = 0 HIGHER, and conc of
reactants get LOWER
• Most biochemical reactions occur in buffered aqueous
as reaction occurs !
solutions near pH = 7. So biochemists have adopted a
convention, in which the standard state is defined as
having pH = 7 (DGo‟, delta G zero primed).
Biochemical Standard State
Biochemical standard state denoted by the symbol DGo’
means [H+] = 1x10-7 M, the concentration of water is constant
= 55.5 M, and concentration of all other species is 1 M
• Primes (’) are used to indicate biochemical standard state
DGo’ =
D Ho’ -
TDSo’
DG o'   RT loge Keq '
• DGo’ informs on the chemical nature of reactants and products:
their tendency to react and the relative stability of reactants & products
• If reaction starts with 1M of all species, Keq and DGo’ inform on what
concentrations will exist once the reaction has reached equilibrium.
Organisms Require a Continual Input of Energy
Catabolism of fats releases more energy per “C” than carbohydrates.
FATS
• Complete oxidation of Glucose is an exergonic reaction:
C6H12O6 + 6 O2  6 CO2 + 6 H2O
DGo’ = - 2850 kJ/mol
- 475 kJ/mol C
• Complete oxidation of Palmitate (a typical fatty acid):
C16H32O2 + 23 O2  16 CO2 + 16 H2O DGo’ = - 9781 kJ/mol
- 611 kJ/mol C
• Oxidative metabolism (catabolism) occurs in a stepwise fashion so that
the free energy released can be recovered in a manageable form, as
“packets of energy” stored in a few types of high-energy intermediates
(Ex: 1,3-BPG, PEP, Acetyl CoA, and eventually ATP).
1,3-BPG + ADP  3PG + ATP substrate level phosphorylation
Have direct phosphoryl transfer between reactants
• Breakdown of these high-energy intermediates via subsequent exergonic
reactions (energy releasing), DRIVES endergonic reactions (energy
requiring); the two reactions (DG - & DG +) are energetically COUPLED!
13
Energy Transformations in Biochemistry
Organisms Require a
Continual Input of Energy
In many enzyme catalyzed biochemical
processes, energy is converted with high
efficiency into different forms:
In mitochondria, the free energy (DG) released
during glucose and fatty acid metabolism is
Foodstuffs
Light
converted (transduced) :
• First into reduction potential (NADH & FADH2)
• Then during electron transport chain, into the
Chemotrophs ATP Phototrophs
+) gradient across the
free
energy
of
an
ion
(H
(respiratory
(photosynthesis)
mitochondrial membrane
catabolism)
1. Perform mechanical work in
muscles contraction & cellular
movements
2. Active transport of molecules & ions
3. Synthesis of macromolecules and
biomolecules from presursors
1) As glucose is oxidized in
catabolism, where do the
electrons go?
4H
+
• Finally into chemical energy
– free energy of adenosine triphosphate (ATP)
ADP + Pi  ATP (cell’s energy transmitter)
• Later hydrolysis of ATP releases its energy
BIOENERGETICS
Provides rationale for types and sequence of
reactions in metabolism
ATP  ADP cycle is the fundamental mode of
energy exchange in biological systems
1) What is the NET charge of each species?
• ATP is a nucleotide consisting of an adenine, a
ribose, and a triphosphate unit. The active form of
ATP is usually a complex of ATP with Mg2+ or Mn2+
2) ATP is an energy-rich molecule because its triphosphate unit contains two
_________________________between Pa & Pb, Pb & Pg
15
3) Pa is attached to ribose 5’-OH via a ________________ bond
ATP Is Continuously Formed and Consumed
• Some biosynthetic reactions are driven by hydrolysis of nucleoside
triphosphates that are analogous to ATP namely, guanosine triphosphate
(GTP), uridine triphosphate (UTP), and cytidine triphosphate (CTP).
• However, although all of the nucleotide triphosphates are energetically
equivalent, ATP is nonetheless the primary cellular energy carrier.
• ATP is an immediate donor of free-energy rather
than a long-term energy storage molecule
• Average Human has ~ 100g of ATP
• Turnover very high:
Resting human: uses ~40 kg/24hr
Strenuous exercise: 0.5 kg/min
 for 2hr run use 60kg (132lbs)
• Typically ATP molecule is consumed within 1 minute of its formation
Q: How does coupling to ATP hydrolysis make possible
an energetically unfavorable reaction?
