BIOL 4087

Basic Biochemistry
Instructor: Bing-Hao Luo
Email: luo@lsu.edu
Room: 264 Life Sciences Building
Office hour: Tue & Thu. 3-4 PM (or by
appt.)

https://moodle3.lsu.edu/course/view.php?id=27323
 Lecture 1. Introduction

• Syllabus
• What is Biochemistry
• Thermodynamic Law
• Important Chemical Bonds and
Non-covalent interactions
 Basic Biochemistry
(BIOL 4087) 2009
Recommended Textbooks:
Biochemistry 8th Edition by Berg, Tymoczko, Gatto and
Stryer

Fundamentals of Biochemistry 3nd Edition by Voet, Voet and

Pratt.

Lehninger Principles of Biochemistry 7th Edition by Nelson

and Cox

Principles of Biochemistry 5th Edition by Moran, Horton,

Scrimgeour and Perry

These textbooks are highly recommended, it is NOT required.

Grading Scheme
• Exam 1: 100 points
• Exam 2: 100 points
• Exam 3: 100 points
• Final Exam (comprehensive): 200 points

There are 500 possible points. Grade to be determined

by dividing your point total by 500 points:
A+ = 95-100%; A = 90-94%; A- = 85-89%
B+ = 80-84%; B = 75-79%; B- = 70-74
C+ = 65-69; C = 60-64%; C- = 55-59
D+ = 50-54; D = 45-49%; D- = 40-44
F = <39%
Make-up Exams
Make-up Examinations will only be allowed with an excuse
considered valid by the University. If you miss an exam, you
must contact the instructor within 24 hrs if you wish to schedule a
make-up exam.
Some Course Policies
All students are entitled to equal treatment without regard to race, creed,
color, marital status, sexual orientation, religion, sex, national origin, age,
mental or physical disability, or veteran's status.

Academic dishonesty will not be tolerated. Cheating or plagiarism or other

types of academic misconduct will be penalized as described by the Office of
the Dean of Students in the LSU Code of Student Conduct.
Phones and electronic devices are not to be used or even accessible
during exams and/or quizzes.
http://appl003.lsu.edu/slas/dos.nsf/$Content/Code+of+Conduct?OpenDocum
ent#5.1

Academic civility will be expected in the classroom. Disruptive behavior or

harassment or mistreatment of other students will be as described by the
Office of the Dean of Students in the LSU Code of Student Conduct
http://appl003.lsu.edu/slas/dos.nsf/$Content/Code+of+Conduct?OpenDocum
ent#5.1
 Goals
• Basic biochemical concepts

• Links of biochemical processes

and human diseases

• Contemporary biomedical research

 Five major objectives
• Protein structure and functions (including
AA structures and properties)***
– On all EXAMS v important
• DNA-based information technologies
• Metabolism and its regulation**
• DNA replication
• Protein synthesis and regulation of gene
expression
 Tentative Lecture Schedule (I)
•Jan 9 Lecture 1. Introduction
•Jan 14 Lecture 2. Water, pH, Buffers
•Jan 16 Lecture 3. Amino Acids
•Jan 21 Martin Luther King Day holiday
•Jan 23 Lecture 4. Peptides and Proteins
•Jan 28 Lecture 5. Three-Dimensional Structure of
Proteins
•Jan 30 Lecture 6. Protein Structure and Functio
•Feb 4 Lecture 7. Enzymes I
•Feb 6 EXAM #1 (Lectures 1-6)
•Feb 11 Lecture 8. Enzymes II
 Tentative Lecture Schedule (II)
•Feb 13 Lecture 9. Carbohydrates and Glycobiology
•Feb 18 Lecture 10. Nucleotides and Nucleic Acids
•Feb 20 Lecture 11. DNA-based Information Technologies
•Feb 25 Lecture 12. Lipids and Membranes
•Feb 27 Lecture 13. Introduction to Metabolism
•Mar 4 Mardi Grass Holiday
•Mar 6 Lecture 14. Glycolysis and gluconeogenesis
•Mar 11 EXAM #2 (Lecture 7-12)
•Mar 13 Lecture 15. Metabolism of Glycogen, Fructose
and Galactose
•Mar 18 Lecture 16. The Citric Acid Cycle
•Mar 20 Lecture 17. Oxidative Phosphorylation
 Tentative Lecture Schedule (III)
•Mar 25 Lecture 18. Pentose Phosphate Pathway
•Mar 27 Lecture 19. Lipid Metabolism
•Apr 1 EXAM #3 (Lectures 13-18)
•Apr 3 Lecture 20. Amino Acid Catabolism & Integration
of Metabolism. & Lecture 21. Nucleotide Metabolism
•Apr 8 Lecture 22. DNA Replication
•Apr 10 Lecture 23. RNA Metabolism
•Apr 15-21 Spring break
•Apr 22 Lecture 24. Protein Synthesis (Translation)
•Apr 24 Lecture 25. Regulation of Gene Expression
•May 2 FINAL EXAM (Thursday, 5:30 P.M. – 7:30 P.M.)
 Examinations
Material for the Exams:
 What is Biochemistry

Biochemistry:

1. The study of the chemical substances and vital

processes occurring in living organisms; biological
chemistry; physiological chemistry.

