UNIT 1 BASIC CHEMISTRY IN BIOCHEMISTRY
1.0 Introduction
Organic molecules are molecules that contain carbon and hydrogen. All living things contain
these organic molecules. These are carbohydrates, lipids, proteins, and nucleic acid. These
molecules are often called macromolecules because they may be very large and they are
typically composed of many smaller molecules bonded together. They can contain thousands
of carbon and hydrogen atoms. These four macromolecules will be discussed in units four-
five. This unit introduces critical aspects as used in biomolecules chemistry.
Objectives
Students should be able to:
Outline the main characteristics and importance of carbon, which enable it to perform
best in living organisms.
Explain functional groups and importance in living matter.
Distinguish between types of bonding in molecule and compounds.
1.1 Carbon and its unique characteristics
Carbon (C) is an element of relative molecular weight 12. It has six protons and six neutrons
in its nucleus. The element has six electrons distributed as shown in Figure 1. The outer shell
(valence shell) holds four electrons since the first is full at maximum of two electrons.
Elements as such have little tendency to donate its electrons but rather they share. Carbon can
therefore form four covalent bonds because it has four electrons in its outer shell. It can form
the following number of bonds. 4 single bonds for example in methane-Figure 1.3
two double bonds Figure 1.3
one double bond and two single bonds Figure 1.4
one triple and one single bond Fig 1.5
Figure 1.1: Orbit Presentation of Carbon
Note that in each case below, there is a total of four bonds. Hydrogen has one proton, no
neutron and one electron. It can readily share with carbon for it to fill its valence of two,
therefore can easily form four covalent bonds forming methane (Fig 1.3)
Figure 1.2: Orbit Presentation of Hydrogen
Activity
Characterize carbon and explain its importance in agriculture and nutrition.
1.2 Nomenclature of organic molecules
The number of carbon atoms usually forms the basis of naming organic compounds amongst
other types of nomenclature. Table 1.1 shows this naming system, giving examples
Table 1.1 Naming based on number of carbons
Number of carbon Naming Example
atoms
1 Meth- Methane, methanol
2 Eth- Ethane, ethanol
3 Prop- Propanol
4 But- Butanol
5 Pent- Pentose ribose
6 Hex- Hexose glucose
7 Hept- Sedoheptulose
Figure 1.3 : Methane molecule showing sharing in single bonds
The diagram above shows a molecule of methane. Lines can be used to represent bonds in the
shorthand formula seen in the upper right side of the diagram.
1
Figure 1.4: Methene molecule showing sharing in double bonds
Figure 1.5: Molecule showing sharing in tripple bonds
The characteristics above give the carbon molecule some unique characteristics such as;
It can form covalent bonds which are rated relatively stronger in comparison to other
bonding such as ionic which can easily dissociate.
It is of low molecular weight, a characteristic that advantages storage molecules in
plants and animals.
It has the ability to form diverse molecules since it can have four same or different
connections and orientations thus can form basis of isomerism
Its ability to form carbon-carbon bonds (catenation) is critical in forming long chains,
which can branch or coil to form rings- critical in forming storage molecules such as
glycogen and amylopectin. Long chains of carbon atoms are common Fig 1.6.
-
Figure1.6: Long Chain and Ring Structure Formations
1.3 Functional Groups
Biomolecules that can be formed by carbon connections are classified into groups in relation
to the way they react. This presents the usefulness of functional groups.A functional group is
a group of atoms of a particular arrangement that gives the entire molecule certain
characteristics (Lehninger, 1982). Organic molecules may have functional groups attached.
Functional groups are named according to the composition of the atom or group of atoms, for
example, COOH is a carboxyl group. Organic chemists use the letter "R" to indicate an
organic molecule. For example, the diagram below can represent a carboxylic acid. The "R"
can be any organic molecule.
Table 1.2 Some Important Functional Groups. Source: IUPAC, 1997.