Q: Is the phosphorylation of glucose (1st step of glycolysis)
a spontaneous reaction?
16
BIOENERGETICS: “High-Energy” Compounds and
Phosphoryl Group Transfer reactions
• Organisms harness the free energy from the degradation of
macromolecules into a common set of smaller molecules, by trapping it
in certain nucleotides (ATP, NADH, FADH2) and certain
thioesters (acetyl CoA)  all of these are derivatives of ATP.
• These energy transmitters release their energy to lower energy species,
via the transfer of functional groups from “high-energy” compounds to
“low-energy” compounds:
• ATP
phosphoryl
• NADH, FADH2
hydrides [electrons]
• Acetyl CoA
2C acetyl groups
Example:
ATP + H2O  ADP + Pi
Q: How much energy (kJ/mol) is released when this reaction occurs?
• Phosphoryl Group Transfer Potential – describes the tendency of a
phosphorylated compound to transfer its phosphoryl group to water, and is
a measure of the large negative free energy of hydrolysis of the
17
compound (the energy ‘captured’ in the compound).
Phosphoryl Group Transfer Potential
• Larger negative free
energy of hydrolysis
indicates a HIGHenergy compound
• Phosphoryl group
transfer potential
(DGo’) is a measure of
the energy „captured‟ in
the compound, based on
its tendency to transfer
its phosphoryl group
to water.
• Smaller value
indicates a LOWenergy compound
acyl phosphate (or analog)
phosphorylated alcohols
Similar to Text Table 15.1
1) What rxn does the free energy change (-30.5) represent?
18
Phosphoryl Group Transfer Potential
• Energy is released
when the terminal Pi
is removed from ATP
O
O
ATP4- + H2O  ADP3- + Pi2- + H+
You need to know the structures and formal charges of all these species at pH 7
-
P
O
OH
-
Pi
orthophosphate
HPO42-
• High-energy
phosphoanhydride
bonds are NOT
present in AMP, or
singly phosphorylated sugar alcohol
OH groups.
1) Write the reaction for which - 49.4 kJ/mol
is the free energy of hydrolysis.
2) What is the direction of the reactions below when the reactants and
products are present in equimolar amounts? Use data in Table above.
(a) ATP + pyruvate
phosphoenol pyruvate + ADP
(b) ATP + glycerol
glycerol-3-phosphate + ADP
DGo’ is negative for transfer of phosphates DOWN the table!
19
Basis for Phosphoryl Transfer Potential of ATP
1) Why is ATP the “energy currency” of the cell?
2) What makes ATP a particularly efficient
phosphoryl-group donor?
•
•
The “energy” of ATP resides in the
thermodynamic instability of its two
phosphoanhydride bonds
Three factors are important:
(1) resonance stabilization
(2) electrostatic repulsion
(3) stabilization due to hydration
1. Products ADP and, particularly, Pi, have greater resonance
stabilization than does ATP. Orthophosphate (Pi) has a number of
resonance forms of similar energy, whereas the terminal g-phosphoryl
group of ATP has a smaller number:
20
Basis for Phosphoryl Transfer Potential of ATP
2. At pH 7, the triphosphate unit of ATP carries about four negative
charges. These charges repel one another because they are in close
proximity. The electrostatic repulsion between them is reduced when
ATP is hydrolyzed.
ATP4- + H2O  ADP3- + Pi2- + H+
Net charge:
ATP = 4 -
ADP = 3 -
3.Water can bind more effectively to
ADP and Pi than it can to the
phosphoanhydride part of ATP,
stabilizing the ADP and Pi by hydration
21
Net charge:
AMP = 2 -
HPO42- = Pi = 2 -
Phosphoryl Transfer Potential of ATP
• Let us compare the standard free energy of hydrolysis of ATP with that of
a phosphate ester, such as glycerol-3-phosphate:
1) Which phosphorylated molecule (ATP or G3P)
has a higher phosphoryl transfer potential
(phosphoryl-group transfer potential)?
• Compare positions in table:
______________________
• because ATP has a
larger negative DGo’hydrolysis
(is higher on table):
22
Metabolites with High Phosphoryl Transfer Potential
1) Are there compounds in biological systems have a higher phosphoryl
transfer potential than that of ATP? _____ , three compounds:
phosphoenolpyruvate (PEP)
[DG° of - 61.9 kJ/mol]
1,3-bisphosphoglycerate (1,3-BPG) [DG° of - 49.4 kJ/mol]
creatine phosphate
[DG° of - 43.1 kJ/mol]
• PEP can transfer its phosphoryl group to ADP to
form ATP; this is how ATP is generated directly
during glycolysis.
