CHEMICAL BASIS

SBC 3013 Cell Biology

 Water
Hydrogen Bonds
1. A hydrogen bond is an attraction
between a hydrogen atom and
an electronegative atom, both
of which are taking part in
separate polar covalent bonds.
2. These are not chemical bonds;
they do not form new
molecules. They are weaker
than ionic or covalent bonds,
easily forming and breaking.
3. These bonds are critical to life
and impart structure to liquid
water, and stabilize nucleic acids
and other large organic
molecules.
Water’s Life-Giving Properties
A.Each Water Molecule is Polar
1.Water is a polar molecule
due to the slight negative
charge at the oxygen end and
a slight positive charge at the
hydrogen end caused by the
unequal sharing of electrons.

2.Water molecules often

form hydrogen bonds with
each other.
B. Water is an Excellent Solvent
1. The solvent properties
of water are greatest
with respect to polar
molecules with which
they interact by pulling
on ions or molecules,
dispersing them.

hydrophilic 2. Polar substances are

(water loving) hydrophilic (water
loving); non-polar ones
are hydrophobic (water
dreading, like oils) and
are repelled by water.
hydrophobic
 C. Cohesion
1. Hydrogen bonding of water
molecules provides cohesion, a
property that helps the
molecules resist separating,
which imparts surface tension.

2. In evaporative processes the

input of heat energy increases
molecular motion so that
hydrogen bonds are broken
faster than they form and water
molecules escape into the air,
thus cooling the surface.

3. Cohesion contributes to pulling

water through plant tissues.
 D. High specific heat capacity
• Specific heat is defined as the amount of heat energy
needed to raise the temperature of one gram of a
substance to 1°C.
• For water the specific heat = 4.184 J/g °C
• Since it takes much more energy to break all the hydrogen
bonds in liquid water, water resists rapid temperature
fluctuations, adding stability to earth's environments
where liquid water is plentiful.
• Water has a very high heat of vaporization. The heat of
vaporization is defined as the energy needed to change
the phase of a liquid to a gas.
• For water at its normal boiling point of 100 °C, the heat of
vaporization is 2260 J g-1
• Again, because of the number and relative strength of
water's hydrogen bonds, it takes a great deal of energy to
break a molecule free of its liquid partners. Heat of
vaporization causes a cooling effect because as the
warmer molecules evaporate from your skin they take the
heat energy with them, leaving you cooler.
 E. Density of Water

• Water’s density it is dependent on its

temperature, but the relation is not linear
• At approximately 4 °C, pure water reaches
its maximum density (~ 1.000 g/cm3)
• As it is cooled further, it expands to
become less dense.
 F. Ice Lattice Structure
Inference
Why does ice float?
• Because ice floats, we can infer that ice must be
less dense than water.
• If water is frozen in a glass jar, the glass jar breaks.
• If a pop can freezes, it will also burst.
• From both of the above we infer that the volume
of the ice has increased.

Conclusion: The volume of ice is increased, with the

mass of liquid water still same.

Why does the volume increase?

Ice Lattice Structure
• In liquid water, the hydrogen
bond between water molecules
is constantly formed, break and
reformed.
• In ice, each molecule forms
stable hydrogen bonded to 4
other molecules.
• Compare the structures of Liquid
Water and Solid Ice .Notice the
empty spaces within the ice
structure, as this translates to a
more open or expanded
structure. The ice structure takes
up more volume than the liquid
water molecules, hence ice is less
dense than liquid water.
 Acids and Bases
1. In year 1884, Svante Arrhenius (Sweden)defined :
a. Acids are compounds that contain hydrogen
and can dissolve in water to release hydrogen
ions (H+) into solution
eg. HCl H O2
H+(aq) + Cl-(aq)
b. Bases are substances that dissolve in water to
release hydroxide ions (OH-) into solution.
eg. NaOH H O 2
Na+(aq) + OH-(aq)

