BIOMOLECULES

Elements of Life

The earths crust contains around 100 or so elements

16 of these are essential for life

Chief Elements
Of Organic
Molecules
H hydrogen
C Carbon
N Nitrogen
O Oxygen
P phosphorus
S Sulphur

Ions

Na+ Sodium
Mg 2+ Magnesium
Cl- Chlorine
K+ Potassium
Ca+ Calcium

Trace Elements

Mn Manganese
Fe Iron
Co Cobalt
Cu Copper
Zn Zinc
B Boron
Al Aluminium
Si Silicon
V Vanadium
Mo Molybdenum
I Iodine

Elements of Life

The four most common elements in living

organisms are:

H, C, O, and N

These account for 99% of the mass and number of

atoms found in all living organisms

H, C, O, and N are biologically important because

they have the ability to form more stable covalent
bonds than any other elements

CARBON

Life on planet earth is based on carbon

It is found in all organic molecules

Carbon is important because it forms strong covalent

bonds meaning it shares electrons with other elements

It forms 4 covalent bonds thus has a valency of 4

Carbon

Carbon is important because of the way atoms

can join to each other forming either chains or
rings
benzene

octane

http://www.green-planet-solar-energy.com/what-is-octane.html

http://images.yourdictionary.com/benzene-ring

These chains and rings are the skeleton of

organic molecules and hence of life itself

Carbon

They are very stable because of the strong

covalent bonds linking the carbon atoms
together are very strong
Atoms or particular groups of atoms of
other elements can be attached at various
positions to the carbon skeleton
Each group has its own particular
properties for example
COOH (carboxyl
group) is responsible for the acidic nature
of fatty acids

http://highered.mcgraw-hill.com/sites/dl/free/0035456775/694192/bioTP_CH3_mgb_f

Carbon

Carbon is also capable of forming double

bonds C C and triple bonds C
C

Compounds consisting of double or triple

bonds are referred to as unsaturated

Thus those with single bonds are called

saturated compounds

Summary of carbon

The important properties of carbons are:

It is a small atom with a low mass

Has the ability to form four strong covalent bonds

It has the ability to form carbon-carbon bonds thus

making large carbon skeletons with a ring or chain

It has the ability to form multiple covalent bonds

with other carbon atoms O and N

BIOMOLECULES

Living organisms are made up of a limited number of

types of atoms which combine to form molecules

These molecules vary in size from simple molecules

such as CO2 and H2O to macromolecules such as
proteins, smaller molecules are soluble and are
easily transported and frequently enter into cells
where they can be used in metabolic processes

Larger molecules tend to be stored or serve a

structural role

Some of these molecules are used to carry genetic

information

Chief Elements
Of Organic
Molecules
H hydrogen
C Carbon
N Nitrogen
O Oxygen
P phosphorus
S Sulphur

Ions

Na+ Sodium
Mg 2+ Magnesium
Cl- Chlorine
K+ Potassium
Ca+ Calcium

Trace Elements

Mn Manganese
Fe Iron
Co Cobalt
Cu Copper
Zn Zinc
B Boron
Al Aluminium
Si Silicon
V Vanadium
Mo Molybdenum
I Iodine

Water

Of all the molecules water is the most

abundant

Makes up 60-95% of fresh mass of an

organism

Constituent of living cells and provides

an environment for some organisms to
live

Properties of water

Solvent
High heat capacity
High heat of vaporization
High heat of fusion
Density and freezing properties
High surface tension
Is a good reagent

Biologically important functions of water

Photosynthesis
cellular respiration
The transport of substances from cells to tissues
A good solvent for polar substances and
assures the existence of enzymatic activity.
Temperature Control
Sexual Reproduction
Used as aLubricant
A mechanism ofSupport
Reactant

Macromolecules

All living things are made up of four

classes of large biological molecules:
carbohydrates, lipids, proteins, and
nucleic acids

