A C C R A T E C H N I C A L U N I V E R S I T Y (A T U)

B A C H E L O R O F T E C H N O L O G Y (B. T E C H)

PROGRAMME

IN

MEDICAL LABORATORY SCIENCE

BIOLOGICAL CHEMISTRY
MLB 103

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 MLB 103
COURSE PARTICULARS

Course Title: BIOLOGICAL CHEMISTRY

No. of Units: 3

Course Duration: Three hours of lectures per week for 12 weeks.

Dept. of Medical Laboratory Science

COURSE OBJECTIVES

By the end of the course, students should be able to;

 Explain the structure and properties of matter.

 Describe the functional groups of organic molecules and their biological roles
 Describe the structure and function of carbohydrates
 Identify the importance of proteins and enzymes
 List biological importance of the parts of a cell

Grading System

This course will be graded as follows:

Continuous assessment 40%(Group work, Mid sem Tests )

Final Examination 60%

TOTAL 100%

COURSE OUTLINE
This course deals with the biochemical mechanism that under pin biological processes. It
includes topics such as;

 Structure and properties of matter

 Origin of element
 Bond formation and molecules
 Functional group chemistry
 Carbohydrates their structure and function
 Protein chemistry
 Nucleic acids

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 Enzymes and catalysis
 Chemistry of bacterial cell

REFERENCES

Champe,P.C.
(2005).Lippincott’sIllustratedreviews:biochemistry.Philadelphia:LippincottWilliams&Wilkin
s.Christian,G.D.(2004).Analyticalchemistry(6thed).NewJersey:John&WileyInc.

Denniston,K.J.,Topping,J.J.,Woodrum,K.R.&Caret,R.L.(2014).General,organicand

biochemistry(8thed).NewYork:McGraw-Hill.

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Structure and Properties of Matter
All the objects around us whether living or non-living are matter. Water we drink, food we eat,
air we breathe, blood running through our bodies, chair we sit on, are all examples of matter.

Matter is anything that has mass and takes up space.

Matter appears in a huge variety of forms such as rocks, Trees, computer, clouds, people, etc.
Matter embraces each and everything within us and around us. Therefore, in order to understand
the world, and the humans and the science of the human body it would be necessary to
understand the matter.

CLASSIFICATION OF MATTER
In modern science there are two main ways of classifying matter:
I) based on physical states:
All matter, in principle, can exist in three states; solid, liquid and gas.
II) Based on composition and properties:
With regards to its composition the classification of matter includes elements, compounds and
mixtures.

CLASSIFICATION OF MATTER BASED ON PHYSICAL STATE

A given kind of matter may exist in different physical forms under different conditions.
Water, for example, at one atmospheric pressure, may exist as solid, liquid or gas with change of
temperature.
Sodium metal is normally solid, but it melts to a silvery liquid when heated to 98 oC. Liquid
sodium changes to a bluish gas if the temperature is raised to 883oC.
Similarly, chlorine, which is normally a gas, can exist as a yellow liquid or solid under
appropriate conditions.
 These three different forms of matter differ from each other in their properties. Solids are
rigid with definite shapes. Liquids are less rigid than solids and are fluid, i.e. they are able
to flow and take the shape of their containers. Like liquids, gases are fluids, but unlike
liquid, they can expand indefinitely.

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Can you think of other differences between a gas and liquid?
A gas can be compressed easily whereas a liquid cannot. You might be aware; natural gas is
compressed and supplied as fuel for vehicles in the name of CNG (compressed natural gas). It is
not possible to compress a liquid. It is still more difficult to compress a solid. All these three
forms of matter (solid, liquid and gas) are generally referred as states of matter.
Taking fluidity/rigidity and compressibility, we can write characteristic properties of solid, liquid
and gas.

As mentioned, a substance can exist in three forms depending upon temperature and pressure.
Water at room temperature (25oC) exists in liquid form and at 0oC and 1atmospheric pressure as
solid. If we go on increasing temperature of water at constant pressure, more and more of it will
go into vapour form and at 100 oC will start boiling. If heating continues at this temperature (100
o
C), entire liquid water will be converted into vapour. This is true with most of the liquids.

Definitely melting and boiling points of different substances will be different. Can you think why
this variation in their melting point and boiling point occurs?
Intermolecular forces are different in different liquids, and therefore their boiling points and
melting points are different.
In gaseous form, intermolecular forces are very weak and unable to keep molecules together in
aggregation. However, in case of solids, these forces are very strong and capable of keeping
molecules in fixed positions. This is the reason solids are rigid and hard and cannot be
compressed. Liquids have properties intermediate to solid and gases as intermolecular forces
between molecules in liquid are definitely more than gases and less than solids but strong enough

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to keep the molecules in aggregation. Due to weak intermolecular forces in gases, molecules in
gases can move freely and can occupy any space available to them. This property of gases is
responsible for their diffusion.
Molecules in gases are far apart and therefore when pressure is applied they can be brought
closer and gases can be compressed.

CLASSIFICATION OF MATTER BASED ON COMPOSITION –

ELEMENTS, COMPOUNDS AND MIXTURES

Another method of classification of matter is based on its composition. A pure substance is

matter that has a definite or constant composition and has distinct properties. Examples are
aluminum, sliver, water, carbon dioxide, nitrogen, oxygen etc. Substances differ from one
another in composition and can be identified by their properties like colour, smell, taste,
appearance, etc. Aluminium has uniform composition. Similarly water has uniform composition.
No doubt there are also matter which do not have uniform composition. Such matter is called
mixture. Some examples of mixtures are air, soft drink, milk, blood etc. Mixtures are either
homogeneous or heterogeneous. Suppose you add 5g of sugar to water kept in a glass tumbler.
After stirring, the mixture obtained is uniform throughout. This mixture is homogeneous
throughout and is called solution. Air is solution of several gases (oxygen, nitrogen, water
vapour, carbon dioxide etc). Can blood be considered as a homogeneous mixture? What are
component of the blood mixture? Of suppose you mix sand with iron filings, sand grains and the
iron filings remain visible and separate. This type of mixture in which the composition is not

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uniform, is called a heterogeneous mixture. If you add oil to water, it creates another
heterogeneous mixture because the liquid thus obtained does not have a uniform composition.

