Introduction to Biochemistry

Why am I here?
How can the world become a better place?
 Introduction
Biochemistry

•What is Biochemistry
•The Aim and Objective of Biochemistry
•Why Biochemistry
•Biomolecules & Biochemical Methods
 Objectives

 Know what biochemistry is and its principle.

 Know the components of a cell and its major types
of bio-molecules.
 Understand how the role of cell organisation and
different types of chemical reactions involved in
maintaining high degree of internal order.
 What is Biochemistry

• Bio - Life
• Chemistry - Science concerned with
molecules and their reactions
• Biochemistry is the chemistry of Life
Biochemistry - an interdisciplinary scientific
discipline whose very fast development is
one of the characteristics of the 20th century
and beginning of a new millennium.
 The scope of biochemistry is to understand the
chemical processes that take place in living
organisms, and in fact, characterize life itself.
 The chemical logic of living things includes synthesis
and degradation of small organic molecules, use of
these simple molecules (building blocks) to
construct macromolecules, which in turn acquire
functionality such as enzymatic activity or capacity to
store information.
 Much of biochemistry concerns regulation and
control of chemical processes of life, as well as
about how living cells produce energy for their
processes.
 What is Biochemistry
 Biochemistry is the application of chemistry to the
study of biological processes at the cellular and
molecular level.

 It emerged as a distinct discipline around the

beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex

molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and

whole organism
 What is Biochemistry?
A. Biochemistry is concerned with structural
chemistry. It seeks to determine the
structures of molecules found in living
systems in order to understand structure-
function relationships.
B. Biochemistry is concerned with chemical
change, this is reflected in the study of
metabolic pathways
 What is Biochemistry?
C. Biochemistry is concerned with information
which has accumulated through evolution and is
preserved in DNA (or sometimes RNA).
These nucleic acid sequences code for amino
acid sequences, which result in folded proteins.
These proteins are often catalysts (enzymes)
and some of them are regulated (able to sense
the chemical state inside the cell and, in some
cases, the outside)
Biochemistry is an intrinsically beautiful and
fascinating body of knowledge.
 Aim of Biochemistry

• To Understand all the chemical processes

associated with living cells
• To Isolate the various molecules and
determine their structure and function
• To Understand how life began
 Principles of Biochemistry
 Cells (basic structural units of living organisms) are highly
organized and constant source of energy is required to
maintain the ordered state.
 Living processes contains thousands of chemical rxns.
Precise regulation and integration of these rxns are required
to maintain life
 Certain important rxns E.g. Glycolysis is found in almost all
organisms.
 All organisms use the same type of molecules: CHO,
proteins, lipids & nucleic acids.
 Instructions for growth, reproduction and developments for
each organism is encoded in their DNA
 Why Biochemistry

• All Diseases are a result of abnormalities of molecules,

chemical reactions and processes
• To know the normal situation so that abnormalities can be
quickly diagnosed, prognosis of the symptoms can be
drafted leading to successful treatment of the illness.
• Major advances in biochemistry and molecular biology has
allowed diagnosis and treatment of many diseases. Eg.
Gene therapy
 Principle Areas of
Biochemistry
 Structure and function of biological
macromolecules
 Metabolism – anabolic and catabolic processes.
 Molecular Genetics – How life is replicated.
Regulation of protein synthesis
High level of knowledge in biochemistry -
necessary for development of other associated
disciplines (molecular biology, genetics,
biotechnology, medical biology etc.)
Why study Biochemistry (scope)
 The chemistry basics of many important processes are
now elucidated
 Flow of genetic information; conversion of energy forms,
molecular motors
 Common chemical principles are the bases of all life
forms
 Genetic information, conversion of energy
 Biochemistry is the basis of medical science and
technology
 Enzymes, cell growth, protein structure, DNA mutations
 Biochemistry is the basis of all advances in medical
science and technology
 bioengineering, biochemical engineering, biomedical
engineering, biotechnology, tissue engineering, etc.
 Medical biochemistry – scope & practice