Macromolecules are large molecules

composed of thousands of covalently
connected atoms

Molecular structure and function are

inseparable

Macromolecules are polymers, built from

monomers

A polymer is a long molecule consisting of

many similar building blocks

These small building-block molecules are

called monomers

Three of the four classes of lifes organic

molecules are polymers

Carbohydrates
Proteins
Nucleic acids

The Synthesis and Breakdown of Polymers

A dehydration reaction occurs when

two monomers bond together through
the loss of a water molecule

The Synthesis and Breakdown of Polymers

Polymers are disassembled to monomers

by hydrolysis, a reaction that is
essentially the reverse of the
dehydration reaction

The Diversity of Polymers

Each cell has thousands of different

macromolecules

Macromolecules vary among cells of an

organism, vary more within a species,
and vary even more between species

An immense variety of polymers can be

built from a small set of monomers

Carbohydrates

Carbohydrates include sugars and the polymers

of sugars and contain the elements C, O, H
Chemical formula Cx(H2O)y
All carbohydrates are :
1. Aldehydes or ketones
2. Contain several hydroxyl groups
.
1.
2.
3.

Carbohydrates are divided into 3 classes

Monosaccharides
Disaccharides
Poly saccharides

Carbohydrates

The simplest carbohydrates are

monosaccharides, or single sugars

Carbohydrate macromolecules are

polysaccharides, polymers composed of
many sugar building blocks

Monosaccharides

Monosaccharides have molecular formulas that

are usually multiples of CH2O

Glucose (C6H12O6) is the most common

monosaccharide

Monosaccharides are classifed by

The location of the carbonyl group (as aldose or

ketose)
The number of carbons in the carbon skeleton

Triose- involved in photosynthesis,

form intermediates in respiration

Pentoses- involved in synthesis of

nucleic acid ribose is found in DNA
and RNA, synthesis of ATP requires
ribose. Ribulose biphospate is a CO2
acceptor in photosynthesis

Hexoses- sources of energy when

oxidised in respiration glucose is the
most common respiratory substrate
and the most commom
monosaccharide. Synthesizes
disaccharides and polysaccharides

Monosaccharides

Though often drawn as linear skeletons, in aqueous

solutions many sugars form rings

Monosaccharides serve as a major fuel for cells and as raw

material for building molecules

Disaccharides

A disaccharide is formed when a dehydration

reaction(condenstaion) joins two monosaccharides
usually hexoses this reaction is reversible by hydrolysis

This covalent bond is called a glycosidic linkage

normally found between carbon atoms 1 and 4

Most common disaccharides are:

Maltose= glucose + glucose

Lactose= glucose + galactose
Sucrose= glucose + fructose

Maltose:- occurs mainly as a breakdown product during

digestion of starch by enzymes called amylases. This
occurs in animals and germinating seeds. Germination
of barley is stimulated by the conversion of starch to
maltose. Maltose is then fermented by yeast to alcohol

Lactose:- is known as milk sugar is the primary energy

source in young mammals. It is digested slowly so
releases energy slowly and steadily

Sucrose:- known as cane sugar most abundant

disaccharide in nature found mostly in plants
transported in large quantities in phloem tissue it makes
a good transport sugar because it is very soluble it is
relatively unreactive chemically thus will not enter
metabolic processes during transport

Reducing sugars

All mono and some disaccharides including

maltose and lactose are reducing sugars

This means they can carry out a type of

chemical reaction known as reduction

They can reduce copper from a valency of 2 to 1

Thus Benedicts test and Fehlings test can be

used to test for the presence of some sugars

Polysaccharides

Polysaccharides, the polymers of

sugars, have storage and structural roles

The structure and function of a

polysaccharide are determined by its
sugar monomers and the positions of
glycosidic linkages