We can create homogeneous and heterogeneous mixtures and if need arises we can separate them
into pure components by physical means without changing the identities of the components
(separating blood into its components). We can recover sugar from its water solution by heating
and evaporating the solution to dryness. From a mixture of iron filings and sand, we can separate
iron filings using magnet. After separation we can see that the components have the same
composition and properties as they did to start with.

Elements

Antoine Laurent Lavoisier (1743-94), a French chemist was first to explain an element. He
defined an element as basic form of matter that cannot be broken down into simpler
substances even by chemical means. Elements serve as the building blocks for various types of
other substances, starting from water up to extremely complex substances like protein. Oxygen,
nitrogen, magnesium, iron, gold all are example of element. Today about 118 elements are
known and with various details about them. An element consists of only one kind of atoms.
These elements are represented by suitable symbols as shown on the periodic table.

The human body at glance may be said to be made up of organs, tissues, cells and so on.
However it is important to also recognize that the human body is known to be made up of several
elements in varied proportions. Fig 1. Shows an image of the distribution of the various elements
in the body.

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Fig. 1. Elements % of total human body weight

Compounds

Most elements can interact with one or more other elements to form compounds. A compound is
a substance that consists of two or more different elements chemically united in a definite
ratio. A pure compound, whatever its source, always contains definite or constant proportions of
the elements by mass. As you know, water is composed of two elements: hydrogen and oxygen.
Property of water is completely different from its constituent elements: hydrogen and oxygen
which are gases. Similarly when sulphur is ignited in air, sulphur and oxygen (from air) combine
to form sulphur dioxide. All sample of pure water contain these two elements combined in the
ratio of one is to eight (1: 8) by mass. For example, 1.0 g of hydrogen will combine with 8.0g of
oxygen. This composition does not change whether we take water from river of India, Ghana or
of United States or the ice caps on Mars. Unlike mixtures compounds can be separated only by
chemical means into their pure components.

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 In conclusion, the relationship among elements, compounds and other categories of matter are
summarised in Fig. 2 below

MATTER
.

MIXTURE
PURE SUBSTANCE

ELEMENT COMPOUND
HOMOGENEO
US HETEROGENOUS

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 HISTORY OF ELEMENTS
The various elements came about as a result of various discoveries by different scientists. Brief
history of some selected elements is as discussed below.

Hydrogen
The discovery of the various elements on the periodic table began several years ago from the
early 1500s the alchemist Paracelsus noted that the bubbles given off when iron filings were
added to sulfuric acid were flammable. In 1671 Robert Boyle made the same observation.
Neither followed up their discovery of hydrogen, and so Henry Cavendish gets the credit. In
1766 he collected the bubbles and showed that they were different from other gases. He later
showed that when hydrogen burns it forms water, thereby ending the belief that water was an
element. The gas was given its name hydro-gen, meaning water-former, by Antoine Lavoisier.

Helium
In 1931, Harold Urey and his colleagues at Columbia University in the US detected a second,
rarer, form of hydrogen. This has twice the mass of normal hydrogen, and they named it
deuterium.
In 1868, Pierre J. C. Janssen travelled to India to measure the solar spectrum during a total
eclipse and observed a new yellow line which indicated a new element. Joseph Norman Lockyer
recorded the same line by observing the sun through London smog and, assuming the new
element to be a metal, he named it helium.

Lithium
In 1882, the Italian Luigi Palmieri found the same line the spectrum of gases emitted by
Vesuvius, as did the American William Hillebrand in 1889 when he collected the gas given off
by the mineral uraninite (UO2) as it dissolves in acid. However, it was Per Teodor Cleve and
Nils Abraham Langer at Uppsala, Sweden, in 1895, who repeated that experiment and confirmed
it was helium and measured its atomic weight.
he first lithium mineral petalite, LiAlSi 4O10, was discovered on the Swedish island of Utö by the
Brazilian, Jozé Bonifácio de Andralda e Silva in the 1790s. It was observed to give an intense

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crimson flame when thrown onto a fire. In 1817, Johan August Arfvedson of Stockholm
analysed it and deduced it contained a previously unknown metal, which he called lithium. He
realised this was a new alkali metal and a lighter version of sodium. However, unlike sodium he
was not able to separate it by electrolysis. In 1821 William Brande obtained a tiny amount this
way but not enough on which to make measurements. It was not until 1855 that the German
chemist Robert Bunsen and the British chemist Augustus Matthiessen obtained it in bulk by the
electrolysis of molten lithium chloride.

Carbon

Carbon occurs naturally as anthracite (a type of coal), graphite, and diamond. More readily
available historically was soot or charcoal. Ultimately these various materials were recognised as
forms of the same element. Not surprisingly, diamond posed the greatest difficulty of
identification. Naturalist Giuseppe Averani and medic Cipriano Targioni of Florence were the
first to discover that diamonds could be destroyed by heating. In 1694 they focussed sunlight on
to a diamond using a large magnifying glass and the gem eventually disappeared. Pierre-Joseph
Macquer and Godefroy de Villetaneuse repeated the experiment in 1771. Then, in 1796, the
English chemist Smithson Tennant finally proved that diamond was just a form of carbon by
showing that as it burned it formed only CO2.

Nitrogen

Nitrogen in the form of ammonium chloride, NH 4Cl, was known to the alchemists as sal
ammonia. It was manufactured in Egypt by heating a mixture of dung, salt and urine. Nitrogen
gas itself was obtained in the 1760s by both Henry Cavendish and Joseph Priestley and they did
this by removing the oxygen from air. They noted it extinguished a lighted candle and that a
mouse breathing it would soon die. Neither man deduced that it was an element. The first person
to suggest this was a young student Daniel Rutherford in his doctorate thesis of September 1772
at Edinburgh, Scotland.

