Module II

Chemical Components of Life

This module will help you gain knowledge on the different biomolecules that composes a living
organism. Living organisms are made up of non-living atoms and molecules. These molecules
carbohydrates, proteins, lipids and nucleic acids are varied, complex and they interact with each other
and constitute the molecular reason of life processes.
Learning Outcomes:

After examining this module, you are expected to:

1. Distinguish the chemical components of the cell;
2. Discuss structure and functions of biomolecules.

Content/Information Sheet

Subtopic 1. Chemical Components of the Cell

Overview:

Earthly life can be understood as form of existence of matter i.e. All living organisms are composed of the
same particles (may it be ions, atoms, and molecule) as the non- living organisms. Chemical and physics
laws are also applicable to both types of organisms.
There are close connections between living and non-living nature but they differ in chemical composition,
structure, complexity and organization. The non-living organisms are chemically composed in varied ways
and the presence of living organisms is based on the presence of few chemical elements especially carbon,
oxygen, nitrogen and hydrogen.
All the chemical compounds in the living system are composed of chemical elements. There 118 chemical
elements, wherein 92 elements are naturally present in nature and rest were laboratory made. The 30
elements from the 92 make up the living matter and they are called biogenic elements.

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Source: www.kr-jihomoravsky.cz › pptv › chemie › Helešicová
Figure 1. Earth’s crust chemical representation.

Out of the 92 elements, 75% of all elements were represented by Oxygen and Silicon (see Figure 1.). These
elements are bonded especially in minerals (in the form of oxides and silicates) and rocks.

Chemical elements in the living systems:

The four basic elements in all living systems are: Carbon, Oxygen, Nitrogen, and Hydrogen. Among the
four elements, Carbon is the basic unit in living matter oxygen together with hydrogen are present in
almost all organic compounds which generate living organisms. Water is the source of hydrogen for
organisms and water and nitrogen are the sources for oxygen. Nitrogen is mainly attached in amino acids,
proteins and nucleic acids.

Table 1. Biogenic elements in living and non-living matter.

Chemical element Percent in Living matter Percent in Non-living mater
Carbon, C 19.37 0.18
Hydrogen, H 9.31 0.95
Oxygen, O 62.8 49.4
Nitrogen, N 5.14 0.63
Source: www.kr-jihomoravsky.cz › pptv › chemie › Helešicová

Biogenic Elements:

Biogenic elements are all elements contained in the living matter and is present in compounds in the
form of ions and unbound like oxygen. Biogenic elements are categorized into macrobiogenic,
microbiogenic and trace elements. Trace and microbiogenic are also called oligobiogenic elements.

Group Description Major Elements Function of major elements

Macrobiogenic Building function, and C,H,O,N,S,P,Na,K,Ca, C- basis of living matter,
elements C,H,O,N represent 95% of Mg, Cl,Fe bond to each other and to
living matter other atoms of other
elements

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O and H – part of water,
maybe inorganic or organic,
O- product of photosynthesis
in autotrophs(plants and
cyanobacteria)
N- component of proteins
and nucleic acids, necessary
for mineral plant nutrition
and plant protein synthesis
in the form of nitrates and
ammonium carbonates
Microbiogenic Catalytic function (part of Cu, I, Mo, Mn, Zn, Co
elements enzymes), represent 0.1%
in living organism
Trace Elements Together with Al, As,B, Br, F, Li, Ni,
microbiogenic elements, Se, Si, Ti, V
they are parts of enzymes
and have catalytic function
too., Content is 0.001% in
organisms

Chemical Composition of Living Systems

Living organisms are composed of biomolecules. Based on their molecular weights, substances in living
organism are divided into:

1. Inorganic or Low molecular substances (Mr<10,000):

a. Water
b. Inorganic(mineral) substances
c. Intermediate of metabolic pathways (carboxylic acids etc.)
d. Final products of metabolic pathways like amino acids,, monosaccharides, lipids, nucleotides)
2. Organic or High molecular substances(Mr>10,000) or Biological macromolecules or biopolymers
A. Proteins- amino acids
B. Polysaccharides- monosaccharides
C. Nucleic acids- nucleotides

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Source: www.kr-jihomoravsky.cz › pptv › chemie › Helešicová
Figure 2. Proportions of substances in Living systems.