Storage Polysaccharides

Starch, a storage polysaccharide of plants, consists

entirely of glucose monomers

Plants store surplus starch as granules within chloroplasts

and other plastids

Starch is made up of amylose and amylopectin

Amylose is a straight chain structure consisting of several

thousand glucose residues joined by 1,4 glycosidic bonds

Amylopectin has twice as much glucose residues as amylose

compact and has many branches with 1,6 glycosidic bonds

Storage Polysaccharides

Glycogen

Made from glucose

Humans and other vertebrates store glycogen mainly in liver

and muscle cells

These organs are the centers of high metabolic activity where

it provides a useful energy reserve

Its conversion is controlled by hormones insulin and glucagon

Its structure is very similar to amylopectin but shows more

branching

is a storage polysaccharide in animals

Structural Polysaccharides

Cellulose a polysaccharide is a major

component of the tough wall of plant cells

Like starch, cellulose is a polymer of

glucose, but the glycosidic linkages differ

The difference is based on two ring forms

for glucose: alpha () and beta ()

Structural Polysaccharides

Polymers with glucose are helical

Polymers with glucose are straight
In straight structures, H atoms on one strand
can bond with OH groups on other strands
Parallel cellulose molecules held together this
way are grouped into microfbrils, which form
strong building materials for plants
50% of carbon in plants occurs as cellulose
and is the most abundant organic molecules
on earth it is also found in some fungi and
non-vertebrate animals

Structural Polysaccharides

Enzymes that digest starch by hydrolyzing

linkages cant hydrolyze linkages in cellulose

Cellulose in human food passes through the

digestive tract as insoluble fber

Some microbes use enzymes to digest cellulose

Many herbivores, from cows to termites, have

symbiotic relationships with these microbes

Structural Polysaccharides

Chitin another structural

polysaccharide, is found in the
exoskeleton of arthropods it closely
resembles cellulose in structure and
function. It forms bundles of long parallel
chains like cellulose

Chitin also provides structural support

for the cell walls of many fungi

Lipids

Lipids are the one class of large biological molecules

that do not form polymers

The unifying feature of lipids is having little or no

affinity for water

Lipids are hydrophobic becausethey consist mostly of

hydrocarbons, which form non-polar covalent bonds

The most biologically important lipids are fats,

phospholipids, and steroids

Fats

Fats are constructed from two types of smaller molecules:

glycerol and fatty acids

Glycerol is a three-carbon alcohol with a hydroxyl group

attached to each carbon

A fatty acid consists of a carboxyl group attached to a long

carbon skeleton

Fats

Fats separate from water because water molecules

form hydrogen bonds with each other and exclude
the fats
In a fat, three fatty acids are joined to glycerol by an
ester linkage, creating a triacylglycerol, or
triglyceride

Fats

Fatty acids vary in length (number of

carbons) and in the number and
locations of double bonds

Saturated fatty acids have the

maximum number of hydrogen atoms
possible and no double bonds

Unsaturated fatty acids have one or

more double bonds

Fats

Fats made from saturated fatty acids are called

saturated fats, and are solid at room temperature

Most animal fats are saturated

Fats made from unsaturated fatty acids are called

unsaturated fats or oils, and are liquid at room
temperature

Plant fats and fsh fats are usually unsaturated

Fats

A diet rich in saturated fats may contribute to

cardiovascular disease through plaque deposits

Hydrogenation is the process of converting

unsaturated fats to saturated fats by adding hydrogen

Hydrogenating vegetable oils also creates

unsaturated fats with trans double bonds

These trans fats may contribute more than

saturated fats to cardiovascular disease

Fats
Certain unsaturated fatty acids are not synthesized in the
human body

These must be supplied in the diet

These essential fatty acids include the omega-3 fatty acids,

required for normal growth, and thought to provide protection
against cardiovascular disease