Oxygen

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In 1608, Cornelius Drebbel had shown that heating saltpetre (potassium nitrate, KNO 3) released
a gas. This was oxygen although it was not identified as such.
The credit for discovering oxygen is now shared by three chemists: an Englishman, a Swede, and
a Frenchman. Joseph Priestley was the first to publish an account of oxygen, having made it in
1774 by focussing sunlight on to mercuric oxide (HgO), and collecting the gas which came off.
He noted that a candle burned more brightly in it and that it made breathing easier. Unknown to
Priestly, Carl Wilhelm Scheele had produced oxygen in June 1771. He had written an account of
his discovery but it was not published until 1777. Antoine Lavoisier also claimed to have
discovered oxygen, and he proposed that the new gas be called oxy-gène, meaning acid-forming,
because he thought it was the basis of all acids.

DALTON’S ATOMIC THEORY

In the fifth century B.C. Indian philosopher Maharshi Kanad postulated that if one goes on

dividing matter (Padarth), he would get smaller and smaller particles and a limit will come

when he will come across smallest particles beyond which further division will not be

possible. He (Kanad) named the particles Parmanu. More or less during the same period

Greek philosophers, Leuappus and Democritus suggested similar ideas. This idea was not

accepted at that time but it remained alive. Not much experimental work could be done

until Lavoisier gave his law: Law of conservation of mass and law of constant

proportions sometimes in 1789. English scientist and school teacher, John Dalton (1766-1844)
provided the basic theory about the nature of matter: All matter whether element,

compound or mixture is composed of small particles called atoms.

Dalton’s theory can be summarized as follows:

 Elements are composed of extremely small indivisible particles called atoms.

 All atoms of a given element are identical, having the same size, mass and chemical
Properties.
 The atoms of one element are different from the atoms of all other elements.
 Compounds are composed of atoms of more than one element. In any compound the
Ratio of the numbers of atoms of any two of the elements present is either an integer or
a simple fraction.
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  A chemical reaction involves only the separation, combination, or rearrangement of
atoms; it does not result in their creation or destruction.

In brief, an atom is the smallest particle of an element that maintains its chemical identity
throughout all chemical and physical changes. Most of the earlier findings and concepts related
to law of conservation of mass and law of constant proportions (Fig. 2.4) could be explained to a
great extent. Dalton’s theory also predicted the law of multiple proportions. However, today we
know that atoms are not truly indivisible; they are themselves made up of particles (protons,
neutrons, electrons, etc), which you will learn

ATOMS AND MOLECULES

We have just seen, the first chemist to use the name ‘atom’ was John Dalton. Dalton used the
word ‘atom’ to mean the smallest particle of an element. He then went on explaining how atoms
could react together to form molecules; which he called ‘compound atoms’. Today we know
what a molecule is. A molecule is an aggregate of two or more than two atoms of the same or
different elements in a definite arrangement held together by chemical forces or chemical bonds.
We can also define a molecule as smallest particle of a compound which can exist alone or freely
under ordinary conditions and shows all properties of that substance (element or compound). A
molecule will be diatomic if there are two atoms, for example, chlorine (Cl 2), carbon monoxide,
CO; will be triatomic if there are three atoms, for example, water (H 2O) or carbon dioxide,
(CO2), will be tetratomic and pentatomic if there are four and five atoms respectively. In general,
a molecule having atoms more than four will be called polyatomic.There are nine atoms in a
molecule of ethyl alcohol and we write formulas as C2H5OH

In Brief an atom is the smallest particle of an element that maintains its chemical identity
throughout all chemical and physical changes

Atomic number: The number of protons determines an element’s atomic number (Z) and
distinguishes one element from another. For example, carbon’s atomic number (Z) is 6 because it
has 6 protons. The number of neutrons can vary to produce isotopes, which are atoms of the
same element that have different numbers of neutrons. The number of electrons can also be
different in atoms of the same element, thus producing ions (charged atoms). For instance, iron,
Fe, can exist in its neutral state, or in the +2 and +3 ionic states.

Mass number: Number of protons plus number of neutrons in the nucleus of an atom of an
element.

Isotopes: Isotopes are atoms having the same atomic number, Z but different mass number, A.

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Compound: Matter that is composed of two or more different kinds of elements chemically
combined in definite proportions.

Homogeneous mixture: A mixture with the same composition throughout

Mole: Mole is amount of substance that contains as many elementary particles as there are atoms
in 0.012 kg of C-12 isotope.

Molar mass: The mass (in gram) of one mole of a substance.

Molar volume: The volume of one mole of a substance.

Molecular mass: The sum of atomic masses of all the atoms of a molecule

BOND FORMATION AND MOLECULES

Atoms, Subatomic Particles And Bond Formation.

Most of the Universe consists of matter and energy. Energy is the capacity to do work. Matter is
anything that mass and occupies space. All matter is composed of basic elements that cannot be
broken down to substances with different chemical or physical properties. Atoms are the smallest
particle into which an element can be divided. The ancient Greek philosophers developed the
concept of the atom, although they considered it the fundamental particle that could not be
broken down. Since the work of Enrico Fermi and his colleagues, we now know that the atom is
divisible, often releasing tremendous energies as in nuclear explosions or (in a controlled fashion
in) thermonuclear power plants.

Subatomic particles were discovered during the 1800s. For our purposes we will concentrate
only on three of them, summarized in Table 1. The proton is located in the center (or nucleus) of
an atom, each atom has at least one proton. Protons have a charge of +1, and a mass of
approximately 1 atomic mass unit (amu). Elements differ from each other in the number of
protons they have, e.g. Hydrogen has 1 proton; Helium has 2.