 Provincial Screening programs

 (Neonatal and Prenatal)
 Lipid Screening
 Chronic Disease Screening
 Iron overload and Deficiency screening
 Cancer Screening
 Tumour Markers
Biochemistry and Human Biology
1. biochemistry is an intrinsically beautiful
and fascinating body of knowledge.
 We now know the essence and many of the details of the
most fundamental processes in biochemistry, such as how a
single molecule of DNA replicates to generate two identical
copies of itself and how the sequence of bases in a DNA
molecule determines the sequence of amino acids in an
encoded protein. Our ability to describe these processes in
detailed, mechanistic terms places a firm chemical foundation
under other biological sciences.
 Moreover, the realization that we can understand essential life
processes, such as the transmission of hereditary
information, as chemical structures and their reactions has
significant philosophical implications.
 What does it mean, biochemically, to be human?
 What are the biochemical differences between a human being, a
chimpanzee, a mouse, and a fruit fly?
 Are we more similar than we are different?
 2, biochemistry is greatly influencing medicine and
other fields.

 The molecular lesions causing sickle-cell anemia,

cystic fibrosis, hemophilia, and many other genetic
diseases have been elucidated at the biochemical
level.
 Some of the molecular events that contribute to
cancer development have been identified.
 An understanding of the underlying defects opens
the door to the discovery of effective therapies.
 Biochemistry makes possible the rational design
of new drugs, including specific inhibitors of
enzymes required for the replication of viruses
such as human immunodeficiency virus (HIV).
 Genetically engineered bacteria or other
organisms can be used as "factories" to
produce valuable proteins such as insulin
and stimulators of blood-cell development.
 Biochemistry is also contributing richly to
clinical diagnostics.
 For example, elevated levels of telltale
enzymes in the blood reveal whether a patient
has recently had a myocardial infarction
(heart attack).
 DNA probes are coming into play in the precise
diagnosis of inherited disorders, infectious
diseases, and cancers.
 Agriculture, too, is benefiting from advances in
biochemistry with the development of more
effective, environmentally safer herbicides and
pesticides and the creation of genetically
engineered plants that are, for example, more
resistant to insects.

All of these endeavors are being accelerated by

the advances in genomic sequencing.
3. advances in biochemistry are enabling researchers to tackle
some of the most exciting questions in biology and medicine.

 How does a fertilized egg give rise to cells as different

as those in muscle, brain, and liver?
 How do the senses work?
 What are the molecular bases for mental disorders
such as Alzheimer disease and schizophrenia?
 How does the immune system distinguish between
self and nonself?
 What are the molecular mechanisms of short-term
and long-term memory?
 The answers to such questions, which once seemed
remote, have been partly uncovered and are likely to
be more thoroughly revealed in the near future.
 Biochemistry is Multidisciplinary

• Various disciplines contribute to

understanding biochemistry:
Physics Genetics
Chemistry Physiology
Cell biology Evolution
 Biomolecules
• Body is composed of a few elements that combine to
form many molecules (C, H, N, O, Ca, P, K, Na, S, Cl, Mg, Fe, Mn, I)
• Major complex molecules (Proteins, Polysacharides (carbohydrates),
Lipids, DNA, RNA)

• The Human body has the following major constituents

•Proteins (17%),
•Fat (14%),
•Carbohydrates (2%),
•Water (62%),
•Minerals (6%).
 Bio-molecules
 Just like cells are building blocks of tissues likewise molecules are
building blocks of cells.
 Animal and plant cells contain approximately 10, 000 kinds of
molecules (bio-molecules)
 Water constitutes 50-95% of cells content by weight.
 Ions like Na+, K+ and Ca+ may account for another 1%
 Almost all other kinds of bio-molecules are organic (C, H, N, O, P,
S)
 Infinite variety of molecules contain C.
 Most bio-molecules considered to be derived from hydrocarbons.
 The chemical properties of organic bio-molecules are determined
by their functional groups. Most bio-molecules have more than one.
 Organization of Life
 elements
 simple organic compounds (monomers)
 macromolecules (polymers)
 supramolecular structures
 organelles
 cells
 tissues
 organisms
 Biochemistry and Evolution

• Prokaryotes - do not have a membrane-

bounded nucleus
• Eukaryotes - possess nucleus and other
complex internal structures
• Prokaryotes and eukaryotes appear to have
evolved from a common ancestor over three
billion years ago
 Range of the
sizes of objects
studies by
Biochemist and
Biologist