The major function of fats is energy storage

Humans and other mammals store their fat in adipose cells

Adipose tissue also cushions vital organs and insulates the

body

Saturated vs. Unsaturated Fatty Acids

Saturated fats (butter, dairy products, meat) are fats which are evenly
flled out with hydrogen, which remains solid at room temperature.
The introduction of double bonds in the hydrocarbon chain results in
the formation of the unsaturated fatty acids (vegetable oils). The
fatty acid with a single double bond is called mono unsaturated fatty
acid (e.g. oleic acid), and if it has multiple double bonds, its
polyunsaturated (e.g. linoleic acid). By virtue of their tightly packed
structure, the saturated fatty acids increase the levels of bad
cholesterol (LDL) and clog the arteries. On the other hand, the
unsaturated fatty acidsincrease the levels of good cholesterol (HDL)
by taking the LDL to the liver to be broken down and removed from
the body.
Poly unsaturated fatty acids remain liquid at room temp. If it needs to
be solidifed, it has to be hydrogenated, or saturated with hydrogen
by breaking the carbon double bonds and attaching hydrogen. The
mono unsaturated fats are considered good fats because of the lower
cholesterol content.
Essential fatty acids are poly unsaturated fatty acids that your body
cant manufacture and, therefore, has to be provided through your
diet. It is divided into two groups omega 3 and omega 6. Omega 6
is http://www.ftday.com/ftness-articles/nutrition/fats/saturated-vs-unsaturated-fattyfound in corn oil, sunflower oil, and soybean oil, while omega 3 is
acids.html#b
present
in salmon, trout and tuna. For a healthy diet, concentrate on

Phospholipids

In a phospholipid, two fatty acids and a phosphate

group are attached to glycerol
The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head

Phospholipids

When phospholipids are added to water, they selfassemble into a bilayer, with the hydrophobic tails pointing
toward the interior
The structure of phospholipids results in a bilayer
arrangement found in cell membranes
Phospholipids are the major component of all cell
membranes

Steroids

Steroids are lipids characterized by a

carbon skeleton consisting of four fused
rings
Cholesterol, an important steroid, is a
component in animal cell membranes
Although cholesterol is essential in animals,
high levels in the blood may contribute to
cardiovascular disease

Proteins

Proteins account for more than 50% of

the dry mass of most cells

Protein functions include structural

support, storage, transport, cellular
communications, movement, and
defense against foreign substances

Proteins

Proteins are made up of amino acids

There are over 170 amino acids and are known to occur
in cells and tissues
Amino acids are organic molecules with carboxyl and
amino groups
Amino acids differ in their properties due to differing
side chains, called R groups- gives each their
uniqueness

Amino acids

Plants are able to make all the amino acids they

require from simpler substances

Animals are unable to synthesize all they need

and therefore must obtain ready made amino
acids from their diet

These are known as essential amino acids

Amino acids are ampotheric they have both

basic and acidic parts

Polypeptides

Amino acids are linked by peptide bonds

Once these bonds are formed

The protein folds into a particular shape as a

result of four other types of bonds

Ionic bonds
Hydrogen bonds
Disulphide bonds
Hydrophobic interactions

 Amino acids are linked by peptide

bonds
A polypeptide is a polymer of
amino acids
Polypeptides range in length from
a few to more than a thousand
monomers
Each polypeptide has a unique
linear sequence of amino acids,
with a carboxyl end (C-terminus)
and an amino end (N-terminus)
Polypeptides are unbranched
polymers built from the same set
of 20 amino acids
A protein is a biologically

A functional protein consists of one or more

polypeptides precisely twisted, folded, and
coiled into a unique shape

The sequence of amino acids determines a protein

three-dimensional structure A proteins structure
determines its function

Four Levels of Protein Structure

The primary structure of a protein is its unique

sequence of amino acids

Secondary structure, found in most proteins,

consists of coils and folds in the polypeptide
chain

Tertiary structure is determined by interactions

among various side chains (R groups)