The neutron is also located in the atomic nucleus (except in Hydrogen). The neutron has no
charge, and a mass of slightly over 1 amu. Some scientists propose the neutron is made up of a
proton and electro n-like particle.

The electron is a very small particle located outside the nucleus. Because they move at speeds
near the speed of light the precise location of electrons is hard to pin down. Electrons occupy
orbitals, or areas where they have a high statistical probability of occurring. The charge on an

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electron is -1. Its mass is negligible (approximately 1800 electrons are needed to equal the mass
of one proton).

Table 1. Subatomic particles of use in biology.

Name Charge Location Mass

-27
Proton +1 atomic nucleus 1.6726 X 10 kg
Neutron 0 atomic nucleus 1.6750 X 10-27 kg
Electron -1 electron orbital 9.1095 X 10-31 kg

The atomic number is the number of protons an atom has. It is characteristic and unique for each
element. The atomic mass (also referred to as the atomic weight) is the number of protons and
Figure 1. Note that each of these isotopes of hydrogen has only one proton. Isotopes differ from
each other in the number of neutrons, not in the number of protons.

Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

neutrons in an atom. Atoms of an element that have differing numbers of neutrons (but a
constant atomic number) are referred to as isotopes.eg

Isotopes, shown in Figure 1 and Figure 2, can be used to determine the diet of ancient peoples
by determining proportions of isotopes in mummified or fossilized human tissues. Biochemical
pathways can be deciphered by using isotopic tracers. The age of fossils and artifacts can be

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determined by using radioactive isotopes, either directly on the fossil (if it is young enough) or
on the rocks that surround the fossil (for older fossils like dinosaurs). Isotopes are also the source
of radiation used in medical diagnostic and treatment procedures.

Some isotopes are radioisotopes, which spontaneously decay, releasing radioactivity.

Other isotopes are stable. Examples of radioisotopes are Carbon-14 (symbol 14C), and
deuterium (also known as Hydrogen-2; 2H). Stable isotopes are 12C and 1H.

Figure 2. Carbon has three isotopes, of which carbon-12 and carbon-14 are the most
well known.

Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer
Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com),

The Periodic Table of the Elements, a version of which is shown in Figure 3, provides
a great deal of information about various elements.

Figure 3. The Periodic Table of the Elements. Each Roman numeraled column on the
label (at least the ones ending in A) tells us how many electrons are in the outer shell
of the atom. Each numbered row on the table tells us how many electron shells an
atom has. Thus, Hydrogen, in column IA, row 1 has one electron in one shell.
Phosphorous in column VA, row 3 has 5 electrons in its outer shell, and has three
shells in total.

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Image from James K. Hardy.

Electrons and energy

Electrons, because they move so fast (approximately at the speed of light), seem to straddle the
fence separating energy from matter. Albert Einstein developed his famous E=mc 2 equation
relating matter and energy over a century ago. Because of his (and others) work, we think of
electrons both as particles of matter (having mass is a property of matter) and as units (or quanta)
of energy. When subjected to energy, electrons will acquire some of that energy, as shown in
Figure 4.

Figure 4. Excitation of an electron by energy, causing the electron to "jump" to another electron
(energy) level known as the excited state. Image from Purves et al., Life: The Science of Biology,
4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.

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An orbital is also an area of space in which an electron will be found 90% of the time. Orbitals
have a variety of shapes. Each orbital has a characteristic energy state and a characteristic shape.
The s orbital is spherical. Since each orbital can hold a maximum of two electrons, atomic
numbers above 2 must fill the other orbitals. The px, py, and pz orbitals are dumbbell shaped,
along the x, y, and z axes respectively. These orbital shapes are shown in Figure 5.

Energy levels (also referred to as electron shells) are located a certain "distance" from the
nucleus. The major energy levels into which electrons fit, are (from the nucleus outward) K, L,
M, and N. Sometimes these are numbered, with electron configurations being: 1s22s22p1, (where
the first shell K is indicated with the number 1, the second shell L with the number 2, etc.). This
nomenclature tells us that for the atom mentioned in this paragraph, the first energy level (shell)
has two electrons in its s orbital (the only orbital it can have), and second energy level has a
maximum of two electrons in its s orbital, plus one electron in its p orbital.

Figure 5. Geometry of orbitals. S-orbitals are spherical, p-orbitals are shaped like a
dumbbell or figure 8. Image from Purves et al., Life: The Science of Biology, 4th
Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission.

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Chemical Bonding
During the nineteenth century, chemists arranged the then-known elements according to
chemical bonding, recognizing that one group (the furthermost right column on the Periodic
Table, referred to as the Inert Gases or Noble Gases) tended to occur in elemental form (in other
words, not in a molecule with other elements). It was later determined that this group had outer
electron shells containing two (as in the case of Helium) or eight (Neon, Xenon, Radon, Krypton,
etc.) electrons.

As a general rule, for the atoms we are likely to encounter in biological systems, atoms tend to
gain or lose their outer electrons to achieve a Noble Gas outer electron shell configuration of two
or eight electrons. The number of electrons that are gained or lost is characteristic for each
element, and ultimately determines the number and types of chemical bonds atoms of that
element can form. Atomic diagrams for several atoms are shown in Figure 6.

Figure 6. Atomic diagrams illustrating the filling of the outer electron shells. Images
from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com),

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Ionic bonding

Ionic bonds are formed when atoms become ions by gaining or losing electrons. Chlorine is in a
group of elements having seven electrons in their outer shells (see Figure 6). Members of this
group tend to gain one electron, acquiring a charge of -1. Sodium is in another group with
elements having one electron in their outer shells. Members of this group tend to lose that outer

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electron, acquiring a charge of +1. Oppositely charged ions are attracted to each other, thus Cl -
(the symbolic representation of the chloride ion) and Na + (the symbol for the sodium ion, using
the Greek word natrium) form an ionic bond, becoming the molecule sodium chloride, shown in
Figure 7. Ionic bonds generally form between elements in Group I (having one electron in
their outer shell) and Group VIIa (having seven electrons in their outer shell). Such bonds
are relatively weak, and tend to disassociate in water, producing solutions that have both
Na and Cl ions.