• It is significant that ATP has a phosphoryl
transfer potential that is intermediate among the
biologically important phosphorylated molecules.
• This intermediate position enables ATP to
function efficiently as a carrier of phosphoryl
groups (accept Pi from some, give Pi to others)
2) What is a common structural feature of
these 3 high energy species?
_____________________________________________
or analog
23
Intermediate position of ATP, relative to “high-energy”
and “low-energy” phosphorylated compounds
• ATP’s intermediate phosphoryl
group transfer potential,
DGo’= - 30kJ/mol, makes it a
conduit for transfer of free energy
from higher-energy compounds to
lower-energy compounds.
Phosphoryl groups
groups flow
flow from
from
•• Phosphoryl
high-energy donors,
donors, via
via the
the
high-energy
ATP-ADPsystem,
system, to
to low-energy
low-energy
ATP-ADP
acceptors
acceptors
(A) make ATP
(B) use ATP
(A) So PEP & 1,3-BPG can
spontaneously transfer a phosphoryl
group to ADP to make ATP, known as
Substrate Level Phosphorylation !
(B) ATP can in turn transfer its
A thermodynamically unfavorable
phosphoryl group to an ROH
reaction can be driven by a
ATP is used by kinases to phosphorylate ROH
thermodynamically favorable
1) How does coupling to ATP hydrolysis
24
reaction to which it is coupled.
make possible an unfavorable reaction?
Bioenergetics Questions
1) Which of the statement(s) about the structure of ATP are correct?
A)
B)
C)
D)
E)
Its contains three phosphoanhydride bonds.
(two answers)
It contains two phosphate ester bonds.
The sugar moiety is linked to the triphosphate by a phosphate ester bond.
The nitrogenous base is called adenine.
ATP is an activated carrier of electrons.
3. A metabolic intermediate with a high-energy phosphoryl group, that
results in ATP synthesis is:
Use info in Table 15.1 (on slide #18)
A) pyruvate
Must have larger negative DGo’hydrolysis
B) 3-Phosphoglyceric acid
than ATP ( _______________ )
C) Fructose-1,6-bisphosphate
D) Glyceraldehyde 3-phosphate
25
E) phosphoenolpyruvate
Phosphoryl Group Transfer Potential
O
O
-
P
O
OH
-
Themodynamics:
the overall DG’ for
a chemically
coupled series of
reactions equals the
sum of the DG’ of
the individual steps.
use Hess’Law
DGo’ is negative for transfer of phosphates DOWN the table!
1) Write the reaction for which -30.5 kJ/mol is the free energy of hydrolysis:
2) How much energy is required to phosphorylate glucose using Pi as the
phosphate source?
• If reverse reaction, change sign:
Energetic Coupling of Reactions in Biochemistry
Themodynamics: the overall DG’ for a chemically
coupled series of reactions equals the sum of the
DG’ of the individual steps. For example:
use
Hess’Law
A
B
B+C
D
DGo'= +5 kcal/mol
DGo'= -8 kcal/mol
A
C+D
DGo'= -3 kcal/mol
If add reactions, add free energies
1) Is the phosphorylation of glucose by ATP a spontaneous process?
Rxn 1: Phosphorylation of Glucose, DG’ is
positive, so Endergonic
Rxn 2: Hydrolysis of ATP DG’ is large negative, so
Exergonic
Rxn 3: is sum of Rxns 1 & 2: DG’ for overall
reaction is small negative, so Exergonic
Thus overall Rxn 3 proceeds spontaneuously even
though reaction 1 is non-spontaneous.
• When small endergonic (+ DGo’) plus large exergonic (- DGo’) reactions are
added to yield an overall small exergonic (- DGo’) reaction, then the coupled
27 !
reaction will occur in direction written, and process can occur spontaneously
Energy Coupled Reactions in Glycolysis Involving ATP
(coupled reactions are spontaneous)
(A) Utilize ATP to drive endergonic phosphorylation reaction of ROH
Step 1 of
Glycolysis:
Kinase
Reaction
Step 10 of
Glycolysis:
Substrate
Level
Phosphorylation
HESS’ LAW: add rxns & add free energies
reverse rxn, so change sign
(B) Utilize highly exergonic phosphoryl transfer to drive ATP synthesis
28
Stryer Textbook Problem 22:
Identify the more reduced molecule in each pair.