Quaternary structure results when a protein

consists of multiple polypeptide chains

 Primary structure is a
series of amino acids in
a polypeptide chain
The frst person to work
out a complete amino
acid sequence is Fred
Sanger
There are thousands of
different proteins in the
human body composed
of different
arrangements of the 20
fundamental amino
acids

Primary structure, the sequence of

amino acids in a protein, is like the
order of letters in a long word

Primary structure is determined by

inherited genetic information

The coils and folds of secondary structure result

from hydrogen bonds between repeating
constituents of the polypeptide backbone normally
formed between CO and NH groups
Typical secondary structures are a coil called an
helix and a folded structure called a pleated
sheet
A protein which is entirely helical is keratin
Keratin is found in hair, nails, wool,claws, beaks,
feathers and horn
A protein which is strictly a pleated sheet is
fibrion which is the protein found in silk and used
by silk worms when spinning their cocoon threads

Figure 5.20c

Secondary structure

helix

pleated sheet

Hydrogen bond

strand, shown as a flat

arrow pointing toward
the carboxyl end

Hydrogen bond

http://www.biog1105-1106.org/demos/105/unit1/fbrous_v_glob.h

Figure 5.20b

Secondary
structure

Tertiary
structure

Quaternary
structure

helix
Hydrogen bond
pleated sheet
strand
Hydrogen
bond

Transthyretin
polypeptide

Transthyretin
protein

Tertiary structure is determined by interactions

between R groups, rather than interactions between
backbone constituents

Usually the polypeptide chain bends and folds

extensively forming a precise compact globular shape

These interactions between R groups include

hydrogen bonds, ionic bonds, hydrophobic
interactions, and van der Waals interactions

Strong covalent bonds called disulfide bridges may

reinforce the proteins structure

Figure 5.20f

Hydrogen
bond

Hydrophobic
interactions and
van der Waals
interactions

Disulfide
bridge
Ionic bond

Polypeptide
backbone

Figure 5.20e

Tertiary structure

Transthyretin
polypeptide

Myoglobinis an iron- and oxygenbindingproteinfound in the muscle

tissue of vertebrates in general and in
almost all mammals. It is related
tohemoglobin, which is the iron- and
oxygen-binding protein in blood,
specifcally in the red blood cells.
The only time myoglobin is found in the
bloodstream is when it is released
following muscle injury. It is an abnormal
fnding, and can be diagnostically

Quaternary structure results when two or

more polypeptide chains form one
macromolecule

Collagen is a fbrous protein consisting of

three polypeptides coiled like a rope

Hemoglobin is a globular protein consisting of

four polypeptides: two alpha and two beta
chains

Figure 5.20g

Quaternary structure

Transthyretin
protein
(four identical
polypeptides)