Figure 7. TOP: Formation of a crystal of sodium chloride. Each positively charged

sodium ion is surropunded by six negatively charged chloride ions; likewise each
negatively charged chloride ion is surrounded by six positively charged sodium ions.
The overall effect is electrical neutrality. Image from Purves et al., Life: The Science
of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com), used with permission. BOTTOM: Table Salt Crystal (SEM
x625). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with
permission.

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Covalent bonding

Covalent bonds form when atoms share electrons. Since electrons move very fast they can be
shared, effectively filling or emptying the outer shells of the atoms involved in the bond. Such
bonds are referred to as electron-sharing bonds. An analogy can be made to child custody: the
children are like electrons, and tend to spend some time with one parent and the rest of their time
with the other parent. In a covalent bond, the electron clouds surrounding the atomic nuclei
overlap, as shown in Figure 8.

Figure 8. Formation of a covalent bond between two Hydrogen atoims. Image from
Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

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Carbon (C) is in Group IVa, meaning it has four electrons in its outer shell. Thus to become a
"happy atom", Carbon can either gain or lose four electrons. By sharing the electrons with other
atoms, Carbon can become a happy atom,. alternately filling and emptying its outer shell, as with
the four hydrogens shown in Figure 9.

Figure 9. Formation of covalent bonds in methane. Carbon needs to share four

electrons, in effect it has four slots. Each hydrogen provides an electron to each of
these slots. At the same time each hydrogen needs to fill one slot, which is done by
sharing an electron with the carbon.

Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer
Associateswww.sinauer.comwww.whfreeman.com

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The molecule methane (chemical formula CH 4) has four covalent bonds, one between Carbon
and each of the four Hydrogens. Carbon contributes an electron, and Hydrogen contributes an
electron. The sharing of a single electron pair is termed a single bond. When two pairs of
electrons are shared, a double bond results, as in carbon dioxide. Triple bonds are known,
wherein three pairs (six electrons total) are shared as in acetylene gas or nitrogen gas. The types
of covalent bonds are shown in Figure 10.

Figure 10. Ways of representing covalent bonds. Image from Purves et al., Life: The
Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH
Freeman (www.whfreeman.com), used with permission.

Sometimes electrons tend to spend more time with one atom in the bond than with the other. In
such cases a polar covalent bond develops. Water (H2O) is an example. Since the electrons spend
so much time with the oxygen (oxygen having a greater electronegativity, or electron affinity)
that end of the molecule acquires a slightly negative charge. Conversely, the loss of the electrons
from the hydrogen end leaves a slightly positive charge. The water molecule is thus polar, having
positive and negative sides.

Hydrogen bonds, as shown in Figure 11, result from the weak electrical attraction between the
positive end of one molecule and the negative end of another. Individually these bonds are very

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weak, although taken in a large enough quantity, the result is strong enough to hold molecules
together or in a three-dimensional shape.

Hydrogen Bonding

Hydrogen bonding differs from other uses of the word "bond" since it is a force of attraction
between a hydrogen atom in one molecule and a small atom of high electronegativity in another
molecule. That is, it is an intermolecular force, not an intramolecular force as in the common use
of the word bond.

When hydrogen atoms are joined in a polar covalent bondwith a small atom of high
electronegativity such as O, F or N, the partial positive charge on the hydrogen is highly
concentrated because of its small size. If the hydrogen is close to another oxygen, fluorine or
nitrogen in another molecule, then there is a force of attraction termed a dipole-dipole
interaction. This attraction or "hydrogen bond" can have about 5% to 10% of the strength of a
covalent bond.

Hydrogen bonding has a very important effect on the properties of water and ice. Hydrogen
bonding is also very important in proteins and nucleic acids and therefore in life processes. The
"unzipping" of DNA is a breaking of hydrogen bonds which help hold the two strands of the
double helix together.

Figure 11. TOP: Formation of a hydrogen bond between the hydrogen side of one
water molecule and the oxygen side of another water molecule. BOTTOM: The
presence of polar areas in the amino acids that makeup a protein allows for hydrogen
bonds to form, giving the molecule a three-dimensional shape that is often vital to that
protein's proper functioning. Images from Purves et al., Life: The Science of Biology,
4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com)

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Chemical reactions and molecules |
Molecules are compounds in which the elements are in definite, fixed ratios, as seen in Figure
12. Those atoms are held together usually by one of the three types of chemical bonds discussed
above. For example: water, glucose, ATP. Mixtures are compounds with variable formulas/ratios
of their components. For example: soil. Molecular formulas are an expression in the simplest
whole-number terms of the composition of a substance. For example, the sugar glucose has 6
Carbons, 12 hydrogens, and 6 oxygens per repeating structural unit. The formula is written
C6H12O6.

26
Figure 12. Determination of molecular weights by addition of the weights of the atoms
that make up the molecule. Image from Purves et al., Life: The Science of Biology, 4th
Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman
(www.whfreeman.com),

Chemical reactions occur in nature, and some also can be performed in a laboratory setting. One
such reaction is diagrammed in Figure 13. Chemical equations are linear representations of how
these reactions occur. Combination reactions occur when two separate reactants are bonded
together, e.g. A + B -----> AB. Disassociation reactions occur when a compound is broken into
two products, e.g. AB -----> A + B.

Figure 13. Diagram of a chemical reaction: the combustion of propane with oxygen,
resulting in carbon dioxide, water, and energy (as heat and light). This chemical
reaction takes place in a camping stove as well as in certain welding torches. Image
from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

27
Biological systems, while unique to each species, are based on the chemical bonding properties
of carbon. Major organic chemicals (those associated with or formed by the actions of living
things) usually include some ratios of the following elements: C, H, N, O, P, S.