1 angstrom = 0.1 nm
 Elements of Life

Most abundant, essential for all organisms: C, N, O, P, S, H

Less abundant, essential for all organisms : Na, Mg, K, Ca, Cl
Trace levels, essential for all organism: Mn, Fe, Co, Cu, Zn
Trace levels, essential for some organisms: V, Cr, Mo, B, Al, Ga, Sn, Si,
As, Se, I,
Important compounds, functional groups
 Many Important Biomolecules are Polymers

lipids proteins carbo nucleic acids

monomer f a t t y a c id a m in o a c id g lu c o s e n u c le o ti d e

polymer p h o s p h o l i p i d p r o t e in s u b u n it c e ll u lo s e D N A

supramolecular
m e m b ra n e p r o t e in c o m p le x c e ll w a ll c h ro m o s o m e
structure
 Lipids

monomer f a t t y a c id

polymer p h o s p h o l i p i d

supramolecular
m e m b ra n e
structure
 Proteins

monomer amino acid

polymer protein subunit

supramolecular
structure Enzyme complex
 Nucleic Acids

monomer n u c le o ti d e

polymer D N A

supramolecular
c h r o m a t in
structure
Prokaryote Cell
Cellular Organization
of an E. coli Cell

200 – 300 mg protein / mL cytoplasm

Eukaryote Cell
 The Cell
•
 Biochemical Methods
• 3 Major Processes
•(1) Isolation
•(2) Determination of Structure
•(3) Analysis
Biochemical Methods
Biochemical Methods
• Elements such as C, H, N, O, etc.
combine to form biomolecules such as
proteins, lipids, carbohydrates, DNA and
RNA.
• Isolation and analysis using various
techniques allow diagnosis of malfunction
and subsequently proper treatment of
diseases
 Major Classes of small Bio-molecules

• Building blocks of proteins.

 1. Amino • 20 commonly occurring.
acids: • Contains amino group and carboxyl group
function groups (behavioral properties)
• R Group (side chains) determines the
chemical properties of each amino acids.
• Also determines how the protein folds and
its biological function.
• Individual amino acids in protein connected
by peptide bond.

• Functions as transport proteins, structural

proteins, enzymes, antibodies, cell
receptors.
 Sugars
 Carbohydrates most abundant organic molecule
found in nature.
 Initially synthesized in plants from a complex series
of reactions involving photosynthesis.
 Basic unit is monosaccharides.
 Monosaccharides can form larger molecules e.g.
glycogen, plant starch or cellulose.

Functions
 Store energy in the form of starch (photosynthesis in
plants) or glycogen (in animals and humans).
 Provide energy through metabolism pathways and cycles.
 Supply carbon for synthesis of other compounds.
 Form structural components in cells and tissues.
 Intercellular communications
 Fatty acids

 Are monocarboxylic acid contains even number C atoms

 Two types: saturated and unsaturated
 Fatty acids are components of several lipid molecules.
 E,g. of lipids are triacylglycerol, streiods (cholestrol, sex
hormones), fat soluble vitamins.

Functions
 Storage of energy in the form of fat
 Membrane structures
 Insulation (thermal blanket)
 Synthesis of hormones
 Biochemical Reactions
 Metabolism: total sum of the chemical reaction happening in a
living organism (highly coordinated and purposeful activity)
a. Anabolism- energy requiring biosynthetic pathways
b. Catabolism- degradation of fuel molecules and the production of
energy for cellular function

 All reactions are catalyzed by enzymes

 The primary functions of metabolism are:

a. acquisition & utilization of energy
b. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHO
c. Removal of waste products
Even though thousands of rxns sound very large
and complex in a tiny cell:

 The types of rxn are small

 Mechanisms of biochemical rxns are simple
 Reactions of central importance (for energy
production & synthesis and degradation of major cell
components) are relatively few in number
Frequent reaction encountered in biochemical
processes

1. Nucleophilic Substitution
 One atom of group substituted for another

2. Elimination Reactions
 Double bond is formed when atoms in a molecule is removed

3. Addition Reactions:
 Two molecules combine to form a single product.
 Hydration Reactions
 Water added to alkene > alcohol (common addition rxn)
4. Isomerization Reactions.
 Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions

 Occur when there is a transfer of e- from a donor to an
electron acceptor

6. Hydrolysis reactions
 Cleavage of double bond by water.
 Energy for Cells

 Living cells are inherently unstable.