Phosphoryl Group Transfer Potential
• Energy is released
when the terminal Pi
is removed from ATP
Pyrophosphate
PPi is:
ATP4- + H2O  ADP3- + Pi2- + H+
Know structures & formal
Orthocharges of all these species at pH 7 phosphate
O
O
-
O
-
P
O
OH
O
-
P
O
OH
-
DGo’ is negative
for transfer of
phosphates DOWN
the table, from
molecule with
higher phosphoryl
transfer potential
to make a
molecule with
lower phosphoryl
transfer potential
1) Write the reaction for which – 43.1 kJ/mol is the free energy
is the
of
hydrolysis.
free energy of hydrolysis.
2) How much energy is required to phosphorylate ADP using Pi as the phosphate
source?
3) What is the direction of the reaction below when the reactants and
products start in equimolar amounts? At standard conditions, will ATP be used
or formed? Use data in Table above.
ADP + creatine phosphate
ATP + creatine
Bioenergetics Questions
1) Glucose-1-phosphate is converted to Fructose-6-phosphate in
two successive reactions:
2) The first reaction of glycolysis is:
Glucose + ATP 
Glucose-6-phosphate + ADP
Use the standard free energy of hydrolysis of ATP & glucose-6-P as given in text
Table 15.1. Select the FALSE statement below at standard conditions.
A) This reaction is catalyzed by a kinase, and is an overall spontaneous reaction.
B) A phosphorylated alcohol (like that in glucose-6-phosphate) has a low
phosphoryl group transfer potential.
C) ATP has intermediate phosphoryl group transfer potential.
D) This reaction in glycolysis is called substrate level phosphorylation.
E) This is a reaction that lies far from equilibrium.
Creatine Phosphate Is a Reservoir of Energy in Muscle
• Creatine phosphate in vertebrate muscle serves as a reservoir of highpotential phosphoryl groups (~P) that can be readily transferred to ATP.
Indeed, we use creatine phosphate to regenerate ATP from ADP every
time we exercise strenuously. This reaction is catalyzed by creatine kinase.
1
162
Creatine Phosphate: DG°‟ of hydrolysis is - 43.1 kJ/mol is
greater than DG°‟ of hydrolysis of ATP - 30.5 kJ/mol
’
___
1
K’eq = [products] / [reactants] so K’eq > 1 means DGo’ negative
• The equilibrium constant (Keq) of this reaction at pH = 7 is 162, where
products are clearly favored. Thus the reaction will occur in the written
32
direction (making ATP) !
Sources of ATP During Exercise
• In resting muscle, [ATP] = 4 mM, [ADP] = 0.013 mM, [creatine
phosphate] = 25 mM, and [creatine] = 13 mM. The amount of ATP in
muscle suffices to sustain contractile activity for less than a second.
• Indeed, creatine phosphate is the major source of phosphoryl groups for
ATP regeneration for runner during the first 4 seconds of a 100-meter sprint
• After that, ATP must be generated through metabolism.
• In the initial seconds, exercise
is powered by existing high
phosphoryl transfer compounds
(ATP then creatine phosphate).
• Subsequently, the ATP
must be regenerated by
metabolic pathways:
• first anaerobic (lactate)
• then aerobic (CO2)
< 1sec
1-4 secs
A. First few minutes
can produce small
amount of ATP
faster anaerobically
marathon runner
33
Overview of Carbohydrate Catabolism
1. Draw Structures
2. Label Pathways
Substrate Level
2 x pyruvate
Phosphorylation
(3C)
2 x CO2
GLYCOLYSIS
CO2
2 x Acetyl CoA
CO2CoAS
(2C)
O
O
Make
2 ATP
H
O
C
H
HO
H
OH
H
OH
H
OH
PDHC
CH3
2 NADH
CH2OH
2 NADH
O
C
O
makes
26 ATP
Oxidative
Phosphorylation
CH3
Pyruvate
CITRIC
ACID
CYCLE
4C oxaloacetate
D-glucose
(6C)
Total output for
ONE molecule of glucose
-O
CH3
2 GTP
6 NADH
2 FADH2
2 CO2
4 x CO2
(1C)
CoAS
O
CH3
Acetyl
CoA
6C citrate
ELECTRON
TRANSPORT
CHAIN
Result for
one glucose:
Make 30
ATP
PDHC = Pyruvate Dehydrogenase Complex