2. Arrhenius theories have limitations. For example,

the Arrhenius definition does not explain why
some substances, such as common baking soda
(NaHCO3), can act like a base even though they
do not contain hydroxide ions.
 2. In 1923, Thomas Lowry (England) and J.N. Brønsted
Acids (Denmark) defined:
a. an acid is a material that donates a proton (H+)
and b. a base is a material that can accept a proton.
Bases The Brønsted-Lowry definition also explains why
substances that do not contain OH- can act like
bases. Baking soda (NaHCO3), for example, acts like a
base by accepting a hydrogen ion from an acid as
illustrated below:
Acid Base Salt
HCl + NaHCO3 H2CO3 + NaCl
the carbonic acid formed (H2CO3) undergoes rapid
decomposition to water and gaseous carbon dioxide,
and so the solution bubbles as CO2 gas is released.
 Acids and Bases
3. Under the Brønsted-Lowry definition, both acids
and bases are related to the concentration of
hydrogen ions present.
4. Acids increase the concentration of hydrogen
ions, while bases decrease the concentration of
hydrogen ions (by accepting them).
5. The acidity or basicity of something, therefore,
can be measured by its hydrogen ion
concentration.
6. In 1909, the Danish biochemist Sören Sörensen
invented the pH scale for measuring acidity.
 pH
3. The pH scale is described by the formula:
pH = -log [H+]

Note: concentration is commonly abbreviated by

using square brackets, thus [H+] = hydrogen ion
concentration. When measuring pH, [H+] is in
units of moles of H+ per liter of solution.

For eg., a solution with [H+] = 1 x 10-7 moles/liter

has a pH equal to 7
 The
pH
Scale

1. The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).

3. Each one unit change reflects a 10 X change in H+ concentration.
 Buffers
1. Buffers are chemicals, often weak
acids or bases and its salt, that help
keep the pH of a solution stable.
2. Buffer molecules act by combining
with, or releasing, H+ to prevent
changes in pH.
3. Example:
Bicarbonate (HCO3-) , Carbon
Dioxide and Hemoglobin are
body’s major buffers. The normal
blood pH is tightly regulated 7.35-
7.45. If the pH drops below 6.8 or
rises above 7.8 death might occur
Resource:
http://www.youtube.com/watch?v=
i_pTaTveCCo&feature=related
MOLECULES OF LIFE
From Structure to Function
• The Molecules of Life are organic
compounds that contain :
1. Carbon (C)
2. At least one hydrogen (H) atom.

• Most have one or more

functional group covalently
bonded to carbon atoms, which
form the backbone of most
organic compounds.

• Familiar examples include:

carbohydrates, fats, proteins, and
nucleic acids—molecules used for
energy, structural materials,
metabolic reaction, and carriers of
genetic information.
 Functional Groups
1.Atoms or clusters of atoms that
covalently bond to carbon in
organic molecules.

2.The number, kind, and

arrangement of these groups give
rise to specific properties such as
polarity and acidity.
 What Cells Do to Organic Compounds?
1. Metabolism is a term that refers to activities where
cells acquire and use energy to stay alive, grow, and
reproduce. Inside cells, organic molecules are
constructed, split, or re-arranged to form new
organic compounds. There are five common classes
of reactions that involve organic molecules:
a. Functional group transfer from one compound to
another

eg. during muscle activity creatine phosphate will

give up its phoshate to ADP(Adenosine di-phosphate)
resulting in Creatine and ATP (Adenosine tri-
phophate).
 What Cells Do to Organic Compounds?
b. Electron transfer : Electrons carry
energy and this energy is released by
transfering electrons from one
substance to another.

eg: NADH an electron carrier being broken down into NAD+ and
H+ along with 2 electrons. These electrons are picked up by a
system of proteins in the plasma membrane of certain
organelles. These proteins then pass the electrons along from
one to the other resulting in energy being released to do work.
 What Cells Do to Organic Compounds?
c. Rearrangement: Many times a molecule's
chemical structure will be rearranged into
another molecule that has the same
empirical formula(i.e., same number of
atoms of each element)

For instance, during cellular respiration

glucose is combined with phosphates,
transferred from ATP and rearranged to
form fructose 1-6 bi-phosphate.
What Cells Do to Organic Compounds?
d. Cleavage: Cells, and organisms in
general, take large molecules and break
them down into smaller molecules.
Eg: when you eat a steak and then digest
the proteins, the proteins are broken
down into amino acids.