Figure 5.20h

Collagen

Figure 5.20i

Heme
Iron
subunit

subunit

subunit

subunit

Hemoglobin

Figure 5.20j

Primary Structure refers to the linear sequence of amino acids that make up the polypeptide chain. This
sequence is determined by the genetic code, the sequence of nucleotide bases in the DNA. The bond between
two amino acids is a peptide bond. This bond is formed by the removal of a H20 molecule from two different
amino acids, forming a dipeptide. The sequence of amino acids determines the positioning of the different R
groups relative to each other. This positioning therefore determines the way that the protein folds and the fnal
structure of the molecule.
The secondary structure of protein molecules refers to the formation of a regular pattern of twists or kinks of the
polypeptide chain. The regularity is due to hydrogen bonds forming between the atoms of the amino acid
backbone of the polypeptide chain. The two most common types of secondary structure are called the alpha helix
and pleated sheet.
Tertiary structure refers to the three dimensional globular structure formed by bending and twisting of the
polypeptide chain. This process often means that the linear sequence of amino acids is folded into a compact
globular structure. The folding of the polypeptide chain is stabilized by multiple weak, noncovalent interactions.
These interactions include:
Hydrogen bonds that form when a Hydrogen atom is shared by two other atoms.
Electrostatic interactions that occur between charged amino acid side chains. Electrostatic interactions are
attractions between positive and negative sites on macromolecules.
Hydrophobic interactions: During folding of the polypeptide chain, amino acids with a polar (water soluble) side
chain are often found on the surface of the molecule while amino acids with non polar (water insoluble) side
chain are buried in the interior. This means that the folded protein is soluble in water or aqueous solutions.
Covalent bonds may also contribute to tertiary structure. The amino acid, cysteine, has an SH group as part of its
R group and therefore, the disulfde bond (S-S ) can form with an adjacent cysteine. For example, insulin has two
polypeptide chains that are joined by two disulfde bonds.
Quaternary structure refers to the fact that some proteins contain more than one polypeptide chain, adding an
additional level of structural organization: the association of the polypeptide chains. Each polypeptide chain in
the protein is called a subunit. The subunits can be the same polypeptide chain or different ones. For example,
the enzyme -galactosidase is a tetramer, meaning that it is composed of four subunits, and, in this case, the
subunits are identical - each polypeptide chain has the same sequence of amino acids. Hemoglobin, the oxygen
carrying protein in the blood, is also a tetramer but it is composed of two polypeptide chains of one type (141
amino acids) and two of a different type (146 amino acids). In chemical shorthand, this is referred to as a22 .

Sickle-Cell Disease: A Change in Primary Structure

A slight change in primary structure can

affect a proteins structure and ability to
function

Sickle-cell disease, an inherited blood

disorder, results from a single amino acid
substitution in the protein hemoglobin

Figure 5.21

Normal hemoglobin

1
2
3
4
5
6
7

Sickle-cell hemoglobin

Primary Secondary
Structure and Tertiary
Structures

1
2
3
4
5
6
7

Quaternary
Structure

Function

Red Blood
Cell Shape

Molecules do not
Normal
hemoglobin associate with one
another; each carries
oxygen.
subunit

10 m

Exposed
Sickle-cell Molecules crystallize
hydrophobic hemoglobin into a fiber; capacity
region
to carry oxygen is
reduced.

subunit

10 m

What Determines Protein Structure?

In addition to primary structure, physical and

chemical conditions can affect structure

Alterations in pH, salt concentration,

temperature, or other environmental factors
can cause a protein to unravel

This loss of a proteins native structure is

called denaturation

A denatured protein is biologically inactive

Figure 5.22

naturation
e
D

Normal protein

Re
naturation

Denatured protein

Protein Folding in the Cell

It is hard to predict a proteins structure

from its primary structure
Most proteins probably go through
several stages on their way to a stable
structure
Chaperonins are protein molecules
that assist the proper folding of other
proteins
Diseases such as Alzheimers,
Parkinsons, and mad cow disease are
associated with misfolded proteins

Figure 5.23

Polypeptide

Correctly
folded
protein

Cap

Hollow
cylinder

Chaperonin Steps of Chaperonin 2The cap attaches, causing3 The cap comes
(fully assembled)Action:
off, and the
the cylinder to change
1An unfolded poly- shape in such a way that properly folded
protein is
peptide enters the it creates a hydrophilic
environment for the
released.
cylinder from
folding
of
the
polypeptide.
one end.

Scientists use X-ray crystallography to

determine a proteins structure
Another method is nuclear magnetic
resonance (NMR) spectroscopy, which
does not require protein crystallization
Bioinformatics uses computer programs
to predict protein structure from amino
acid sequences

Figure 5.24

EXPERIMENT
Diffracted
X-rays
X-ray
source X-ray
beam
Crystal Digital detectorX-ray diffraction
pattern
RESULTS
RNA

DNA

RNA
polymerase II

Figure 5.24a

EXPERIMENT
Diffracted
X-rays
X-ray
source X-ray
beam
X-ray diffraction
Crystal Digital detector
pattern

Figure 5.24b

RESULTS
RNA

DNA

RNA
polymerase II