Biological Molecules

From small to large

1. The larger biological molecules are made from smaller molecules.
Polysaccharides are made from monosaccharaides, proteins from amino acids,
nucleic acids from nucleotides, lipids from fatty acids and glycerol.
2. Polysaccharides, proteins and nucleic acids are formed from repeating
identical or similar subunits
called monomers, and are therefore polymers. These build up into large
molecules called macromolecules.
3. The smaller units are joined together by condensation reactions.
Condensation involves removal of water. The reverse process, adding water, is
called hydrolysis and is used to break the large molecules back down into
smaller molecules.
4. The linkages that join monosaccharaides are called glycosidic bonds. The
linkages that join amino acids are called peptide bonds.
Carbohydrates
5. Carbohydrates have the general formula Cx(H2O)y and comprise
monosaccharaides, disaccharides and polysaccharides.
6. Monosaccharaides (e.g. glucose) and disaccharides (e.g. sucrose) are very
water-soluble and together are known as sugars.
7. Monosaccharaides are the smallest carbohydrate units. Glucose is the most
common. They are important energy sources in cells and also important building
blocks for larger molecules like polysaccharides.

By: Dr.Mufaddal

Page 1

8. Monosaccharaides may have straight-chain or ring structures and may exist

in different isomeric forms such as -glucose and -glucose.
9. Benedicts reagent can be used to test for reducing and non-reducing sugars.
The test is semi quantitative.
10. Polysaccharides include starch, glycogen and cellulose.
11. Starch is an energy storage compound in plants. It is made up of two types
of molecule, amylose and amylopectin, both made from -glucose. Amylose is
an un-branching molecule, whereas amylopectin has a branching structure.
Iodine solution can be used to test for starch.
12. Glycogen is an energy storage compound in animals, which is also made
from -glucose. Its structure is similar to that of amylopectin, but with more
branching.
13. Cellulose is a polymer of -glucose molecules. The molecules are grouped
together by hydrogen bonding to form mechanically strong fi bres with high
tensile strength that are found in plant cell walls.
Lipids
14. Lipids are a diverse group of chemicals, the most common of which are
triglycerides (fats and oils).
15. Triglycerides are made by condensation between three fatty acid molecules
and glycerol. They are hydrophobic and do not mix with water. They are energy
storage compounds in animals, as well as having other functions such as
insulation and buoyancy in marine mammals.
16. Phospholipids have a hydrophilic phosphate head and two hydrophobic fatty
acid tails. This is important in the formation of membranes.
17. The emulsion test can be used to test for lipids.
Proteins
18. Proteins are long chains of amino acids which fold into precise shapes. The
sequence of amino acids in a protein, known as its primary structure,
determines the way that it folds and hence determines its three dimensional
shape and function.
19. Many proteins contain areas where the amino acid chain is twisted into a
-helix; this is an example of secondary structure. The structure forms as a
result of hydrogen bonding between the amino acids.
By: Dr.Mufaddal

Page 2

Another secondary structure formed by hydrogen bonding is the -pleated

sheet.
20. Further folding of proteins produces the tertiary structure. Often, a protein
is made from more than one polypeptide chain. The association between the
different chains is the quaternary structure of the protein. Tertiary and
quaternary structures are very precise and are held in place by hydrogen bonds,
disulfide bonds (which are covalent), ionic bonds and hydrophobic interactions.
21. Proteins may be globular or fibrous. A molecule of a globular protein, for
example hemoglobin, is roughly spherical. Most globular proteins are soluble
and metabolically active. Hemoglobin contains a non-protein (prosthetic) group,
the Haem group, which contains iron. This combines with oxygen. A molecule of
a fibrous protein, for example collagen, is less folded and forms long strands.
Fibrous proteins are insoluble. They often have a structural role. Collagen has
high tensile strength and is the most common animal protein, being found in a
wide range of tissues.
22. Biuret reagent can be used to test for proteins.
Water
23. Water is important within plants and animals, where it forms a large part of
the mass of each cell. It is also an environment in which organisms can live.
24. As a result of extensive hydrogen bonding, water has unusual properties
that are important for life: it is liquid at most temperatures on the Earths
surface; its highest density occurs above its freezing point, so that ice fl oats
and insulates water below from freezing air temperatures; it acts as a solvent
for ions and polar molecules, and causes non-polar molecules to group
together; it has a high surface tension, which affects the way it moves through
narrow tubes and forms a surface on which some organisms can live. Water can
also act as a reagent inside cells, as in hydrolysis reactions and in
photosynthesis as a source of hydrogen.