Chemical Group Formula Structural Prefix Suffix Example
class Formula
methanol
Alcohol Hydroxyl ROH R-O-H Hydroxy Ol
Methanol
Carboxylic Carboxyl RCOOH "Carboxylic carboxy- -oic acid "Acetic acid"
acid acid"
Acetic acid
(Ethanoic acid)
Butanone1
Ketone
-oyl- (-
COR')
Ketone Carbonyl RCOR' -one
or
oxo- (=O) Butanone
(Methyl ethyl ketone)
Aldehyde formyl- (-
COH)
Aldehyde Carbonyl RCHO -al Ethanal
or
(Acetaldehyde)
oxo- (=O)
Amide methylamine
"Primary
Primary amine"
RNH2 amino- -amine
amine
Methylamine
(Methanamine)
"Dimethyl disulfide"
Disulfide disulfanyl
Disulfide Disulfide RSSR' - disulfide
(-SSR') (Methyldisulfanyl)me
thane (prefix) or
Dimethyl disulfide
(suffix)
phosphon
ooxy- "Glyceraldehyde 3-
"Phosphate phosphate"
or
group"
ROP(=O)(O O- Phosphat
Phosphate Phosphate
H)2 phosphon e
o- Glyceraldehyde 3-
(phospho phosphate (suffix)
-)
1.3.1 Reactions of the Functional Groups
Some functional groups are polar and others can ionize. For example, if the hydrogen ion is
removed from the COOH group, the oxygen will retain both of the electrons it shared with
the hydrogen and will have a negative charge. The hydrogen that is removed leaves behind its
electron and is now a hydrogen ion (proton). If polar or ionizing functional groups are
attached to hydrophobic molecules, the molecule may become hydrophilic due to the
functional group. Some ionizing functional groups are: -COOH, -OH, -CO, and -NH2. They
ionize to COO-, O-, CO- and NH3+ respectively
The first carbon atom after the carbon that attaches to the functional group is called the alpha
carbon; the second, beta carbon, the third, gamma carbon, and so on. If there is another
functional group at a carbon, it may be named with the Greek letter, for example the gamma-
amine in gamma-aminobutanoic acid is on the third carbon of the carbon chain attached to
the carboxylic acid group.
1.3.2 Importance of functional groups
Functional groups are the reacting atom or groups of atoms. They are the responsible for
general classification of biomolecules like alcohols, carboxylic acids and carbonyl, among
others. Reaction type is already defined and perceived, despite size of molecule involved, the
same pathway for the reacting groups of atoms remain. They further differentiate even
closely similar molecules and compounds like aldehydes and ketones.
1.4 Isomerism
Different molecules that are composed of the same number and kinds of atoms are called
isomers. Glucose and fructose (shown below) are both C6H12O6 but the atoms are arranged
differently in each molecule. Three kinds of isomers are described below.
1.4.1Constitutional isomerism
The molecules differ in their overall construction as shown above for glucose and fructose,
although having same molecular formula and classified all as hexose sugars
(Lehninger,1982).
Figure 1.8: Constitutional isomers
1.4.2 Geometric isomerism
The isomers maintain the same carbon skeleton but a double bond occurs between carbon
atoms (Holum, 1996). The location of atoms connected to a double-bonded carbon atom
differs. The two molecules below are geometric isomers because the double bond cannot
rotate. If the bond between the two carbon atoms below were a single bond, they would not
be isomers because atoms attached by single bonds can rotate. The carbon atoms would be
able to rotate from one orientation to another if the bond were a single bond.
Figure 1.9 Geometric isomers
1.4.3 Stereoisomerism
The stereoisomer is a special type geometric isomer. The connectivity is the same between
two stereoisomers; the difference is their arrangement in three dimensional space. They are
not super imposable. They are mirror images of each other. Another term used is chiral, this
would be used to describe a carbon that is a stereocenter, the chiral carbon, or a molecule
with a stereocenter is a chiral molecule (Holum, 1996).