 Constant flow of energy prevents them from
becoming disorganized.
 Cells obtains energy mainly by the oxidation of bio-
molecules (e- transferred from 1 molecule to another
and in doing so they lose energy)
 This energy captured by cells & used to maintain
highly organized cellular structure and functions
How do complex structure of cells maintain high internal order?

1. Synthesis of bio-molecules

2. Transport Across Membranes

- Cell membranes regulate the passage of ions and molecules
from one compartment to another.

3. Cell Movement
- Organised movement- most obvious characteristics of living
cells. The intricate and coordinated activities required to
sustain life require the movement of cell components.

4. Waste Removal
- Animal cells convert food molecules into CO 2, H20 & NH3. If
these not disposed properly can be toxic.
 Chemical Bonds
 Holds combined atoms together
 NOT physical, instead energy used
 Formed by electrons
 Types
 Ionic bonds
 Covalent bonds
 Polar and Non-polar bonds
 Hydrogen bonds
 Chemical bonds
 Covalent
 Coordinate
 Ionic
 Hydrogen bonds
 Van der Waal’s forces
 Hydrophobic interactions

 Normality and molarity of solutions

 bonding
 There are several different types of bonds
that are important to understand for
Biology.
 Covalent= shares electrons
 Ionic = swaps electrons
 Polar Covalent= somewhere in between.
 The reality is that most bonds have both
ionic and covalent characteristics= polar.
 Molecular Interactions -
electrostatics
 Biochemistry is ruled by non-covalent
interactions (although covalent bonds are
important) qq
 F  1 2
Important in protein folding, protein interactions,
r2D
protein purification, DNA physical properties, etc.
 In biomolecules
 Dielectric constant (D, ) plays a major role;
 water 78.54 at 25oC
 Methanol 32.63 It is found that the static dielectric
constant and mean polarizability of a
 Ethanol 24.3 simple fluid share the singularity of the
 Cyclohexane 2.02 internal energy at the critical point.
 Bond Strength
 While it takes more energy to break ionic
bonds in a dry environment, in living things
molecules are in aqueous environments.
 Therefore in Biology: Covalent bonds are stronger
than Ionic bonds, and H-bonds are weaker than
both.
 Keep in mind that in large numbers H-
bonds can be strong.
Atom – the smallest unit of matter “indivisible”

Helium
atom
 electron shells
a) Atomic number = number of Electrons

b) Electrons vary in the amount of energy

they possess, and they occur at certain
energy levels or electron shells.

c) Electron shells determine how an atom

behaves when it encounters other
atoms
 Electrons are placed in shells
according to rules:
1) The 1st shell can hold up to two
electrons, and each shell thereafter can
hold up to 8 electrons.
Octet Rule = atoms tend to gain, lose or share electrons so
as to have 8 electrons
C would like to Gain 4 electrons
N would like to Gain 3 electrons
O would like to Gain 2 electrons
 Why are electrons important?
1) Elements have different electron
configurations
 different electron configurations mean
different levels of bonding
 Electron Dot Structures
Symbols of atoms with dots to represent the
valence-shell electrons

1 2 13 14 15 16 17 18
H He:
      

Li Be  B  C  N  O : F  :Ne :

    

      

Na Mg  Al  Si  P

 S :Cl  :Ar :
    
Chemical bonds: an attempt to fill electron shells

1. Ionic bonds –
2. Covalent bonds –
3. Metallic bonds
Forming Chemical Bonds

• According to the Lewis model

– an atom may lose or gain enough electrons to
acquire a filled valence shell and become an ion.
An ionic bond is the result of the force of
attraction between a cation and an anion.
– an atom may share electrons with one or more
other atoms to acquire a filled valence shell. A
covalent bond is the result of the force of
attraction between two atoms that share one or
more pairs of electrons.
 IONIC BOND
bond formed between
two ions by the
transfer of electrons
 Formation of Ions from Metals
 Ionic compounds result when metals react with
nonmetals
 Metals lose electrons to match the number of
valence electrons of their nearest noble gas
 Positive ions form when the number of
electrons are less than the number of protons
Group 1 metals  ion 1+
Group 2 metals  ion 2+
 Group 13 metals  ion 3+
 Formation of Sodium Ion
Sodium atom Sodium ion
Na  – e  Na +

