Biochemistry 440b
Fall 2016
Useful Information for Examination 1
Physical Constants
Avogadro's number
Boltzman's constant
Gas constant ( N x k )
N
k
R
Planck's constant
electron charge
Faraday constant ( N x e )
h
e
F
velocity of light
c
6.02 x
The Boltzmann Equation is an expression of the
Principle of Multiplicity
Ludwig Boltzmann in the 19th Century was the one who recognized
the importance of Multiplicity.
He defined Entropy, S:
S = kB ln(W )
The equilibrium state is defined as the state wit
Stability of Biological Macromolecules and Assemblies
Applications of equilibrium thermodynamics H, G, S, Cp
1. Entropy, water and the hydrophobic force
2. Ionic solutes, non-polar solutes and amphiphilic solutes
3. Lipid shape and the phospholipid bilaye
The thermodynamics of transport in biology
Transport of metabolites across biological membranes
a) into or out of cells
b) into or out of cellular organelles
The lipid bilayer is impermeable to most metabolites, so transport
Is usually mediated by protein
What do we mean by Protein Stability and how is it
measured?
We need to understand this to analyze the effects of mutations on proteins
Two-state analysis is often sufficient for small globular proteins
F
I1
I2
I3
U
unfolded
folded
Intermediates
< 5% of t
Partitioning of a nonpolar molecule in a micelle
is similar to partitioning in a nonpolar solvent
water
water
nonpolar solvent
micelle
Micelle Size and Shape
Which shape micelle is more stable in solution?
Surface area per molecule (S/m) is the critical p
One can calculate the heat of reaction for any biochemical
reaction without a calorimeter
using tabulated HEATS OF FORMATION
f H
o
Heat of Formation:
o
H
f
The heat of formation is the heat of reaction for
a reaction in which the reactants are all elemen
BIO-Physical Chemistry
Foundations and Applications of Physical Biochemistry
Robert B. Gennis
1
Chapter 1: An introduction to thermodynamics- work, heat, energy
and entropy
1.1 Introduction
BOX 1.1 A word about mathematics
1.2 Potentials, Forces, Tendenci
Chapter 3: Thermodynamics of Biochemical Reactions
3.1 Introduction
3.2 Representation of a biochemical reaction
3.3 Maximal available work that can be obtained from a biochemical reaction
3.4 The spontaneous direction of the reaction and the equilibrium
Chapter 2: Gibbs Free Energy and the Chemical Potential
2.1 Free Energy Functions and Maximal Work Capacity
2.11 The special case of an isolated system.
2.12 The special case of a system held at constant temperature: introducing
Helmholz Free Energy.
2.13
We will now look at several reactions involved in oxidative phosphorylation
Complex I
Complex II
4H+/2e-
0 H+ pumped
4H+/2e-
NADH:ubiquinone
oxidoreductase
Complex III
Complex IV
2H+/2e-
4H+/2e-
Succinate:
ubiquinone
oxidoreductase
Ubihydroquinone:
cytoch
Review for the Exam
What Do you need to Do ?
Pay Attention to the Homework and the two practice problems
Home Works 5-8 are included
Total Points 100
Office Hour Tomorrow incase you guys have last minute
questions
How Will the Exam look
like
7 Problems
5
What does this mean?
State 1
(dU sys TdS sys )
wsys
dU sys TdS sys wsys
work
heat
State 2
The work, heat and energy are all negative
in this transition from State 1 to State 2.
ANY OTHER PATHWAY
PATHWAY ACCOMPLISHING
THE MOST WORK
Express this inequality
Biochem 440B
Fall 2016
Problem Set 2
Due Thursday September 8, 2016
1) The standard state reaction enthalpy for the combustion of palmitic acid has been
determined.