2. The chemical composition of a particular living system

or biological substance.

Biochemistry by Berg etc.

Biochemistry is the study of the chemistry of life

processes
 What is life?

Definition from Wikipedia: Life is a characteristic that

distinguishes objects that have signaling and self-
sustaining processes (biology) from those that do not,
either because such functions have ceased (death), or
else because they lack such functions and are classified
as inanimate.
1John 2:16 Because
In the Bible,all that is in the
there areworld,
three the lust of the
flesh and the lust of the eyes and the vainglory of life (Bios,
Greeklife),
biology, physical words
is not offor
the“life”
Father but is of the world.

John 10:11 I am the good Shepherd; the good Shepherd

lays down His life (Psuche, psychology, soul life) for the
sheep.

John 10:10 I have come that they may have life (Zoe,
eternal, divine life, spiritual life) and may have it abundantly.

John 3:16 For God so loved the world that He gave His
only begotten Son, that every one who believes into Him
would not perish, but would have eternal life (Zoe).

1 Thess 5:23 And the God of peace Himself sanctify you

wholly and may your spirit and soul and body be preserved
complete, without blame, at the coming of our Lord Jesus
 Life can be studied as a hierarchical structure
The structure of living organisms including those of entire populations and
ecosystems is organized in a hierarchical fashion that allows a systematic
exploration of the question ‘What is life (physical life)?’. In the biological sciences,
the following structural levels are recognized:
Level Examples and Special consideration
Ecosystem Rain forest, desert, fresh water lake, digestive tract of animal for bacteria
Includes all living organisms and non living matter such as air, water and minerals
Community All species in an ecosystem
Only includes living things from bacteria, to fungi, to plant to animal
Population All individuals of a single species
Includes only individuals from a specific species such as a plant, an animal, a bacterial colony
Organism One single individual
Serves as a representative of the species and describes overall form and function of an
organism
Organ system A specialized functional system of an organism
The nervous system or immune system of an animal
Organ A specialized structural system of an organism
The brain or the thymus of an animal
Tissue A specialized substructure of an organ
The nervous tissue and epithelial tissue are both part of the brain
Cell A single cell
A neuron, a skin cell, a root cell, bacteria, yeast, paramecium
Molecule A single large or small molecule such as a protein, DNA, sugar or fatty acid
Molecules are the smallest part of biological systems; they can be studied for their chemical,
physical properties, but are of particular interest for their usefulness in biological systems.
Structural hierarchy in Molecular organization of cells
 Biochemistry Is a Modern Science

• Urea was synthesized by heating the inorganic

compound ammonium cyanate (1828).
• This showed that compounds found exclusively
in living organisms could be synthesized from
common inorganic substances.
 Two notable breakthroughs in the
history of biochemistry
(1) Discovery of the role of enzymes as
catalysts
(2) Identification of nucleic acids as
information molecules

Flow of information: from nucleic acids to

proteins
DNARNAProtein
 The Chemical Elements of Life

• Only six nonmetallic elements: oxygen, carbon,

hydrogen, nitrogen, phosphorous, and sulfur
account for >97% of the weight of most organisms
• These elements can form stable covalent bonds
• Water is a major component of cells
• Carbon is more abundant in living organisms than
it is in the rest of the universe
 Functional groups in biochemistry
• Functional groups - specific parts of molecules
involved in biochemical reactions
Functional groups in biochemistry
 Many Important Biomolecules
are Polymers

• Biopolymers - macromolecules created by

joining many smaller organic molecules
(monomers)
• Condensation reactions join monomers
(H2O is removed in the process)
• Residue - each monomer in a chain
 Molecular mass

• Molecular weight is more correctly termed the

relative molecular mass (Mr) - the molecular
mass relative to 1/12 mass of a carbon atom (12C)
• Mr is a relative quantity and is dimensionless
• A typical protein may have an Mr = 38,000
• The absolute molecular mass of this protein =
38,000 daltons (1 dalton = 1 atomic mass unit)
 Thermodynamic Laws
Heat, Work and Energy
• Heat: dq=C dT
• Work: dw = Fx dx
• Energy: ∆ E = q + w
At constant pressure, then ∆ E = qp - P(V2-V1)
• Enthalpy: H = E + PV
The ∆H, the heat change at constant
pressure, can be measured experimentally.
 Probability
The ∆H, the heat change at constant pressure,
can be measured experimentally.