2-8-1 2-8 ( = Ne)

11 p+ 11 p+
11 e- 10 e-
0 1+
 Formation of Magnesium Ion
Magnesium atom Magnesium ion


Mg  – 2e  Mg2+

2-8-2 2-8 (=Ne)

12 p+ 12 p+
12 e- 10 e-
0 2+
 Some Typical Ions with
Positive Charges (Cations)
Group 1 Group 2 Group 13
H+ Mg2+ Al3+
Li+ Ca2+
Na+ Sr2+
K+ Ba2+
 Ions from Nonmetal Ions
In ionic compounds, nonmetals gain
electrons from metals

Nonmetal add electrons to achieve the octet

arrangement

Nonmetal ionic charge:

3-, 2-, or 1-
 Fluoride Ion
unpaired electron octet
  1 -

:F + e : F:
 

2-7 2-8 (= Ne)

9 p+ 9 p+
9 e- 10 e-
0 1-
ionic charge
 Ionic Bond
 Between atoms of metals and nonmetals
with very different electronegativity
 Bond formed by transfer of electrons
 Produce charged ions all states.
Conductors and have high melting point.
 Examples; NaCl, CaCl2, K2O
Ionic Bonds: One Big Greedy Thief Dog!
1). Ionic bond – electron from Na is transferred to Cl,
this causes a charge imbalance in each atom. The Na
becomes (Na+) and the Cl becomes (Cl-), charged
particles or ions.
 Ionic Bonds
 Electrons (1 or more) are transferred
between atoms
 Results in an ion (an atom with a + or – charge)
 Anion
 Electron acceptor; net (-) charge (more electrons)
 Cation
 Electron donor; net (+) charge (more protons)
 Common in metallic elements (Na, C, K) and
in Cl, F, I
Example of an Ionic Bond
 Ionic Compounds
 Salts
 Form crystals
 Common:
 NaCl, KCl
 COVALENT BOND
bond formed by the
sharing of electrons
 Covalent Bond
 Between nonmetallic elements of similar
electronegativity.
 Formed by sharing electron pairs
 Stable non-ionizing particles, they are not
conductors at any state
 Examples; O2, CO2, C2H6, H2O, SiC
Bonds in all the polyatomic
ions and diatomics
are all covalent bonds
 NONPOLAR
COVALENT BONDS

when electrons are

shared equally
H2 or Cl2
2. Covalent bonds- Two atoms share one or more
pairs of outer-shell electrons.
Oxygen Atom Oxygen Atom

Oxygen Molecule (O 2)
POLAR COVALENT
BONDS

when electrons are

shared but shared
unequally
H2 O
Polar Covalent Bonds: Unevenly
matched, but willing to share.
- water is a polar molecule because oxygen is more
electronegative than hydrogen, and therefore electrons
are pulled closer to oxygen.
METALLIC BOND
bond found in
metals; holds metal
atoms together
very strongly
 Metallic Bond
 Formed between atoms of metallic
elements
 Electron cloud around atoms
 Good conductors at all states, lustrous,
very high melting points
 Examples; Na, Fe, Al, Au, Co
Metallic Bonds: Mellow dogs with plenty
of bones to go around.
Ionic Bond, A Sea of Electrons
 Metals Form Alloys