Assignment

 describe radioisotopes and list three ways they are used in biology.

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Various functional groups of organic molecules and their biological
roles
Functional Groups

Functional groups refer to specific atoms bonded in a certain arrangement that give a compound
certain physical and chemical properties.

The Role of Functional Groups

In organic chemistry, a functional group is a specific group of atoms or bonds within a

compound that is responsible for the characteristic chemical reactions of that compound. The
same functional group will behave in a similar fashion, by undergoing similar reactions,
regardless of the compound of which it is a part. Functional groups also play an important part in
organic compound nomenclature; combining the names of the functional groups with the names
of the parent alkanes provides a way to distinguish compounds.

The atoms of a functional group are linked together and to the rest of the compound by covalent
bonds. The first carbon atom that attaches to the functional group is referred to as the alpha
carbon; the second, the beta carbon; the third, the gamma carbon, etc. Similarly, a functional
group can be referred to as primary, secondary, or tertiary, depending on if it is attached to one,
two, or three carbon atoms.

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Functional Groups and Reactivity

Functional groups play a significant role in directing and controlling organic reactions. Alkyl
chains are often nonreactive, and the direction of site-specific reactions is difficult; unsaturated
alkyl chains with the presence of functional groups allow for higher reactivity and specificity.
Often, compounds are functionalized with specific groups for a specific chemical reaction.
Functionalization refers to the addition of functional groups to a compound by chemical
synthesis. Through routine synthesis methods, any kind of organic compound can be attached to
the surface. In materials science, functionalization is employed to achieve desired surface
properties; functional groups can also be used to covalently link functional molecules to the
surfaces of chemical devices.

In organic chemistry, the most common functional groups are carbonyls (C=O), alcohols (-OH),
carboxylic acids (CO2H), esters (CO2R), and amines (NH2). It is important to be able to
recognize the functional groups and the physical and chemical properties that they afford
compounds.

Alcohols

The alcohol functional group: Alcohols are characterized by the presence of an -OH group,
which is generally in a bent shape, like that of water. (R-OH)

Alcohols are able to participate in many chemical reactions. They often undergo deprotonation in
the presence of a strong base. This weak acid behavior results in the formation in an alkoxide salt
and a water molecule. Alcohols can react with carboxylic acids to form an ester, and they can be
oxidized to aldehydes or carboxylic acids.

Alcohols have many uses in our everyday world. They are found in beverages, antifreeze,
antiseptics, and fuels. They can be used as preservatives for specimens in science, and they can
be used in industry as reagents and solvents because they display an ability to dissolve both polar
and non-polar substances.

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Ethers

Ethers are a class of organic compounds characterized by an oxygen atom connected to two alkyl
or aryl groups.

Ethers: The general structure of ether. Ether is characterized by an oxygen bonded to two alkyl
or aryl groups, represented here by R and R’. The substituents can be, but do not need to be, the
same. hey follow the general formula R-O-R’. The C-O-C linkage is characterized by bond
angles of 104.5 degrees, with the C-O distances being about 140 pm. The oxygen of the ether is
more electronegative than the carbons. Thus, the alpha hydrogens are more acidic than in regular
hydrocarbon chains.

Nomenclature of Ethers

There are two ways to name ethers. The most common way is to identify the alkyl groups on
either side of the oxygen atom in alphabetical order, then write “ether.” For example, ethyl
methyl ether is the ether that has an ethyl group and a methyl group on either side of the oxygen
atom. If the two alkyl groups are identical, the ether is called di[alkyl] ether. For example,
diethyl ether is the ether with an ethyl group on each side of the oxygen atom.

The other way of naming ethers is the formal, IUPAC method. This way, the form is: [short alkyl
chain][oxy][long alkyl chain]. For example, the IUPAC name for ethyl methyl ether would be
methoxyethane.

In cyclic ethers, the stem of the compound is known as a oxacycloalkane. The “oxa” is an
indicator of the replacement of the carbon by an oxygen in the ring. An example is
oxacyclopentane, a five-membered ring in which there are four carbon atoms and one oxygen
atom.

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Tetrahydrofuran (THF): The common name of the cyclic ether “oxacyclopentane” is
tetrahydrofuran, or THF. It is a common organic solvent that is miscible with water.

Properties of Ethers

Ethers are rather nonpolar due to the presence of an alkyl group on either side of the central
oxygen. The presence of the bulky alkyl groups that are adjacent to it means that the oxygen
atom is largely unable to participate in hydrogen bonding. Ethers, therefore, have lower boiling
points compared to alcohols of similar molecular weight. However, as the alkyl chain of the
ethers becomes longer, the difference in boiling points becomes smaller. This is due to the effect
of increased Van der Waals interactions as the number of carbons increases, and therefore the
number of electrons increases as well. The two lone pairs of electrons present on the oxygen
atoms make it possible for ethers to form hydrogen bonds with water. Ethers are more polar than
alkenes, but not as polar as esters, alcohols or amides of comparable structures.

Aldehydes and Ketones

Aldehydes and ketones are classes of organic compounds that contain a carbonyl (C=O) group.

In organic chemistry, a carbonyl group is a functional group which has a carbon double bonded
to an oxygen atom: C=O.

Ketones

When a carbonyl functional group is placed within a molecule, it is known as a ketone. Ketones
are organic compounds with the structure RC(=O)R’, where R and R’ can be a variety of carbon-
containing substituents. IUPAC nomenclature rules dictate that ketone molecules are named by
changing the suffix of the parent carbon molecule to “-one.” If the position of the ketone must be
specified, then a number is placed between the parent chain name and the “-one” prefix (e.g.,
propan-2-one), or at the beginning of the IUPAC name. The prefixes “oxo-” and “keto-” are used
to describe the ketone functional group.