This phenomenon only occurs around carbon atoms that have four different connections. The
example below shows 4 different connections, atom, for instance a methyl group, could be
substituted for these individual atom as in figure 1.10. The stereochemistry of these
molecules can become overwhelming. As such other prefixes must be introduced to describe
the stereochemistry, alpha, and beta, . The alpha structure has the hydroxyl group down
and the beta group has the hydroxyl group up as shown in figure 1.10.
Figure 1.10 Presentation of stereoisomers
When this occurs, the two mirror images are called enantiomers.
The two isomers will have the same name except for a prefix(s) Your hands are mirror
Figure 1.11. These prefixes originate in one of the properties of images of each other;
compounds with stereocenters, rotation of plane polarized light they are the same, but .
or in the convention of drawing the structures (dextro (D) and opposites.
levo (L) rotatory). This may not seem like an important point,
but as it turns out, even though these two molecules’ structures H
are almost exactly the same, they do react differently, C O
H C OH
sometimes with terrible consequences or resulting in competitive enzyme inhibition
H C OH
To determine the number of isomers a molecule will form: H C OH
H C OH
H
Ribose
ib s
1. Count the number of stereocenters in the molecule (x)
2. Take two to that power, thus, 2x
For an example, the ribose molecule to the right has 3 stereocenters, thus
ribose have 23 = 8 different isomers
CH2OH CH2OH
H O OH O H
H
H H
OH H OH H
HO H HO OH
- D Glucose H HO H HO - D Glucose
Figure 1.11 D and L isomers
Activity
One of the following three carbons is chiral, which is it and why are the other two not chiral?
1.4 Macromolecules and Monomers
Many of the common large biological molecules (macromolecules) are synthesized from
simpler building blocks (monomers). Table 1.3 gives the monomer and polymer it can form.
The macromolecules are synthesised from condensation reactions.
1.4.1 Synthesis and degradation of biomolecules
[Link] Condensation
In biological systems, macromolecules are often formed by removing H from one atom and
OH from the other (see the diagram below). The H and the OH combine to form water (Carr
and Cordell, 1992). Small molecules (monomers) are therefore joined to build
macromolecules by the removal of water. Figure 1.12 shows that sucrose (a sugar) can be
produced by a condensation reaction of glucose and fructose. This is called a condensation or
dehydration reaction .Energy is required to form the bond.
Table 1.3 Monomers and their polymers
Example of a Macromolecule Monomer
Polysaccharide (complex carbohydrate) monosaccharide (simple sugar)
Lipid glycerol, fatty acid
Protein amino acid
Nucleic acid Nucleotide
Figure 1.12: Condensation and Hydrolysis Reactions in sucrose formation and
breakdown
[Link] Hydrolysis
This is a type of reaction in which a macromolecule is broken down into smaller molecules
(Carr and Cordell, 1992). It is the reverse of condensation and reaction is shown by the
upward arrow in figure 1.12.
1.5 Bonding in Biomolecules
1.5.1 Covalent Bonds
Elements near the middle of the periodic table form covalent bonds. Energy cost to reach
stability level is considered. In Carbon, it would use more energy to lose or gain electrons
therefore sharing is best (McMurry, 2003). Such sharing is referred to as covalent bonding.
There are four major non-covalent forces involved in the structure and function of
biomolecules:
1.5.2 Charge-charge interactions or electrostatic interactions (ionic bonds)
Occur between two oppositely charged particles, thus a positive and a negative. They are the
strongest non-covalent force that occurs over greater distances. They can however be
weakened significantly by water molecules (can interfere with bonding). Common salt
(NaCl) is easily dissolved in water. Charge-charge interactions contribute minimally to
protein stability because most ionic bonds are found on the surface of a protein (Cowan,
1997).
