The Chemical Nature of
Cells
Biology, Unit 3
Area of Study 1
Water: A unique compound
 Water is the most abundant compound in our bodies and
is the main solvent for many of the organic molecules
present.
 Water makes the ideal medium for chemical reactions
that take place in the body.
 The sum total of these reactions is called metabolism.

Water: A unique compound

 Although a water molecule has an overall neutral
charge, the oxygen at the end of a covalent bond is
slightly negative and the hydrogen atoms are slightly
positive areas.
 Individual molecules of water are highly attracted to
each other such that the negative oxygen of one
molecule of water is attracted to the positive hydrogen
of another water molecule.
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Water: A unique compound

 they tend to stick together, held by hydrogen bonds,
which are weaker than covalent bonds.
Water: A unique compound

 Although water molecules are attracted to each other, the
hydrogen bonds that hold them together are relatively weak
and continually breaking. At the same time, hydrogen bonds
are continually rejoining.
 As the temperature of water falls, the rate of molecule
movement decreases, and at 4°C there is no longer sufficient
movement to break the hydrogen bonds.
 If the temperature of fluid water increases significantly to
100C, the movement of water molecules increases to a point
where hydrogen bonds no longer hold them together.
Water is a versatile solvent
 Water is the predominant solvent in living
organisms.
 Its versatility as a solvent is due to its cohesive
nature.
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Acid or alkaline?
 Pure water has a pH of 7 and is a neutral solution.
 pH is a scale that provides a measure of hydrogen
ions in a solution.
 The range of the pH scale is from 0 to 14.
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 pH of body fluids is kept relatively constant
because hydrogen ions are continually being
produced and used in cells.
Organic molecules
 Carbon-containing
compounds present in living
matter.
 large molecules made of
smaller sub units
(monomers) that are
bonded together (polymers)
in various ways.
Monomers
Polymers
sugars
(monosaccharides
)
polysaccharides
amino acids
proteins
fatty acids
fats, lipids,
membranes
nucleotides
nucleic acids
Carbohydrates

 The basic unit is a sugar molecule, a monosaccharide.

 Carbohydrates containing one or two sugar units are referred
to simple carbohydrates; those containing many sugar
molecules are called complex carbohydrates.
 Carbohydrates play an important role as a source of energy
for plants and animals, as food storage in the form of starch
for plants and glycogen in animals, and as structural elements
in plants.
Classification of carbohydrates
Simple carbohydrates
 Simple carbohydrates have:
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Monosaccharides

 Usually has formula C6H12O6
 Some monosaccharides have the same molecular
formula - their different properties arise from their
differences in structural formula - the way their atoms
are arranged within the molecule.

Disaccharides

 Example: sucrose, the sugar used in tea/coffee.
 Sucrose is the form in which carbohydrate is transported
in plants, and is formed from the combination of
glucose with fructose.

Structure and function of some
simple sugars
Polysaccharides

 Most common sugar component is glucose.
 starch, glycogen and cellulose are all composed of
glucose, yet their structure and properties are different
from one another.

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 insoluble in water.
Polysaccharide - Glycogen

 When carbohydrates are digested, glucose is absorbed into the
bloodstream that carries it to the liver and then to all cells of the body.
 Excess to body requirements is converted into glycogen by the liver for
storage.
 The liver is able to sore about 100 gram of glycogen.
 Glycogen is also stored in muscle tissue (upto 300 g)

 a circular molecule that has a protein as its ‘starting point’ (the protein
is called a primer) and lots of branches each containing the same
number of sugar units.
Starch
 Glucose is distributed around a plant in the form of sucrose,
and while some plants do store excess requirements in this
form, starch is the chief form of storage by most plants.
 storage can occur in a number of different sites, eg:
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potatoes and ginger store in a modified stem
sweet potatoe stores in modified roots
onions store in modified leaves
seeds store in their endosperm and provide from the young plant until
it becomes established.
Cellulose
 structural polysaccharide (C6H10O5)n

 molecules are long and unbranched
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Proteins
 although water is the main compound in living cells,
more than half of the remainder, about 18%, is protein.
 there are thousands of different proteins in each cell
and many of these control all metabolic processes
within cells.