One possible conclusion is that chemical

equilibria are governed by energy considerations
and that the system will always proceed to the
lowest energy state. But is it true?

Example: The conversion of liquids to gases

requires heat, that is, ∆H is positive, even at
temperatures above the boiling point. Clearly, the
lowest energy state is not necessarily the most
stable state.
The missing ingredient: Probability.
 Entropy
Entropy, S, is a measure of the disorder (or
probability) of a state.

A simple illustration: consider three balls of equal

size that are numbered 1, 2, and 3. How many
different ways these balls can be arranged?

Six different ways:

123 132 213 231 312 321
 Entropy
Entropy, S, is defined as: S = kB ln W
Where kB is the Boltzmann constant, W is the
randomness of the system or the number of
ways.

The more disordered a state, or the larger the

number of available microstates, the higher
the entropy.
 The Second Law
The second law states that disordered states
are more probable than ordered states.

Entropy, S, is defined as:

S = kB ln W

dS = dqrev / T
or
dqrev
∆S = ∫ T
 Third Law of Thermodynamics

The third law can be stated as follows: The

entropy of perfect crystals of all pure elements
and compounds is zero at absolute zero. (0K)

S = kB ln W

It is worth noting that a perfect crystal has one

microstate, and therefore, an entropy of zero
according to this equation.
 Free Energy
Gibbs free energy:
G = H - TS

At constant temperature,
∆G = ∆H - T∆S

∆G < 0, the change in state occurs spontaneously

∆G > 0, the reverse change in state occurs
spontaneously
∆G = 0, the system is at equilibrium (at constant
pressure and temperature)
 Chemical Equilibria
aA (PA) + bB (PB) ↔ cC (PC) + dD (PD)

G = H – TS = E + PV –TS
dG = dE + PdV + VdP – TdS – SdT

Since dE = dq + dw = TdS – SdV for a reversible process,

dG = VdP – SdT

For a chemical reaction of ideal gases at constant

temperature,
dG = VdP = nRTdP/P

If we select 1 atm as our standard state, the last equation is

now integrated from P0 = 1 to P,
G = Go + nRTln(P/P0) = Go + RTlnP
 Chemical Equilibria
aA (PA) + bB (PB) ↔ cC (PC) + dD (PD)

G = Go + nRTln(P/P0) = Go + RTlnP

∆G = c∆GC + d∆GD - a∆GA - b∆GB

= c∆GC + d∆GD - a∆GA - b∆GB + cRTlnPC + dRTlnPD
- aRTlnPA – bRTlnPB
c d
PC PD
= ∆Go + RT ln( a b )
PA PB

At equilibrium, at constant temperature and pressure, ∆G =

0, c d
PC PD
∆Go = -RT ln( a b ) = - RT lnK
PA PB

K is the equilibrium constant.

 Chemical Equilibria
What about free energy in solutions? Conceptually
there is no difference.

aA + bB ↔ cC + dD

G = Go + nRTln(c/c0)
c d
cC cD
∆Go = -RT ln( c a c b ) = - RT lnK
A B

K is the equilibrium constant.

Question:
If ∆Go < 0, K?
 Important Chemical Bonds
in Biochemistry
• Covalent bonds
– Sharing of a pair of electrons
– For C-C bond, 1.54 Å ~85 kcal/mol
– For C=O double bond, 1.34 Å ~175 kcal/mol
– 1 Å (Ångström) = 1×10−10 metres

• No-covalent interactions
– Reversible
– Low energy (1-3 kcal/mol)
 Non-covalent interactions
• Electrostatic interactions

• Hydrogen bonds

• Van der Waals interactions

• Hydrophobic interactions
Electrostatic Interactions
(typical 1-2 kcal/mol)

E = kq1q2/Dr2 (Coulomb’s law)

q1, q2 are the charges on the two atoms,

r, the distance between the two atoms (in Å)
D, dielectric constant.
K is the proportionality constant. (332 kcal/mol)
Materials Dielectric Constant (D)
Vacuum 1.000
Air 1.0006
Glass 5-10
Rubber 2.5-35
Wood 2.5-8
Pure water 88–80.1 –55.3 –34.5
(0– 20°C–100°C–200°C)
 Hydrogen bonds
Typically 1-5 kcal/mol

Donor or acceptor must be strongly electronegative

and have an unshared electron pair.
Strong H-bonds are arranged in a straight line.
Hydrogen bonds network in protein
van der Waals interactions
Typically, 0.5-1.0 kcal/mol.
Dipole–dipole forces

~ 3-4 A
 Hydrophobic Interactions
• Hydrophobic force
– Water tends to squeeze hydrophobic
molecules together

• Hydrophobic force contributes to the

stabilization of structures of biological
molecules.