Ketone: A ketone is a type of organic compound where a carbonyl group bonds to two other
carbon atoms of the carbon backbone.

ketones are often more volatile than alcohols and carboxylic acids of comparable molecular
weights. Ketones have alpha -hydrogens which participate in keto-enol tautomerism. In the
presence of a strong base, enolate formation and subsequent deprotonation of the enolate will
occur.

Aldehydes

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Aldehyde: An aldehyde is characterized by the presence of a carbonyl functional group at the
end of a compound’s carbon skeleton.

An aldehyde is an organic compound that contains a carbonyl group with the central carbon
bonded to a hydrogen and R group (R-CHO). Aldehydes differ from ketones in that the carbonyl
is placed at the end of the carbon skeleton rather than between two carbon atoms of the
backbone. Like ketones, aldehydes are sp2 hybridized and can exist in the keto or enol tautomer.
Aldehydes are named by dropping the suffix of the parent molecule, and adding the suffix “-al.”
For instance, a three-carbon chain with an aldehyde group on a terminal carbon would be
propanal. If there are higher order functional groups on the compound, the prefix “oxo-” can be
used to indicate which carbon atom is part of the aldehyde group. If the location of the aldehyde
must be specified, a number can be used in between the parent chain and suffix, or at the
beginning of the compound name.

Similarities of Aldehydes and Ketones

Both aldehydes and ketones exist in an equilibrium with their enol forms; the enol form is
defined as an alkene with a hydroxyl group affixed to one of the carbon atoms composing the
double bond. The keto form predominates at equilibrium for most ketones. However, the enol
form is important for some reactions because the deprotonated enolate form is a strong
nucleophile. The equilibrium is strongly thermodynamically driven, and at room temperature the
keto form is favored. The interconversion can be catalyzed by the presence of either an acid or a
base.

Carboxylic Acids

Carboxylic acids are organic acids that contain a carbon atom that participates in both a hydroxyl
and a carbonyl functional group.

A carboxyl group (COOH) is a functional group consisting of a carbonyl group (C=O) with a
hydroxyl group (O-H) attached to the same carbon atom. Carboxyl groups have the formula –C
(=O)OH, usually written as -COOH or CO2H. Carboxylic acids are a class of molecules which

33
are characterized by the presence of one carboxyl group. As proton donors, carboxylic acids are
characterized as Brønsted-Lowry acids. Acids with two or more carboxylic groups are called
dicarboxylic, tricarboxylic, etc. Salts and esters of carboxylic acids are called carboxylates.
Carboxylate ions are resonance-stabilized. This increased stability leads to increased acidity
compared to that of alcohols. Generally, in IUPAC nomenclature, carboxylic acids have an “-oic
acid ” suffix, although “-ic acid” is the suffix most commonly used.

A carboxylic acid: Carboxylic acids are organic oxoacids characterized by the presence of at
least one carboxyl group, which has the formula -C(=O)OH, usually written as -COOH or -
CO2H.

Physical Properties of Carboxylic Acids

Carboxylic acids act as both hydrogen bond acceptors, due to the carbonyl group, and hydrogen
bond donors, due to the hydroxyl group. As a result, they often participate in hydrogen bonding.
Carboxylic acids usually exist as dimeric pairs in nonpolar media because of their tendency to
“self-associate.” This tendency to hydrogen bond gives them increased stability as well as higher
boiling points relative to the acid in aqueous solution. Carboxylic acids are polar molecules; they
tend to be soluble in water, but as the alkyl chain gets longer, their solubility decreases due to the
increasing hydrophobic nature of the carbon chain. Carboxylic acids are characterized as weak
acids, meaning that they do not fully dissociate to produce H+ cations in a neutral aqueous
solution.

Hydrogen bonding between carboxylic acids: Carboxylic acids hydrogen bond with
themselves, giving them an increased level of stability.

Esters

Esters are functional groups produced from the condensation of an alcohol with a carboxylic
acid, and are named based on these components.

Esters are an important functional group in organic chemistry, and they are generally written
RCOOR’ or RCO2R’.

Esters: An ester is characterized by the orientation and bonding of the atoms shown, where R
and R’ are both carbon-initiated chains of varying length, also known as alkyl groups.

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As usual, R and R’ are both alkyl groups or groups initiating with carbon. Esters are derivative of
carboxylic acids where the hydroxyl (OH) group has been replaced by an alkoxy (O-R) group.
They are commonly synthesized from the condensation of a carboxylic acid with an alcohol:

RCO2H+R′OH→RCO2R′+H2O

Esters are ubiquitous. Most naturally occurring fats and oils are the fatty acid esters of glycerol.
Esters are typically fragrant, and those with low enough molecular weights to be volatile are
commonly used as perfumes and are found in essential oils and pheromones. Polymerized esters,
or polyesters, are important plastics, with monomers linked by esteric units like this:

CO2RCO2RCO2R… etc.

Nomenclature

The word “ester” was coined in 1848 by German chemist Leopold Gmelin, probably as a
contraction of the German Essigäther, meaning acetic ether.

Ester names are derived from the parent alcohol and acid. For example, the ester formed by
ethanol and ethanoic acid is known as ethyl ethanoate; “ethanol” is reduced to “ethyl,” while
“ethanoic acid” is reduced to “ethanoate.” Other examples of ester names include methyl
propanoate, from methanol and propanoic acid, and butyl octanoate, from butane and octanoic
acid.

Ethyl ethanoate: The name ethyl ethanoate is derived from the components from which it is
synthesized: ethanol and ethanoic acid. In this diagram, the red part of the molecule represents
the portion formerly attributed to ethanol (minus a H), and the green part of the molecule
represents the ethanoic acid portion (minus an OH). Esterification is a form of dehydration
synthesis, so the H and OH components are removed as water.

In the case of esters formed from common carboxylic acids, more colloquial terms are sometimes used.
For example, ethanoic acid is more commonly known as acetic acid, and thus its esters contain “acetate”
instead of “ethanoate” in their names. Other such substitutions include “formate” instead of
“methanoate,” “propionate” instead of “propanoate,” and “butyrate” instead of “butanoate.”