Metals do not combine with metals. They form

Alloys which is a solution of a metal in a metal.
Examples are steel, brass, bronze and pewter.
(0.90% carbon 1.0%–1.4% manganese,
0.50% chromium, 0.50% nickel, and 0.50% tungsten)
(tin, lead, copper)
(30% zinc, and 1% tin)
(copper, manganese, nickel, and zinc)
Weak Chemical Forces and Their
Relative Strengths and Distances
 H bonding
 Hydrogen bond – sharing of a H atom between
two other atoms - in biochem usually O and N
 Orientation is very important – colinear is
strongest
 Typical H-bond strengths 3-7 kcal/mol (vs. 83
kcal/mol for C-C bonds)
 Prevalence – protein folding, DNA structure,
enzyme mechanics, etc.
 Molecular Interactions
– Hydrogen Bonds
 Hydrogen bonds form between a hydrogen atom
covalently bonded to an electronegative atom (such as
oxygen or nitrogen) and a second electronegative atom
that serves as the hydrogen bond acceptor.
 Hydrogen bonds, at a strength of 12 to 30 kJ/mol, are
stronger than van der Waals forces and have an
additional property: H bonds tend to be highly directional,
forming straight bonds between donor, hydrogen, and
acceptor atoms.
 Hydrogen bonds are more specific than van der Waals
interactions because they require the presence of
complementary hydrogen donor and acceptor groups.
Van der Waals Attractive Forces
 Van der Waals forces are the result of induced electrical interactions
between closely approaching atoms or molecules as their
negatively-charged electron clouds fluctuate instantaneously in time.
These fluctuations allow attractions to occur between the
positively charged nuclei and the electrons of nearby atoms.
 Van der Waals interactions include dipole–dipole interactions,
whose interaction energies decrease; dipole-induced dipole
interactions, which fall off and induced dipole-induced dipole
interactions, often called dispersion or London dispersion
forces.
 Dispersion forces contribute to the attractive intermolecular forces
between all molecules, even those without permanent dipoles, and are
thus generally more important than dipole–dipole attractions. Van
der Waals attractions operate only over a limited interatomic distance
and are an effective bonding interaction at physiological temperatures
only when a number of atoms in a molecule can interact with several
atoms in a neighboring molecule. For this to occur, the atoms on
interacting molecules must pack together neatly. That is, their
molecular surfaces must possess a degree of structural
complementarity.
Molecular Interactions – Van der Waal’s
 Non-specific attractive forces
 appear when atoms are 3-4Å
apart
 ~ 1 kcal/mol; similar to weak
induced dipole interactions
 Very weak individually, but
number of bonds, geometry,
and steric complimentarity in
biomolecules make it a major
contributor to interactions
 Importance of water
 When looking at the periodic table, the closest related
compounds to water (H2O) would be H2S or maybe H3N
(i.e. NH3, or ammonia) or HF (hydrofluoric acid).
 It is important to understand the nature of hydrogen
bonding, particularly between water molecules
Dipole: Oxygen is more electronegative than
hydrogen, therefore, the oxygen-hydrogen bonds
are polar. Due to the bent geometry, the overall
molecule has a dipole.

Molecular dimensions
• The O-H bond length is ~ 1.0Å (0.1nm)
• The van der Waals distance for hydrogen is ~1.2Å
• The van der Waals distance for oxygen is ~1.4Å