1.5.3 Hydrogen bonds
The bonds will be discussed under properties of water. They are more important when they
occur between and within molecules to stabilize structures such as proteins and nucleic acids
(Cowan, 1997). Many hydrogen bonds ultimately form between polypeptide backbone and
water, between backbone and R-groups, between R-groups, and between R-groups and water.
Those hydrogen bonds within interior of protein are more stable than those on the surface
because these bonds do not then compete with water molecules.
1.5.4 Disulfide bonds/bridges
Disulfide bonds form between the sulfur atoms of two cysteine side chains in a protein
(Southerland, 1990)The side chains undergo a reversible oxidation of the sulfhydryl groups
of the cysteine, which results in covalent bonding of the sulfur atoms (S-S). This bonding is
called a "disulfide bridge". Typically, disulfides do not form on the surface of proteins
because of the presence of reducing agents in the cytoplasm. According to Cowan (1997),
these bonds are of great importance concerning the shaping of protein structure. Their
formation guides the folding of peptide chains as the proteins are produced. Structural
proteins that have to be rigorously stable (for example, keratin, which is found in nail, horn
and crustacean shell) often contain a large number of disulfide bonds.
1.5.5 Van der Waals forces
They occur between neutral atoms and can be attractive or repulsive, depending upon the
distance of the two atoms. They are much weaker than hydrogen bonds. The actual distance
between atoms is the distance at which maximal attraction occurs. Distances vary depending
upon individual atoms.
1.5.6 Hydrophobic interactions
Non polar molecules are hydrophobic (means "water fearing"). They do not dissolve in water.
Hydrophobic interactions are rated very weak but are very important in protein shape and
membrane structure (Lehninger, 1982). They occur between non-charged molecules. Proteins
are more stable when their hydrophobic R-groups are in the interior of a protein and away
from water (Cowan, 1997). Nonpolar side chains then interact with each other. Polar side
chains remain in contact with water on the protein surface.
Non polar molecules are hydrophobic.
Polar and ionic molecules are
hydrophilic.
Figure 1.7 Hydrophobic and hydrophilic molecules
Portions of large molecules may be hydrophobic and other portions of the same molecule
may be hydrophilic. This denotes the importance of functional groups.
1.6 Summary
Carbon forms the major backbone of all chemical life due to its unique properties. There are
however some molecules such as sulphur, hydrogen, phosphorus and nitrogen involved in
basic chemistry of living organisms.
Atoms or groups of atoms (functional groups) divide the molecules into classes like; alcohols,
carboxylic acids and so on. Functional groups positioning helps distinguish alike molecules
such as glyceraldehydes and dihydroxyacetone, glucose and fructose, among many other
examples. Nomatter the size of the carbon chain, functional group presents the reacting part
of a molecule.
Molecules react through these functional groups to build up macromolecules. If they remove
water molecules, the reaction is a condensation reaction. In instances where such molecules
are split and water is needed or used in bond breaking, the reaction is a hydrolytic one.
There are many molecules that have the same molecular formula and relative molecular
weight but are differentiated by their functional groups, hence the difference in reactions they
take part in. Such molecules are referred to as isomers. Isomerism differs in form; structural,
geometric and stereoisomerism.
Molecules are formed through ionic and covalent bonding. The molecules usually interact
through different forces such as hydrophobic, hydrogen bonding, disulfide bridges and so on.
Reading Material
Carr, M and Cordell, B. (1992). Biochemistry. Nelson L.t.d. London.
Cowan, J.A. (1997). Inorganic Biochemistry: An Introduction. 2nd Edition. Library of
Congress.
Hames,B. D., Hooper, N.M., and Houghton, J.D. (1997). Instant Notes in Biochemistry.
Bios Scientific, University of Leeds.
Holum, J.R. (1996). Organic and Biological Chemistry. John Wiley, Canada.
Lehninger, A.L. (1982). Principles of Biochemistry. Worth Publishers, New York.
Southerland, W.M. (1990). Foundations of Medicine: Biochemistry. Howard University,
Washington D.C.