The most common form of cleavage is

called hydrolysis because it involves
essentially adding water to the bounds
joining the small subunits of larger
molecules, breaking those bonds.
What Cells Do to Organic Compounds?
e. Condensation: The small molecules resulting from
cleavage can then be used by the cell to make just
the complex molecules it needs.
For example, the amino acids from a steak or other
protein source are recombined in protein synthesis
to build the proteins the cell needs and these may
be quite different in function from the original
muscle proteins in the steak.

The common type of condensation reactions in cells

is called dehydration synthesis because it involved
removing a hydroxyl group from one molecule and a
hydrogen from the other molecule when the two
molecules are joined resulting in water as a by-
product.

2. Most metabolic reactions require enzymes

(specialized proteins) that speed up (catalyzed) these
chemical reactions.
 Carbohydrates
A. Carbohydrates are used for structural materials
and energy. Most consist of C, H, and O in a 1:2:1
ratio

B. Simple Sugars
1. Single sugar unit (monosaccharides) are the
simplest carbohydrates.

2. Most are water soluble, easily transported in

fluids, and taste sweet.

3. Simple sugars, like glucose, are used by cells

for energy and as a structural building block.

4. Other sugars are part of the nucleotide

monomers of RNA and DNA.
 Disaccharides
Disaccharides consist of two
monosaccharides linked together
by a dehydration synthesis.
Sucrose, lactose, maltose
Short Chain Carbohydrates
1. Oligosaccharides are covalently
bonded short chains of sugar
monomers.
2. Oligo means a few and
oligosaccharides have a few simple
sugars linked together but not
thousands as do polysaccharides
3. Oligosaccharides are often bonded
to lipids or proteins that have roles
in cell membrane functions and
immunity.
Complex Carbohydrates
1. Called polysaccharides, straight or branched chains of
many (often hundreds or thousands) sugar monomers
of the same or different types covalently linked
together.

2. Common polysaccharides made from glucose

monomers covalently bonded together in different
ways include starch, cellulose, and glycogen.

a.Plants store glucose in large spiral-shaped,

hydrophobic molecules called starch. Hydrolysis
breaks these molecules down when sugar is
needed.

b.Cellulose, tightly bundled chains of glucose

produced in plants, used to form structural
elements in cell walls.

c.Glycogen is a stored form of glucose common in

animal tissues.

d. Chitin, a polysaccharide modified with nitrogen-

containing groups, strengthens the
exoskeleton in many animals like crabs and
insects. In most fungi, chitin reinforces the cell wall.
 LIPIDS/FATS
1. Lipids, or triglycerides, have three fatty acid
tails linked to a glycerol and include
examples such as butter and vegetable oils.

2. Triglycerides are the most abundant energy

source in vertebrates, stored in adipose
(fat) tissue that insulates and cushions
parts of the body.

3. At 9 kcal/gram, lipids contain more than

twice the energy of carbohydrates.
Triglyceride
A. Lipids function as the body’s main energy
reserve as well as form structural materials in
locations like cell membranes. Lipids are
fatty, oily, or waxy organic compounds that
are insoluble in water – hydrophobic
1. Lipids can be saturated, with only single
carbon-to-carbon bonds, or unsaturated
with double carbon-to-carbon bonds.
3. Saturated fats have fatty acid tails
with carbon backbones that have only
single covalent bonds. This permits
the fatty acid tails to pack together
tightly, allowing animal fats to remain
solid at room temperature.

4. Fatty acid tails in unsaturated fats

have one or more double covalent
bonds, making the tails more rigid and
preventing them from packing
together tightly. Most vegetable oils
are unsaturated and remain liquid at
room temperature.
 2.Unsaturated lipids may be cis or trans depending
on the arrangement of hydrogens on either side of
the double bond.