By: Dr.Mufaddal

Page 3

Multiple - choice Test

1 The results of testing a solution for the presence of three biological molecules
are shown in the table.

Which biological molecules are present in the solution?

A
B
C
D

reducing sugar and protein

reducing sugar and starch
protein only
starch only

2 The diagrams show the structure of four monosaccharaides.

Which row in the table below identifies -glucose and -glucose?

By: Dr.Mufaddal

Page 4

3 Which reaction involves the hydrolysis of glycosidic bonds?

A cellulose glucose
B glucose glycogen
C protein amino acids
D triglyceride fatty acids and glycerol
4 The diagram shows a tripeptide made from three glycine amino acids.

Which of the bonds numbered 1 to 8 represent peptide bonds?

A
B
C
D

1 and 7
2 and 8
3 and 6
4 and 5

5 The following bonds are among those found in proteins: disulfide, hydrogen,
ionic and peptide bonds.
Which row shows the bonds involved in primary, secondary and tertiary protein
structures?

By: Dr.Mufaddal

Page 5

6 Which of the following describes a molecule of hemoglobin?

A
B
C
D

a central haem group enclosed by four coiled globin polypeptides

a central globin group enclosed by four coiled haem polypeptides
four coiled globin polypeptides, each with a central haem group
four coiled haem polypeptides, each with a central globin group

7 Which statement about the properties of water is not correct?

A Evaporation of water is an effective means of cooling an organism.
B Large volumes of water are slow to change temperature as the
environmental temperature changes.
C The solid form of water, ice, is denser than the liquid form.
D Water is an excellent solvent for ions and polar molecules.
8 Amylopectin is formed from amylose by a plant cell detaching short lengths of
an amylose chain and reattaching them as branches.
Which bonds are broken and which are formed when amylose is converted into
amylopectin?

9 The graph shows the variation in melting point of triglycerides with different
numbers of carbon atoms in their fatty acid chains.

By: Dr.Mufaddal

Page 6

What explains these results?

A Triglycerides with longer fatty acid chains have stronger intermolecular
forces and so have a lower melting point.
B Triglycerides with longer fatty acid chains have weaker intermolecular
forces and so have a higher melting point.
C Triglycerides with shorter fatty acid chains have stronger intermolecular
forces and so have a higher melting point.
D Triglycerides with shorter fatty acid chains have weaker intermolecular
forces and so have a lower melting point.
10 In spider silk, the polypeptide chains have the amino acid sequence Gly-AlaGly-Ala repeated many times, and the chains pack together as shown in the
diagram. The diagram shows the R groups of the two amino acids.

Which of the following describes this structure?

A
B
C
D

-helix held together by hydrogen bonds

-helix held together by ionic bonds
-sheet held together by hydrogen bonds
-sheet held together by ionic bonds

Answer to multiple-choice test

1 A
2 C
3 A
4 C
5 B
6 C
7 A
8 B
9 D
10 C
By: Dr.Mufaddal

Page 7

Carbohydrates - Monosaccharaides, Disaccharides

Carbohydrates:
- Sugar polymers
- Molecules contain C, H, O atoms
- H atoms are twice as many as C or O atoms (C6H12O6)
Monosaccharides

The simplest carbohydrates

They are sugar: C = 3 = triose; C = 4 = tetrose; C = 5 = pentose; C = 6 =
hexose
Examples of hexose sugars: glucose, fructose, galactose (C6H1206)
Molecules often have the form of a ring, made up of some C atoms and one
O atom.

Glucose molecules have 2 forms: -glucose and -glucose.

By: Dr.Mufaddal

Page 8

Disaccharides

Different disaccharides can be formed by linking different

monosaccharaides. The bond that joins them together = glycosidic bond.

Condensation reactions (dehydration): 2 monosaccharaides covalently

joined; H20 is formed.

By: Dr.Mufaddal

Page 9

Hydrolysis reaction (splitting by water): disaccharides are split into 2

monosaccharaides by breaking the glycosidic bond; a molecule of H20 is
added.

Functions of monosaccharaides and disaccharides

Good sources of energy in living organisms, used in respiration for making

ATP.
Transportable through the body because of the solubility: glucose is
transported dissolved in blood plasma (animal), sucrose is transported in
phloem sap (plant).
All monosaccharaides and some disaccharides are reducing sugars (reduce
blue Benedict's solution to produce an orange-red precipitate). Sucrose is
a non-reducing sugar.