However, in simple calculations water

is often represented as a sphere
with a radius of 1.4Å. This is
because the oxygen will withdraw the
electron cloud from the hydrogen, and
thus, the van der Waals distance of
hydrogen is reduced.
 Water Structure
 Water has a "structure"
 Each water molecule can participate in up
to four hydrogen bonding interactions:
 The two hydrogens are potential "donors"
in a hydrogen bond interaction
 The two oxygen lone pairs are each
potential "acceptors" in a hydrogen bond
interaction
 Each H-bond is about 23kJ/mol in
strength
 As a liquid, neighbor molecules move
around and H-bonds are constantly
breaking and new ones reforming
 average lifespan of a single H-bond in
water is about 10ps
 The combination of so many H-bonds
between the water molecules results in
the unusually high boiling point and
melting point of water
 Water structure
 The distance between Oxygen atoms in a typical H-bond between water
molecules is about 2.8Å (0.28nm)
 The O-H covalent bond length is ~1.0Å. Therefore the H-bond distance
between the donor H and the acceptor O is typically 1.8Å, but can vary
from 1.6Å to 2.4Å.
 The typical distance of 2.8Å between O atoms in adjacent water molecules
explains why a 1.4Å radius sphere model for waters can be useful
 The orientation is important; the O-H bond vector points directly at
the acceptor lone pair, and vice versa
 Ice
 Cooling reduces thermal energy and you can
get a phase transition to a solid form of water
(i.e. "ice")
 A regular (crystalline) H-bond lattice forms (as
opposed to the transient nature in the liquid
form). This regular lattice is actually less-
densely packed than the liquid form. Thus, ice
floats in liquid water.
 The lattice is a regular arrangement based on
the near-tetrahedral geometry of the Oxygen
 Six molecules can form a closed H-bond ring
in ice, resulting in hexagonal appearance of
snowflakes
 Water molecules in ice have low entropy
 Water as a polar solvent
 Water molecules will separate, surround and disperse a
polar solute
 Water molecules surrounding a polar or charged solute will
orient according to H-bonding or electrostatic principles of
dipole-dipole interactions (i.e. oppositely charged ends of
dipoles will orient towards each other)
 The water molecules surrounding a solute are referred to
as the "hydration or solvation shell" of waters
 The ability of water molecules to surround and separate
oppositely charged ion pairs in a solution is referred to as
the dielectric constant of water.
 What this equation says is that if a substance can prevent
opposite charges from attracting each other (i.e. ions in q1q2
water are "shielded" by the solvation shell from other ions) F
then it has a high dielectric (i.e. Attractive force between r 2D
ions is small)
 Water has a dielectric of 78.5, and Hexane has a dielectric
of 1.9 (will not shield charged ions from each other)
 Hydrophobic Interactions
 Water cannot hydrogen bond with non-polar molecules (aliphatic,
aromatic hydrocarbons)
 Water will form an ice-like lattice arrangement ("clathrate") around
non-polar solutes in solution.
 This arrangements of water molecules is
entropically costly.
 Entropic cost will be minimized if the non-
polar solute adopts a shape with the
smallest surface area (i.e. a sphere). This
is why oil forms a sphere in water.
 Remember, nature wants to maximize
entropy – 2nd Law of Thermodynamics
Removing non-polar groups from aqueous solution frees up water
molecules in the clathrate, increases entropy, and is a lower free energy
condition (i.e. spontaneous). Oil drops in an aqueous environment will
coalesce into a single large spherical drop (i.e. the "hydrophobic effect").
 Amphipathic molecules
 Amphipathic and amphiphilos
molecules possess both polar
and nonpolar groups
 "amphi" means both, "pathos"
means passion, "philos" means
loving
 Such molecules have both a
polar region and a non-polar
region
 In aqueous solution they have the
ability to self organize according
to the hydrophobic effect, i.e. they
will assemble to as to remove the
non-polar group from solution

All of these properties of water and concepts of intermolecular interactions

of water/solutes are extremely important in the consideration of molecular
properties of DNA, RNA, proteins, carbohydrates, lipids, and
supramolecular assemblies
Covalent Bonds
 Polar Covalent Bonds
 Because Oxygen has an electronegativity
value of 3.44 and Hydrogen has a value of
2.1, the difference is significant enough
that at any given time the electrons are
more likely to be found closer to the O.
 Oxygen is a well known electron thief.
 While there is no official charge on either
atom, we have a “partial charge” 
 Hydrogen Bonds
 Because Hydrogen has such a low
electronegativity value, when it is bonded
to something with a stronger value the
polarization allows the charge of the
H to form a weak bond with the 
charge of another polar molecule.
 Water!
 A Single Water Molecule can form up to 4
H-bonds with other molecules at a time,
and when combined with other water
molecules that can make 4 of their own H-
bonds, the net strength of those bonds is
significant.
 Water Part 2
 All of the special properties of water are
caused by the polarity of the molecules
and the H-bonds it makes.
 Specific Heat- it takes a significant amount
of energy to break enough H-bonds for the
molecules to speed up.
 Large bodies of water have a significant
effect on the local climate by moderating
temperature fluctuations.
 Expansion of ice
 Most substances have a density that is
directly related to temperature. As heat is
added the molecules take up more space
and expand. As they cool, they take up
less space and become denser.
 Water is unique because of the H-bonds.
Liquid water does not form all 4 bonds per
molecule, but when the molecules are
moving slow enough all 4 can form and lock
into a crystal.
 Water Phase Changes
 When going from a liquid to a gas, H-
bonds have to be broken- it requires an
increase in energy.
 When Water evaporates is takes energy
from the environment, which in turn cools
off the environment. (sweating cools us)
 When water freezes, it is releasing energy
to the environment.
 Solutions
 Ions Dissociate in water.
 Covalent molecules that form H-bonds
with each other can break the H-bonds
and separate into individual molecules.
(dissolving sugar in water- each sucrose
molecule gets surrounded and shielded by
water molecules)
 Thermodynamics and Kinetics
 First Law – total energy of system and
surroundings is constant
 Second Law – total entropy of a system
and surroundings always increases
 Biochemistry – usually only think about
system, but remember the surroundings