Chapter 1

Life: Foundations of Biochemistry

Instructor: Rashid Syed

Textbook: Biochemistry (4th Edition ) by Donald Voet Judith G. Voet

Cell: The Universal Building Block

Living organisms are made of cells

Simplest living organisms are single-celled
Larger organisms consist of many cells with different functions
Not all of the cells are the same

All cells share some common features

Three Distinct Domains of Life Defined

by: Cellular and Molecular Differences

Bacterial Cell Structure

Components of Bacterial Cell

Structure

Composition

Function

Cell wall
Cell membrane
Nucleoid
Ribosomes
Pili
Flagella
Cytoplasm

Peptidoglycan
Lipid + protein
DNA + protein
RNA + protein
Protein
Protein
Aqueous solution

Mechanical support
Permeability barrier
Genetic information
Protein synthesis
Adhesion, conjugation
Motility
Site of metabolism

Eukaryote Cells: More Complex

Have nucleus by definition
protection for DNA; site of DNA metabolism
selective import and export via nuclear membrane pores
some cells become anuclear (red blood cells)

Have membrane-enclosed organelles

Mitochondria for energy in animals, plants, and fungi
Chloroplasts for energy in plant
Lysosome for digestion of un-needed molecules

Spatial separation of energy-yielding and energyconsuming reactions helps cells to maintain

homeostasis and stay away from equilibrium

Bacterial, animal, and plant cells are different

Bacterial, animal, and plant cells are different

Biochemistry: the Chemistry of Living Matter

The basis of all life is the chemical reactions that

take place within the cell.

Chemistry allows for:

A high degree of comlexity and organization
Extraction, transformation, and systematic use of
energy to create and maintain structures and to do
work
The interactions of individual components to be
dynamic and coordinated.
The ability to sense and respond to changes in
surrounding
A capacity for fairly precise self-replication while
allowing enough change for evolution

Organisms Classification based on different

energy and carbon sources

Living systems extract energy

From sunlight
plants
green bacteria
cyanobacteria

From fuels
animals
most bacteria

Energy input is needed in order to maintain life

The Molecular Logic of Life

We look at the chemistry that is behind:
Accelerating reactions
Organization of metabolism and signaling
Storage and transfer of information

The ABCs of Life

The Molecular Hierarchy of Structure

Biological Polymers (Macromolecules)

Biochemistry: Unique Role of Carbon

30 Elements Essential for Life

Other than carbon, elements H, O, N, P, S are also common
Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play important roles
in metabolism

Common Functional Groups of Biological Molecules

Biological molecules typically have several

functional groups

The function of molecules strongly

depends on three-dimensional structure
Stereoisomers: molecules with the same chemical bonds
and chemical formula but different configuration (the
fixed spatial arrangement of atoms)
Geometric Isomers (cis vs. trans)
have different physical and chemical properties
Enantiomers (mirror images)
have identical physical properties (except with
regard to polarized light) and react identically with
achiral reagents
Diastereomers
have different physical and chemical properties

Cis vs. Trans

Cis vs. Trans

Enantiomers and Diastereomers

Enantiomers and Diastereomers

Interactions between biomolecules are specific

Macromolecules have unique binding pockets

Only certain molecules fit in well and can bind
Binding of chiral biomolecules is stereospecific

Interactions between biomolecules are specific

Genetic Information
Genetic information is contained in DNA.
Double helical DNA molecule contains
information for its own replication and repair.
This ensures genetic identity and continuity.
The complete human genome is sequenced.
Need to identify the functions of each gene.
Which genetic errors cause disease ?
Gene expression during development.
Genetic changes during evolution.

Flow of Information
Genetic information flows from
DNA DNA RNA Protein Function
DNA is the Blue print
RNA is the Messenger
(RNA also has structural and adapter roles)
Protein is the Performer/Effector
DNA and RNA sequences are made up of
only 4 bases each
Protein sequences contain 20 amino acids.