By: Dr.Mufaddal

Page 10

Carbohydrates Polysaccharides

Molecules contain hundreds/thousands of monosaccharaides linked into long

chains.
Molecules are enormous --> the majority do not dissolve in water --> good
for storing energy (starch and glycogen) or for forming strong
structures (cellulose).
1. Storage Polysaccharides
Glycogen (in animals and fungi)
Made of -glucose molecules linked together by glycosidic bonds.
Most of the bonds are 1-4 links (C1 on one glucose + C4 on the next)
There are some 1-6 links, which form branches in the chain.
The bonds can be hydrolyzed by carbohydrase enzymes to form
monosaccharaides, used in respiration.
The branches increase the rate of hydrolysis.

1-4 and 1-6 links in Glycogen.

By: Dr.Mufaddal

Page 11

Starch (in plants)

A mixture of amylose and amylopectin. Both forms of starch are polymers of
- Glucose. Natural starches contain 10-20% amylose and 80-90%
amylopectin.

Amylose molecule is a very long chain with 1-4 links. The chain coils up into a
spiral, held in shape by H bonds between the glucose units.

Amylopectin differs from amylose in being highly branched. Short side chains
of about 30 glucose units are attached with 1- 6 linkages approximately every
20-30 glucose units along the chain.

2. Structural polysaccharides

Plant cell walls contain the polysaccharide cellulose:

Made of many glucose molecules, linked by 1-4 links.

Adjacent glucose molecules in the chain are upside-down to one another.

By: Dr.Mufaddal

Page 12

The chain is straight (not spiraling).

H bonds between chains --> very strong microfibrils --> cell wall will not
break easily if the plant cell absorbs water; difficult to digest (few organisms
have enzyme that can break the 1-4 bonds).

By: Dr.Mufaddal

Page 13

Tests for Carbohydrates

Tests for Reducing sugars, Non-reducing sugar and Starch.

1. Reducing sugar (Benedict's test)

All monosaccharaides and most disaccharides (except sucrose) will

reduce blue CuSO4 (II), producing a precipitate of red Cu2O(I).

Benedicts reagent is an aqueous solution of CuSO4(II), Na2CO3 and sodium

citrate.
2 cm test solution + 2 cm Benedicts reagent.
Shake, and heat for a few minutes at 95C in a water bath.
The mass of precipitate or intensity of the color indicates the amount of
reducing sugar present ---> the test is semi-quantitative.

By: Dr.Mufaddal

Page 14

2. Non-reducing sugar (Benedict's test)

Principles:
Sucrose is a non-reducing sugar (not reduce CuSO4)---> Benedict's test(-)
If it is hydrolyzed to form glucose and fructose ---> Benedict's test (+).
So sucrose is the only sugar that will give a (-) Benedict's test before hydrolysis
and a (+) test afterwards.
Steps:
Test a sample for reducing sugars to be sure it does not contain reducing
sugars.
Boil the test solution with dilute HCl for a few minutes to hydrolyze the
glycosidic bond.
Neutralize the solution by gently adding small amounts of solid NaHCO3 until it
stops fizzing.
Test for reducing sugar.
3. Starch (Iodine test)

2 cm of test solution + 2 drops of iodine/KI solution.

A blue-black color indicates the presence of starch as a starch-polyiodide
complex is formed.
Starch is only slightly soluble in water, but the test works well in a suspension
or as a solid.

By: Dr.Mufaddal

Page 15

Lipids - Triglycerides and Phospholipids

Lipids:
- Include triglycerides + phospholipids.
- Molecules contain C, H, O atoms
- Very small proportion of O.
- Insoluble in water.
1. Triglycerides
- Made of glycerol 'backbone', attached to 3 fatty acids by ester bonds.

Fatty acids

Have long chains of C and H atoms.

Each C atom has 4 bonds: 2 to C atoms, 2 to H atoms.
Sometime, only 1 H atom attached --> C atom has a 'spare' bond, attached to the next-door C
atom (also has 1 H bonded) ---> double bond.
Unsaturated fatty acid has 1 C-C double bonds (do not contain quite as much H).
Saturated fatty acid has no double bonds.

By: Dr.Mufaddal

Page 16

Lipids containing unsaturated fatty acids ---> unsaturated lipids (in plant)
Lipids containing completely saturated fatty acids ---> saturated lipids (in animal)
Unsaturated lipids tend to have lower melting points than saturated lipids.