The building blocks of proteins

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 Humans are unable to make all 20 amino acids and must
rely on their food for the nine they are unable to make.

 the general formula of an amino acid is:
The building blocks of proteins

 two amino acids join together as a dipeptide when a
peptide bond forms between the amino groups of one
amino acid and the carboxyl group of another amino
acid.

 each type of protein has its own particular sequence of
amino acids.
 polypeptide chains become folded in different ways
depending on their function.
The structure and shape of
proteins

 protein structure is described at four different
levels of organisation.
The structure and shape of proteins
 Primary structure - the specific linear sequence of
amino acids in the protein. Different proteins have
different primary structures and different functions.
The sequence of amino acids in a protein is
determined by the genetic material in the nucleus.
 Secondary structure -
The structure and shape of proteins
 Tertiary structure - the total irregular folding held
together by ionic or hydrogen bonds forming a
complex shape, eg: myoglobin. The bonds form
between side chains of amino acids to from a complex
internal structure.
 Quaternary structure - two or more polypeptide
chains interact to form a protein. The resulting
structure can be, for example, globular as in
haemoglobin or fibrous as in collagen, the most
common of animal proteins.
Examples of proteins
and their function
Type of protein
Function
Example
structural
fibrous support tissue in
skin, bone, tendons,
cartilage, blood vessels,
heart valves and cornea
of the eye
collagen, keratin
enzyme
catalyse reactions
ATP synthase
contractile
muscle movement
myosin, actin
immunoglobulin
defence against disease
antibodies
hormone
regulate body activity
insulin
Receptor
respond to stimuli
insulin receptors
transport
carry other molecules
haemoglobin
Conjugated proteins
 With some proteins, the chains of amino acids conjugate
with other groups, esp. proteins in the nucleus
(nucleoproteins - contain protein and nucleic acid)

 Example of a conjugated protein: haemoglobin
Non-active to active molecule
 Although a molecule may be made from a number of
molecules linked together by sulfide or other bonds,
they may derive from the same initial inactive protein.
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What is a proteome?
 In living organisms, proteins are involved in one way or
another in virtually every chemical reaction. They may
be the enzymes involved, they may be the reactants or
the products, or they may be all three.
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Lipids
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 composed of C, H, O.
 carry more energy per molecule than either
carbohydrates or proteins.
Fats

 triglycerides are a
common form of fats has a single glycerol
molecule to which three
fatty acid molecules are
attached.
 hydrophobic
Phospholipids
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 Have a phosphate group attached to the glycerol and
other small groups attached to the phosphate to make
different kinds of phospholipids.
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Nucleic Acids
There are two kinds of nucleic acid:
 deoxyribonucleic acid (DNA) - located in chromosomes
in the nucleus of eukaryotic cells. It is the genetic
material that contains hereditary information and is
transmitted from generation to generation.
 ribonucleic acid (RNA) - is formed against DNA which
acts as the template.
DNA
 a polymer of nucleotides
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 Each DNA molecule consists of two chains of nucleotides that
are complementary to each other and held together by
hydrogen bonds.
 the sugar and phosphate parts are the same in each
nucleotide.
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DNA
 The nucleotide sub-units are assembled to form a chain
in which the sugar of one nucleotide is bonded with the
phosphate of the next nucleotide in the chain.
 Each DNA molecule contains two chains that bond with
each other because the bases in one chain pair with the
bases in another.
 The base pairs between the two stands, ie A with T, and
C with G, are complimentary pairs.
DNA

 Chromosomes reside in the nucleus of a cell and the DNA they
contain carries genetic instructions that control all functions
of the cell.
How does DNA control all
functions within cells?

 Proteins are formed from polypeptide chains – chains of
amino acids
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How does a DNA molecule
directly influence the production
of a polypeptide chain?
 The sequence of nitrogen bases along one of the chains
of nucleotides in a DNA molecule carries a set of
information.
 This information controls the production of all the
polypeptide chains for which that molecule of DNA is
responsible, and can be thought of as a code.
How does the DNA code work?
 The total process is quite complex and involves action
both in the nucleus of a cell and in the cytosol.
 The DNA code comprises the four bases in the four
nucleotides that make up the DNA structure,
represented by the letters A (adenine), T (thymine), C
(cytosine) and G (guanine).
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How does the DNA code work?
 A particular set of three letters together in a molecule
of DNA codes for a particular amino acid. For example: –
the sequence AAA in a molecule of DNA results in the
amino acid phenylalanine being added into the
polypeptide chain for which the particular DNA
molecule is responsible – the sequence GTA results in
histidine being added and the sequence GCA results in
arginine and so on.
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How does the DNA code work?

 If a mutation occurs in a DNA molecule and leads to a
change in the order of bases, there is likely to be a
change in the amino acids in the polypeptide chain.
 Example: a change in a sequence from AAA  AGA, the
amino acid added is serine and not phenylalanine.
 A change in amino acid sequence in a polypeptide chain
may result in a non-functional protein, or a protein that
may act in a way that causes harm to a cell. It is
generally suggested that many cancers arise as a result
of changes in the genetic material.
RNA
 Ribonucleic acid (RNA) is also a polymer of nucleotides.
 In RNA, each nucleotide consists of a ribose sugar part,
a phosphate part and an N-containing base.
 It differs from DNA in that it is an unpaired chain of
nucleotide bases.
 Each RNA molecule consists of a single strand of
nucleotides.
RNA

RNA
 RNA exists in three different forms, all are produced in
the nucleus against DNA as a template:
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 The strand of nucleotides in each of the RNAs is folded
in a different way.