Formation of Macromolecules
Both DNA and protein are linear polymers
The sequence of amino acids in a protein is determined
by the sequence of the DNA encoding it.
The linear sequence of aa in a protein leads to its folding
into a unique 3-D structure.
The folded structure confers affinity for other
macromolecules or small ligands.
Two or more components with high affinity for each
other self-assemble into supramolecular complexes.
The overall structure of a complex is key to its function.

Assembly of
Supramolecular
Complexes

Structure-Function Relationship
Underlying principle throughout Biochemistry:
Structure determines function.
The structure (sequence) and therefore, the
function, of each gene is unique.
In the double helix, A-T and G-C pairing is based
on chemical structure of A, T, G, and C.
In proteins, not only the sequence of amino acids,
but also the 3D folding patterns and oligomeric
composition affect function.

Chapter 3
Thermodynamics Principles: A Review
Instructor: Rashid Syed

Textbook: Biochemistry (4th Edition ) by Donald Voet Judith G. Voet

Organisms perform energy transductions to

accomplish work to stay alive

ATP: Chemical Currency of Energy

How to speed reactions up

Higher temperatures
Stability of macromolecules is limiting

Higher concentration of reactants

Costly as more valuable starting material is needed

Change the reaction by coupling to a fast one

Universally used by living organisms

Lower activation barrier by catalysis

Universally used by living organisms

Unfavorable and Favorable Reactions

Synthesis of complex molecules and many other metabolic
reactions requires energy (endergonic)
A reaction might be thermodynamically unfavorable (G > 0)
Creating order requires work and energy

Metabolic reaction might have too high energy barrier (G > 0)

Metabolite is kinetically stable

Breakdown of some metabolites releases significant amount of

energy (exergonic)
Such metabolites (ATP, NADH, NADPH) can be synthesized using the
energy from sunlight and fuels
Their cellular concentration is far higher than their equilibrium
concentration

Energy Coupling
Chemical coupling of exergonic and endergonic
reactions allows otherwise unfavorable reactions
The high-energy molecule (ATP) reacts directly
with the metabolite that needs activation

Catalysis
A catalyst is a compound that increases the rate
of a chemical reaction

Catalysts lower the activation free energy G

Catalysts does not alter G
Enzymatic catalysis offers:
acceleration under mild conditions
high specificity
possibility for regulation

Enzymes lower the activation energy to

increase the reaction rate

Series of related enzymatically catalyzed

reactions forms a pathway

Metabolic Pathway
produces energy or valuable materials
Signal Transduction Pathway
transmits information

Pathways are controlled in order to

regulate levels of metabolites

Example of a negative regulation:

Product of enzyme 5 inhibits enzyme 1

Chapter 2

Aqueous Solutions
Instructor: Rashid Syed

Textbook: Biochemistry (4th Edition ) by Donald Voet Judith G. Voet

Water, pH, and Buffers

Structure of water
Hydrogen bond
Interactions of water with biomolecules
Weak acids and bases
Buffers
pH and pKa: The Henderson-Hasselbalch
equation

Water
Most biochemical reactions occur in an aqueous
environment.
There is a significant difference in electronegativity
between H (2.1) and O (3.5). There is a partial positive
charge (+) on H and partial negative charge (-) on O.
The presence of two lone pairs of electrons on O leads to a
bond angle of 104.5o instead of 109.5o .
Because of its bent shape, and the partial charges on H and
O, water is a highly polar molecule.
Water is highly cohesive because of inter-molecular
hydrogen bonding. This results in its higher MP, BP and
heat of vaporization than other common solvents.

Structure and H-bonding of Water Molecules

Hydrogen Bond
The attractive force between a partially negatively
charged electronegative atom and a partially positively
charged H atom is called a Hydrogen Bond.
H-bonds are considerably weaker than covalent bonds.
Bond energy for covalent HO bond = 420 kJ/mol
Bond energy for H-bond = 20 kJ /mol
Non-covalent bonds such as H-bonds, van der waals
interactions and hydrophobic interactions are
individually weak, but collectively they greatly
stabilize the conformation of biomolecules.