CH3(CH2)14COOH(solid) + 23O2(g) D 16CO2(g) + 16H2O(l)
r H o = 9958.7 kJ / mole
The standa
BIOC 440B / CHEM 440B
Introduction to Physical
Biochemistry
Part I
Instructor:
Emad Tajkhorshid
emad@life.illinois.edu
BIOC 440B / CHEM 440B
Moodle Website
https:/learn.illinois.edu/course/view.php?id=19058
Login using your NetID
An e-mail list of all stu
Solutions to Problem Set 3
Biochem/Chem 440b
Fall 2016
1) The following two reactions are part of glycolysis.
fructose 1,6,-bisphosphate + ADP
I fructose 6-phosphate + ATP
dihydroxyacetone phosphate + glyceraldehyde phosphate
II fructose 1,6-bisphos
Solution to Practice Problem 1
A) We have a system A with 10 particles and a total energy of 2 units. Each particle is
allowed to have an energy of either 0 or 1 units only. What is the multiplicity of this system, WA?
S
What is the value of A = ln WA ?
k
Solutions to practice problem 4
1. (a)
+
2 Pi + Nain+
Net reaction: Naout
+ PPi
in
out
r G ' = 2 Pi + Na
PPi Na
'
in out
r G ' = r Gbiochem
+ Na
'
'o
where r Gbiochem = 2 Pi PPi = r Gbiochem
[ Pi ]2
+ RT ln
[ PPi ]
in out
in
out
Na
= ( Na
Na
)
At e
Biochem 440B
Fall 2016
Solutions to Problem Set 2
1. The standard state enthalpy of the reaction is determined by the standard state
heats of formation of each of the reactants and products.
o
o
r H o = 16 f HCO
+ 16 f H Ho 2O (l ) 23 f HOo2 f H palm
2 (g
Biochemistry 440b
Fall 2016
Problem Set 4
Due: Thursday September 22, 2016
1. The sodium/proton antiporter from the bacterium Thermus thermophilus (NapA) has been
characterized and its structure determined by X-ray crystallography (Lee et al, Nature (2013
Solution to Practice Problem 2
1. (a) There are 3 translational degrees of freedom, 3 rotational degrees of freedom and 684
vibrational degrees of freedom.
(b) Average translational kinetic energy from the equipartition theorem is
3
3
RT = (1.99)(310) = 9
Biochem 440B
Fall 2016
Solutions to Problem Set 1
1.
a) Pressure is measured in pascals. What is this in terms of SI base units?
In SI units, pressure is force/area = Newton/(meter)2, or m-1.kg.s-2.
b) What is the relationship between a pascal, an atmosph
Practice Problem 3
1. If r G 'o for the hydrolysis of ATP to ADP and Pi is -35 kJ/mole under the conditions of
interest, what is the value of r G ' for the following conditions:
a) [ATP]=3 mM, [ADP]=0.5 mM, [Pi]= 1 mM; T = 298K
b) [ATP]=0.5 mM, [ADP]=3 mM
Problem Set 3
Biochem/Chem 440b
Fall 2016
Due: Thursday September 15, 2016
1. The following two reactions are part of glycolysis.
fructose 1,6,-bisphosphate + ADP
I fructose 6-phosphate + ATP
dihydroxyacetone phosphate + glyceraldehyde phosphate
II
CHEM 440B / BIOC 440B
Fall 2016
Problem Set 1
Due Thursday September 1, 2016
1. For the most part, we will use the International System (SI) of Units throughout this
course. Review what these are by examining the NIST website:
http:/physics.nist.gov/cuu/U
Practice Problem 4
1. (a) The pyrophosphatase sodium pump can be studied in reconstituted membrane vesicles
in which the active site is on the outside and sodium is pumped inside the vesicle. Sodium
transport is thus easily measured using radioactive sodi
Practice Problem 1
Simple models can be useful to understand the power of the principle of multiplicity. In lattice
models, for example, we can explore the behavior of a small number of particles (molecules)
distributed in different locations or energy le
EXAM III Review
Topics Covered in the Exam
Ficks law and diffusion
Isothermal titration calorimetry (ITC)
Protein allostery and cooperativity
Monod-Wyman-Changeux (MWC) model
Protein folding and transition state theory
Ficks law and diffusion
Isothermal t