BIOMOLECULES

Elements of Life
 The earths crust contains around 100 or so elements
 16 of these are essential for life
Chief Elements Of Ions Trace Elements
Organic Molecules
H hydrogen Na+ Sodium Mn Manganese
C Carbon Mg 2+ Magnesium Fe Iron
N Nitrogen Cl- Chlorine Co Cobalt
O Oxygen K+ Potassium Cu Copper
P phosphorus Ca+ Calcium Zn Zinc
S Sulphur 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://images.yourdictionary.com/benzene-ring
http://www.green-planet-solar-energy.com/what-is-octane.html

 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_final_OK.pdf
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 Ions Trace Elements
Organic Molecules
H hydrogen Na+ Sodium Mn Manganese
C Carbon Mg 2+ Magnesium Fe Iron
N Nitrogen Cl- Chlorine Co Cobalt
O Oxygen K+ Potassium Cu Copper
P phosphorus Ca+ Calcium Zn Zinc
S Sulphur 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

 Is polar
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 a Lubricant
 A mechanism of Support
 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 life’s 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 Cn(H2nO)n

 All carbohydrates are :

1. Aldehydes or ketones
2. Contain several hydroxyl groups
Carbohydrates

• Carbohydrates are divided into 3

classes
1. Monosaccharides
2. Disaccharides
3. Polysaccharides
Carbohydrates
 Monosaccharides

 The simplest carbohydrates are

monosaccharides, or single sugars.
 Cannot be further hydrolysed.

 General formula (CH2On)

 Monosaccharides
 Monosaccharides are classified by
 The number of carbons in the carbon
skeleton

 Triosehave 3C for eg. Glycerldehyde

 Pentose have 5C for eg. Ribose and
deoxyribose
 Hexoses have 6C for eg. Glucose, fructose,
galactose.
Monosaccharides

 Monosaccharides serve as a major fuel

for cells and as raw material for building
molecules
 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 straight chains/

linear skeletons, in aqueous solutions many
sugars form rings.

 The ring form of Glucose can exist in two

forms; α- glucose ( alpha glucose) and β-
beta glucose.
Monosaccharides- Glucose

 α- glucose and β-beta glucose have a

six membered ring made up of five
carbons and one oxygen.

 They differ only in the orientation of

the –H and –OH groups on Carbon 1.
Monosaccharides- Glucose

The alpha position is defined as the

–OH being on the opposite side of the
ring from carbon 6.
 The beta position is defined as the –

OH being the same side of the ring as

carbon 6.
Monosaccharides
 Disaccharides

 A disaccharide is formed when a dehydration

reaction(condensation) 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
Disaccharides

 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 is a storage polysaccharide in animals
 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
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 microfibrils, 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
can’t hydrolyze  linkages in cellulose

 Cellulose in human food passes through the digestive

tract as insoluble fiber

 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 because they 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 fish 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 filled 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, it’s 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 acids increase 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 solidified, 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 can’t manufacture
and, therefore, has to be provided through your diet. It is divided into two groups –
omega 3 and omega 6. Omega 6 is found in corn oil, sunflower oil, and soybean oil,
while omega 3 is present in salmon, trout and tuna. For a healthy diet, concentrate on
mono unsaturated fats like olive oil and essential fatty acids.

http://www.fitday.com/fitness-articles/nutrition/fats/saturated-vs-unsaturated-fatty-acids.html#b
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 self-assemble
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 functional

molecule that consists of one or more
polypeptides
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’s three-
dimensional structure A protein’s 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 first 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

Hydrogen bond
 pleated sheet

 strand, shown as a flat

arrow pointing toward
the carboxyl end

Hydrogen bond
http://www.biog1105-1106.org/demos/105/unit1/fibrous_v_glob.html
Figure 5.20b

Secondary Tertiary Quaternary

structure structure structure

 helix

Hydrogen bond
 pleated sheet
 strand
Transthyretin
Hydrogen Transthyretin protein
bond polypeptide
 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 protein’s 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
 Myoglobin is an iron- and oxygen-
binding protein found in the muscle tissue of
vertebrates in general and in almost all mammals. It
is related to hemoglobin, which is the iron- and
oxygen-binding protein in blood, specifically 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 finding, and can be diagnostically
relevant when found in blood
 Quaternary structure results when two or more
polypeptide chains form one macromolecule

 Collagen is a fibrous 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 final 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 ß 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
disulfide bond (S-S ) can form with an adjacent cysteine. For example, insulin has two polypeptide chains that are joined by two disulfide 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 ß-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 a2ß2 . For some proteins, quaternary structure is required for full activity (function) of
the protein
Source(s):
http://matcmadison.edu/biotech/resources…
Sickle-Cell Disease: A Change in Primary
Structure

 A slight change in primary structure can affect a

protein’s 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

Primary Secondary Quaternary Red Blood

and Tertiary Function
Structure Structure Cell Shape
Structures

1 Normal Molecules do not

hemoglobin associate with one
2 another; each carries
Normal hemoglobin

3 oxygen.
4
5 
 subunit  10 m
6
7



1 Exposed Sickle-cell Molecules crystallize

hydrophobic hemoglobin into a fiber; capacity
2 region to carry oxygen is
Sickle-cell hemoglobin

3 reduced.
4
5 
6  10 m
7  subunit


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 protein’s native structure is called

denaturation

 A denatured protein is biologically inactive

Figure 5.22

tu

Normal protein Denatured protein

Protein Folding in the Cell
 It is hard to predict a protein’s 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 Alzheimer’s, Parkinson’s, and mad
cow disease are associated with misfolded proteins
Figure 5.23

Correctly
folded
protein
Polypeptide
Cap

Hollow
cylinder

Chaperonin Steps of Chaperonin 2 The cap attaches, causing 3 The cap comes
(fully assembled) Action: the cylinder to change off, and the
1 An unfolded poly- shape in such a way that properly folded
peptide enters the it creates a hydrophilic protein is
cylinder from environment for the released.
one end. folding of the polypeptide.
 Scientists use X-ray crystallography to determine a
protein’s 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 detector X-ray diffraction

pattern

RESULTS

RNA DNA

RNA
polymerase II
Figure 5.24a

EXPERIMENT
Diffracted
X-rays

X-ray
source X-ray
beam

Crystal Digital detector X-ray diffraction

pattern
Figure 5.24b

RESULTS

RNA DNA

RNA
polymerase II