Biologically Important H-Bonds

Interactions of water with Biomolecules

Biomolecules may be polar, non-polar or amphipathic.
Water is a polar solvent; it dissolves most polar or
charged compounds (including high molecular weight
proteins and DNA/RNA) by hydration.
Hydration involves formation of H-bonds between water
and charged ions or polar groups of solutes, thus
neutralizing electrostatic interactions amongst solute
molecules.
Hydrophobic molecules align surrounding water
molecules into highly ordered H-bonded cages.

Water Dissolves Polar Solutes by Hydration

Physics of Noncovalent Interactions

Noncovalent interactions do not involve sharing a pair of electrons.
Based on their physical origin, one can distinguish between:
Ionic (Coulombic) Interactions
Electrostatic interactions between permanently charged species,
or between the ion and a permanent dipole
Dipole Interactions
Electrostatic interactions between uncharged, but polar
molecules
van der Waals Interactions
Weak interactions between all atoms, regardless of polarity
Attractive (dispersion) and repulsive (steric) component
Hydrophobic Effect
Complex phenomenon associated with the ordering of water
molecules around nonpolar substances

Examples of Noncovalent Interactions

Hydrophobic Interactions

Non-polar regions cluster together

Exposure of hydrophobic region is minimized

Ionization of Water
Weak ionization of water:
H2O

H+ + OH-

Free protons do not exist in solution; they get hydrated

H2O + H2O

H3O+ and OH-

The equilibrium constant for the dissociation of water

Keq = [H+] [OH-] / [H2O]
Keq [H2O] = [H+][OH-]
The concentration of water is constant at 55.5 M
Keq[H2O] is a constant referred to as Kw = [H+][OH-]
Keq = 1.8 x 10-16 M by electrical conductivity measurements
Kw = 1 x 10-14 M2 = [H+][OH-]

Acids and Bases, pH

For pure water [H+] = [OH-] = 10-7 M

The ion ratios change in the presence of an acid or base.
An acid is defined as a proton donor
AH = A- + H+
AH is the acid and A- is its conjugate base.
Base is defined as a proton acceptor
B + H2O = BH+ + OHB is the base and BH+ is its conjugate acid
pH = -log [H+]
pOH = -log [OH-] ([H+] and [OH-] in M)
[H+] x [OH-] = 1 x 10-14 M2. Therefore, pH + pOH = 14

The pH scale
An acidic solution is one in
which [H+] > [OH-]
In an acidic solution:
[H+] > 10-7, pH < 7.
A basic solution is when
[OH-] > [H+].
In a basic solution:
[OH-] > 10-7, pOH < 7, and
pH >7.
When the pH = 7, the
solution is neutral.
Physiological pH range is
6.5 to 8.0

pH scale is logarithmic: 1 unit = 10-fold

Weak Acids and pKa

The strength of an acid is determined by its dissociation
constant, Ka.
Dissociation of an acid: HA = H+ + Athe dissociation constant Ka = [H+][A-] / [HA]
Acids that do not dissociate significantly in water are weak
acids.
When Ka < 1, [HA] > [H+][A-] and HA is not significantly
dissociated. Thus, HA is a weak acid when Ka < 1.
The lesser the value of Ka, the weaker the acid.
The value of Ka is represented by pKa: pKa = -log Ka.
The larger the pKa, the weaker the acid.
pKa is a constant for each conjugate acid and its conjugate base
pair.
Most biological compounds are weak acids or weak bases.

pKa Values of Conjugate Acid-Base Pairs

Polyprotic Acids
Some acids are polyprotic acids; they can lose more than
one protons.
In this case, the conjugate base is also a weak acid.
For example: Carbonic acid (H2CO3) can lose two
protons sequentially.
Each dissociation has a unique Ka and pKa value.
Ka1 = [H+][HCO3-] / [H2CO3]
Ka2 = [H+][CO3-2] / [HCO3-]
Note: (The difference between a weak acid and its
conjugate base is one hydrogen)