The chemical formulas of organic esters are typically written in the format of RCO2R’, where R and R’ are
the hydrocarbon parts of the carboxylic acid and alcohol, respectively. For example, butyl acetate,
systematically known as ethanoic acid, is derived from butanol and acetic acid and would be written
CH3CO2C4H9. Alternative presentations are common, including BuOAc and CH3COOC4H9. Cyclic esters are
known as lactones.

Structure and Bonding

Esters contain a carbonyl center, which gives rise to 120 degree C-C-O and O-C-O bond angles
due to sp2 hybridization. Unlike amides, esters are structurally flexible functional groups because
35
rotation about the C-O-C bonds has a lower energy barrier. Their flexibility and low polarity
affects their physical properties on a macroscopic scale; they tend to be less rigid, leading to a
lower melting point, and more volatile, leading to a lower boiling point, than the corresponding
amides. The pKa of the alpha-hydrogens, or the hydrogens attached to the carbon adjacent to the
carbonyl, on esters is around 25, making them essentially non-acidic except in the presence of
very strong bases.

Physical Properties and Characterization

Esters are more polar than ethers, but less so than alcohols. They participate in hydrogen bonds as
hydrogen bond acceptors, but cannot act as hydrogen bond donors, unlike their parent alcohols and
carboxylic acids. This ability to participate in hydrogen bonding confers some water-solubility,
depending on the length of the alkyl chains attached. Since they have no hydrogens bonded to oxygens,
as alcohols and carboxylic acids do, esters do not self-associate. Consequently, esters are more volatile
than carboxylic acids of similar molecular weight.

Amines

Amines are compounds characterized by the presence of a nitrogen atom, a lone pair of
electrons, and three substituents.

The amine functional group contains a basic nitrogen atom with a lone pair of electrons. As such,
the group is derivative of ammonia, in which one or more hydrogen atoms have been replaced by
a carbon-containing substituent. Compounds with the nitrogen group attached to a carbonyl
within the structure are referred to as amides, and they have the structure R-CO-NR’R”. Amine
groups bonded to an aromatic (conjugated cyclic) structure are known as aromatic amines. The
aromatic structure effectively decreases the alkalinity of the amine, while the presence of the
amine group significantly decreases the reactivity of the ring due to an electron donating effect.
The prefix “amino-” or the suffix “-amine” is used when naming an amine compound. An
organic compound with multiple amino groups is called a diamine, triamine, tetramine, etc.

Amine Structure

Amines are generally organized into categories based on their bonding environments. Amines
that have one of their three hydrogen atoms replaced by an alkyl or aromatic substituent are
referred to as primary amines. Secondary amines are those that have two substituents and one
hydrogen bonded to a nitrogen. Tertiary amines are amines whose hydrogens have been
completely replaced by organic substituents. Finally, cyclic amines are those in which the
nitrogen has been incorporated into a ring structure, effectively making it either a secondary or
tertiary amine. The general structure of an amine contains a nitrogen atom, a lone pair of
electrons, and three substituents. However, it is possible to have four organic substituents on the
nitrogen, making it an ammonium cation with a charged nitrogen center.

Tertiary amine: The central carbon is attached to an amine group and three other carbon atoms.

Physical Properties of Amines

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Amines are able to hydrogen bond. As a result, the boiling points of these compounds are higher
than those of the corresponding phosphines, but lower than those of the corresponding alcohols,
which hydrogen bond to a stronger extent. Amines also display some solubility in water.
However, the solubility decreases with an increase in carbon atoms, due to the increased
hydrophobicity of the compound as the chain length increases. Aliphatic amines, which are
amines connected to an alkyl chain, display solubility in organic polar solvents. Aromatic
amines, which are amines that participate in a conjugated ring, donate their lone pair of electrons
into the benzene ring, and thus their ability to engage in hydrogen bonding decreases. This
results in a decrease in their solubility in water and high boiling points.

Acidity and Alkalinity of Amines

Amines of the type NHRR’ and NR’R”R”’ are chiral molecules and can undergo inversion.
Since the barrier for inversion is quite low (~7 kcal/mol), these compounds cannot be resolved
optically. Amines are bases, and their basicity depends on the electronic properties of the
substituents (alkyl groups enhance the basicity; aryl groups diminish it), steric hindrance, and the
degree of solvation of the protonated amine. In general, the effect of alkyl groups raises the
energy of the lone pair of electrons, thus elevating the basicity. Thus, the basicity of an amine
can be expected to increase with the number of alkyl groups on the amine. Additionally, the
effect of the aromatic ring delocalizes the lone pair of electrons on nitrogen into the ring,
resulting in decreased basicity. The solvation of protonated amines changes upon their
conversion to ammonium compounds. Typically, salts of ammonium compounds exhibit the
following order of solubility in water: primary ammonium (RNH3+) > secondary ammonium
(R2NH2+) > tertiary ammonium (R3NH+). Quaternary ammonium salts usually exhibit the lowest
solubility of the series.

Amine Preparation and Reactivity

Imine formation: A primary amine is reacted with an aldehyde to produce an imine.

Industrially, amines are prepared from ammonia by alkylation with alcohols. They can also be
prepared via reduction of nitriles to amines using hydrogen in the presence of a nickel catalyst.
Amines are quite reactive due to their basicity as well as their nucleophilicity. Most primary
amines are good ligands and react with metal ions to yield coordination complexes. One of the
most important reactions for amines is their formation of imines, or organic compounds where
nitrogen participates in a double bond, upon reacting with ketones or aldehydes.

Applications of Amines

Amines are ubiquitous in biology. Many important molecules are amine-based, such as
neurotransmitters and amino acids. Their applications in the world include being starting
material for dyes and models for drug design. They are also used for gas treatment, such as
removing CO2 from combustion gases.

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