Triglycerides are insoluble in water ---> energy storage in plants, animals and fungi. They contain
more energy per gram than polysaccharides.
A. In mammals
Triglycerides are building up beneath the skin in the form of adipose tissue:

It cells contain oil droplets of triglycerides;

Helps to insulate body against heat loss.
Relatively low density ---> buoyancy ---> useful for aquatic mammals living in cold water
(whales, seals).
Forms a protective layer around organs (e.g. kidneys).

By: Dr.Mufaddal

Page 17

B. In plants
Triglycerides = major part of energy stores in seeds:
Cotyledons (sunflower seeds)
Endosperm (castor beans)
2. Phospholipids
Made of glycerol 'backbone', 2 fatty acids and 1 phosphate group.

Fatty acid chains are hydrophobic: no electrical charge ---> not attracted to H2O molecules.
Phosphate group is hydrophilic: has electrical charge ---> attracted to H2O molecules.
In H2O, phospholipid molecules arranges into a bilayer: hydrophilic heads facing outwards into
the water + hydrophobic tails facing inwards, avoiding water.
This is the basic structure of a cell membrane.

By: Dr.Mufaddal

Page 18

3. Emulsion (Ethanol) test for lipids

Dissolve the substance by mixing it with absolute ethanol.

Decant the ethanol into water.
If lipids are present in the mixture, it will precipitates and forms a milky emulsion.

A milky emulsion indicates the presence of lipid.

By: Dr.Mufaddal

Page 19

Proteins - Amino acids, Peptide bonds

Proteins are large molecules made of long chains of amino acids.

1. Amino acids
All proteins have the same basic structure. They consist of an Amino Group
(NH2), a Carboxyl group (COOH), and a Carbon in the middle which bonds
with a Hydrogen atom and an 'R' group, which is specific to individual amino
acids.

There are 20 naturally occurring 'R' groups, making amino acids neutral, acidic,
alkaline, aromatic (has a ring structure) or sulphur-containing). The 20 R
groups correspond to 20 different amino acids. Each different amino acid has a
specific name. For example, Alanine's 'R' group consists of CH3.
2. Peptide bonds
a. Condensation reaction:
2 amino acids are joined by a peptide bond ---> dipeptide + H2O.

By: Dr.Mufaddal

Page 20

b. Hydrolysis reaction:
Dipeptides are split into 2 amino acids by breaking the peptide bond using a
molecule of H20.

By: Dr.Mufaddal

Page 21

Protein- Primary, Secondary, Tertiary, Quaternary Structure

Amino acids can be linked together in any order to form a long chain polypeptide.
Protein molecules can be made up of the same polypeptides or different
polypeptides.
1. Primary structure: The sequence of amino acids in a polypeptide or
protein molecule.

The 3 letters in each circle are the first 3 letters of the amino acid.

By: Dr.Mufaddal

Page 22

2. Secondary structure: The way in which the primary structure of a

polypeptide chain folds.

After synthesis, polypeptide chains are folded or pleated into different

shapes: Alpha helix (regular 3D shape) and Beta-pleated sheet (twisted,
pleated sheet)
The helix is hold by many Hydrogen bonds between amino acids at
different places in the chain, giving the shape great stability.

The typical Alpha helix is about 11 amino acids long.

By: Dr.Mufaddal

Page 23

3. Tertiary structure: The final 3D structure of a protein, involving

coiling or pleating of the secondary structure.

Tertiary structure.

Tertiary structure is held by:

1. Hydrogen Bonds - formed between amino acids at different points in the
chain.
2. Disulphide Bonds - a strong double bond (S=S) formed between the Sulphur
atoms within the Cysteine monomers.
3. Ionic Bonds - formed between 2 oppositely charged 'R' groups (+ and -) found
close to each other.
4. Hydrophobic & Hydrophilic Interactions: amino acids may be hydrophobic
or hydrophilic; in a water based environment, the hydrophobic parts of globular
protein are orientated towards center and the hydrophilic parts are towards
edges.

By: Dr.Mufaddal

Page 24

4. Quaternary structure: 2 polypeptide chains join together to form a

protein.

Some proteins are made up of multiple polypeptide chains, sometimes with

an inorganic component (e.g. a haem group in haemoglogin) called a
Prosthetic Group. These proteins will only be able to function if all subunits
are present.
The polypeptide chains are held by the same type of bonds as in the tertiary
structure.

By: Dr.Mufaddal

Page 25

The tertiary and quaternary structures of a protein, and its properties, are
determined by its primary structure.