Weak Acids and their Conjugate Bases

Titration of a weak acid with a strong base

Normally, a weak acid is mostly in its conjugate acid form
When strong base is added, it removes protons from the solution
(acid is neutralized), Equilibrium shifts to the right and acid is
converted to its conjugate base. The pH increases.
The pH can be determined by using a pH meter or indicator dye.
A titration curve of pH vs moles of OH-/moles of initial HA is
drawn.
When x-axis value is 0.5, the amount of OH- added is exactly
half of the initial acid. The weak acid and its conjugate base are
in equal amounts.
At this point the pH = pKa. (pKa is the pH at which [WA]=[CB])
If more base is added, the conjugate base form predominates till
the equivalance point when all acid is in conjugate base form.

Titration Curve for Acetic Acid

Buffers
Definition: A buffer is a solution that resists a significant
change in pH upon addition of an acid or a base.
Chemically: A buffer is a mixture of a weak acid and its
conjugate base
Example: Bicarbonate buffer is a mixture of carbonic acid
(the weak acid) and the bicarbonate ion (the conjugate
base): H2CO3 + HCO3 All OH- or H+ ions added to a buffer are consumed and the
overall [H+] or pH is not altered
H2CO3 + HCO3- + H+
2H2CO3
H2CO3 + HCO3- + OH2HCO3- + H2O
For any weak acid / conjugate base pair, the buffering
range is when pH = pKa +1.

Mechanism by which Buffers Operate

Example:
CH3COOH + CH3COO- + OH- = 2CH3COO- + H2O (you get more conjugate base)
CH3COOH + CH3COO- + H+ = 2CH3COOH (you get more weak acid)

Antacids
Alka-seltzer contains NaHCO3 which is a salt of
HCO3- a conjugate base of H2CO3
TUMS: contains CaCO3, which is a salt of CO3-2, the
conjugate base of HCO3-.
Antacids neutralize excess H+ by forming the weak
acid. The weak acid remains mostly undissociated.
The conjugate base (antacid) and the weak acid
formed together form a buffer and resist change in pH.

Buffering range for weak acids

Initially, [WA] >>> [CB]
When [WA]=[CB], pH=pKa
The central region of the
curve (pH+1) is quite flat
because:
When [CB]/[WA] = 10,
pH = pKa +1;
When [CB]/[WA] = 0.1,
pH = pKa - 1
Titration curve is reversible, if
we start adding acid, [WA]
increases

The Henderson-Hasselbalch equation

Dissociation of a weak acid is mathematically described by
the Henderson-Hasselbalch equation
Ka = [H+][A-] / [HA] or
Ka = [H+] x [A-] / [HA]
logKa = log[H+] + log {[A-] / [HA]}
-log[H+] = -logKa + log {[A-] / [HA]}
pH = pKa + log {[A-] / [HA]}
So, if CB = conjugate base and WA = weak acid, then:
pH = pKa + log {[CB] / [WA]}
This is the Henderson-Hasselbalch equation
Note: pH = pKa when [CB] = [WA]
When pH > pKa, [CB] > [WA]

Biological Buffers
Biological systems use buffers to maintain pH in the
physiologic range.
Intracellular buffers: proteins, biomolecules with
ionizable functional groups, phosphate.
Extracellular buffers: bicarbonate, phosphate
H2PO4HPO4-2 + H+ pKa = 6.86
H2CO3
HCO3- + H+ pKa = 6.37
H2CO3 is CO2 dissolved in H2O; the amount of CO2
dissolved depends on the partial pressure of CO2.
The equilibrium of each of these reactions is shifted to
maintain the plasma pH at ~ 7.4

The Bicarbonate Buffer System