(note:
trans-
unsaturated lipid
is carcinogenic
 Phospholipids
1. Phospholipids are fats in which one
fatty acid has been replaced with a
phosphate group.

2. These partly hydrophobic, partly

hydrophilic molecules are found in
cell membranes.

Waxes
1. Waxes are fats with long fatty acids
bound to long-chain alcohols or
carbon rings.
 Steroids
1. Steroids are lipids with four
carbon rings and no fatty acid
tails.

2. Cholesterol is the most common

type of sterol in animal tissues.

3. Sterols form the basis for

diverse molecules like bile salts
and hormones. Estrogen and
testosterone are two familiar
examples.
 Proteins
Diversity in Protein’s Structure
and Function.
A.Proteins are large biological
molecules that are very
diverse in form and function.
Proteins are used as
structural elements and as
enzymes, and help move
materials around and in
communication between
cells.
Amino Acids
1. Amino acids are small organic
compounds with an amino
group (-NH 3+), a carboxyl
group (-COO -, the acid), a
hydrogen atom, and one or
more atoms of an R group. In
most cases, these
components are all attached
to the same carbon atom
(remember the carbon can
form up to four covalent
bonds).
Amino Acids
2. The R group represents the
variable portion of the 20
different amino acids. In
simple amino acids the R
group is a single hydrogen
atom, while in complex amino
acids it consists of one or
more carbon atoms with
various functional groups
attached.
Building Proteins
1. Proteins are
build via the
formation of a
peptide bond
between
amino acids.

2. A protein may
be build of
hundreds or
thousands of
amino acids.
Protein Structure
1. Each protein is made from a unique
sequence of amino acids. This is called
its primary structure. Amino acids are
joined together using a type of covalent
bond called a peptide bond.

2. Secondary structure results from twists,

bends, loops, and folds in the primary
structure. While primary protein
structures are unique, there are
common patterns of coils, sheets, and
loops that occur in most proteins.

3. Tertiary structures represent “domains,”

parts of a protein that are organized as
structurally-stable units. Domains are a
compact section of a protein that result
from coils, loops, or sheets that fold up.
4. A quaternary structure results
from two or more polypeptide
chains that bond together or
are closely associated with one
another.
5. A protein’s structure is often
further modified by the action
of enzymes that attach short,
linear, or branched
oligosaccharides to new
polypeptide chains, creating
large molecules called
glycoproteins. Other molecules
like lipids also get attached to
many proteins, further
modifying their structure.
The Importance of Protein Structure
A. Proteins Undone—Denaturation

1. Protein shapes define (dictates) its biological

activity. Therefore, proteins function as long as
they maintain their complex shapes. Heat,
shifts in pH, salts, and detergents may all act to
disrupt bonding patterns and alter a protein’s
shape.

2. Denaturing is the process by which bonding

patterns are broken, altering the secondary,
tertiary, or quaternary shape of the protein.

3. Denaturing causes the protein to loose its

function and is often irreversible.
 Prions
1. Prions are proteins that
induce spontaneous
denaturation in other
similar proteins.

2. These proteins can be

shared by consumption of
infected tissue.
Nucleic Acids
1. Nucleotides are small organic
molecules that function as energy
carriers, enzyme helpers, and
messengers.

2. Nucleotides are composed of one

sugar, at least one phosphate
group, and one nitrogen-
containing base.

3. These organic molecules vary from

one another based on the type,
number, and orientation of these
components.
4. DNA (deoxyribonucleic acid) is a
double stranded polymer comprised of
four different nucleotide monomers
(adenine, guanine, thymine, and
cytosine). DNA encodes the genetic
information for all living things based
on the sequence of the nucleotide
monomers.

5. RNA (ribonucleic acid) is similar to

DNA. Most RNA, however is comprised
of a single stranded polymer of four
nucleotide monomers (uracil instead of
thymine). RNA is involved in the
conversion of the genetic code in DNA
to create proteins.
Thanks