Additional sources: Some parts of the note are taken from A level Notes.

By: Dr.Mufaddal

Page 26

Globular and Fibrous Proteins - Haemoglobin and Collagen

Globular and Fibrous are 2 main types of proteins with a 3D structure.

1. Haemoglobin, a globular protein

Composed of 2 + 2 polypeptide chains + 1 inorganic

prosthetic Haem group.

By: Dr.Mufaddal

Page 27

Hb's function: carry O2 from lungs to respiring tissues.

2. Collagen - a fibrous protein

Composed of 3 polypeptide chains wound around each other. Each chain is

a coil itself of around 1000 amino acids.

By: Dr.Mufaddal

Page 28

Structure strength is increased by forming:

- H bonds between the 3 polypeptide chains.
- Collagen molecules wrapped around each other ---> Collagen
Fibrils
- Collagen Fibrils ---> Collagen Fibers.

Collagen's function: support and elasticity in many animal tissues (human skin, bone and
tendons).

By: Dr.Mufaddal

Page 29

3. Test for proteins

The Biuret Test shows the presence of peptide bonds, which are the basis for
the formation of proteins. These bonds will make the blue Biuret reagent
turn purple.
Add biuret solution. A purple color indicates the presence of protein.

By: Dr.Mufaddal

Page 30

Water

About 80% of the organism's body is H2O.

Its molecule has a small negative charge (-) on the O atom a small positive
charge (+) on each H atom. This is called a dipole. This makes H2O an
excellent solvent.
Hydrogen bond = attraction between (-) and (+) parts of
neighboring H2O molecules.

Solvent properties of water

The dipoles on H2O molecules make water an excellent solvent.

If you stir NaOH into H2O, the Na+ and Cl- separate and spread between
the H2O molecules --> They dissolve in the water.

The Cl- is attracted to the small (+) charge on the H of H2O molecules.

The Na+ is attracted to the small (-) charge on the O of H2O molecules.

By: Dr.Mufaddal

Page 31

Any substance that has fairly small molecules with charges on them, or that
can separate into ions, can dissolve in water.

Being a good solvent, H2O helps:

- To transport substances around the bodies of organisms. The blood plasma
of mammals is mostly water, and carries many substances in solution: glucose,
oxygen, ions (Na...).
- To dissolve reactants ---> enable metabolic reactions.

By: Dr.Mufaddal

Page 32

Thermal properties of water

1. H2O is liquid at normal Earth to

The H bonds between H2O molecules prevent them flying apart at normal to.
Between 0oC and 100oC, water is in the liquid state. The H2O molecules move
randomly, forming transitory H bonds with each other.
Other substances with similar molecule structure, such as hydrogen sulfide
(H2S), are gases at these to (no H bonds to attract their molecules to each
other).

H2O and H2S molecules have similar structure.

2. H2O has a high latent heat of evaporation

When a liquid is heated, its molecules gain kinetic energy, moving faster +
a lot of heat energy is needed to break H bonds between water
molecules. Those molecules with the most energy are able to fly off into the
air.
When H2O evaporates, it absorbs a lot of heat from its surroundings --->
The evaporation of H2O from the skin of mammals when they sweat and the
transpiration from plant leaves has a cooling effect.

3. H2O has a high specific heat capacity

Specific heat capacity is the amount of heat energy that has to be added
to a given mass of a substance to raise its to by 1oC.

The higher the kinetic energy the higher the to: a lot of energy is needed to
rise to (to speed of H2O molecules + break H bonds) ==> Bodies of H2O
(oceans, lake) do not change to as easily as air does. Bodies of
organisms (with large amounts of H2O) do not change to easily.

By: Dr.Mufaddal

Page 33

4. H2O freezes from the top down

Most substances are denser in solid form than liquid form and will sink if
submerged in their liquid state. But H2O is LESS dense in its solid state, and
will float. This has to do with the crystal structure of ice.

When water cools (to) the density of water (molecules lose kinetic energy,
getting closer).
Below 4C this trend is reversed: When H2O approaches freezing point,
molecules form a lattice and stretches its very elastic H bonds --> density
(lower than density at 4C) --> Ice floats on water.

The layer of ice acts as an insulator, slowing down the loss of heat
from H2O beneath it, which tends to remain at 4C.
The H2O under the ice remains liquid, allowing organisms to continue to live in it
even when air temperatures are below the freezing point of H2O.
By: Dr.Mufaddal

Page 34

Inorganic ions

By: Dr.Mufaddal

Page 35