Water :
The simplest and most frequent biomolecule in living systems. The basic and most spread inorganic
compound confined in living organisms for survival(75% average water content). It possesses unique
properties that make it highly essential in biological systems. It has the ability to dissolve substances and
almost anything- thus considered as the UNIVERSAL SOLVENT. Water help create stable, inner
environment, medium for biochemical reactions, transporting medium and a thermoregulatory.

Acids and Bases:

Acids – substances that release hydrogen ions, have sour taste, react with active metals to form hydrogen
gas, turn blue litmus paper to red
Bases – substances that produces OH ion in water, bitter in taste, corrosive to skin, turn red litmus paper
to blue

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Subtopic 2: BIOMOLECULES OR MACROMOLECULES:

Biomolecules are large group of organic molecules on which most living organisms depend on.
Biomolecules are large molecules composed of many atoms that are covalently bound together. There
are four basic classes of biomolecules namely: carbohydrates, proteins, lipids and nucleic acids. These are
made up mainly of carbon and hydrogen with nitrogen, oxygen, sulphur and phosphorus. These
biomolecules may also include small molecules like metabolites and natural products.
https://www.researchgate.net/publication/323551103_UNIT-I_Biomolecules

Table 2. Major Complex Biomolecules in cells

Biomolecule Building Block/repeating unit Major function
Protein Amino acids Fundamental basis of structure and
function of cell(static and dynamic
functions)
Deoxyribonucleic deoxyribonucleotides Repository of hereditary information
acid(DNA)
Ribonucleic acid (RNA) ribonucleotides Essentially required for protein
biosynthesis
Polysaccharide Monosaccharides(glucose) Storage form of energy to meet short
term demands.
Lipids Fatty acids, glycerol Storage form of energy to meet long
term demands, structural components of
membranes
Source: https://www.biologydiscussion.com/biomolecules/biomolecules-top-4-classes-of-biomolecules/11169

I. CARBOHYDRATES(C,H,O)- hydrates of carbon

The most abundant organic molecules in nature, primarily composed of the elements C, H, and oxygen.
Through hydrolysis, carbohydrates maybe defined as polyhydroxy – aldehydes and ketones. Commonly
know as “sugar “ i.e. water soluble and sweet to taste but are collectively called as saccharides.

DESCRIPTION TYPES FUNCTIONS EXAMPLES

-Good source of Simple: -Substrate for Glucose- main fuel of body
heat and energy Monosaccharides respiration and cells
consisting of oxygen, – simple sugars(most source of energy Fructose-participates in
hydrogen and basic of a carbohydrate) -intermediate metabolism
carbon atoms composed of 3-7 carbon substances for Galactose- found in
-Long chains of atoms respiration erythrocytes with b-type
sugars -have one free aldehyde -energy storage, individual
or ketone group(reducing structure and Mannose- important in
agents thus known as transport human metabolism
reducing sugars -recognition of Ribose/deoxyribose – part
-colorless, crystalline molecules that pass of DNA in chromosomes
white solid through the cell
membrane
*carbohydrate
deficiency causes

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fatigue, poor
mental function

Disaccharides a. Sucrose(sugar)= glucose +

– made up of 2 or more fructose
monosaccharides linked b. lactose(milk) =glucose +
by glycosidic bonds galactose
(through dehydration c. maltose(grain for beer)= 2
synthesis) glucose units
(a and b are sweet,
crystalline and water
soluble substances)

Oligosaccharides a. Trioses-
-fromed by condensation 3C/molecule
of 2-9 monomers called b. Pentoses-
oligosaccharides 5C/molecule
c. Hexoses-
6C/molecule

Polysaccharides Starch(polysaccharides in
- polymers (long chains) plants) - (grains of rice,
of monosaccharides corn and cereals),
-unsweet , insoluble, not composed of linear chain
in crystalline form and amylose and branched
complex carbohydrates amylopectin chains
Cellulose(fiber) -
component of rigid plant
cells walls, main structural
component of cell wall in
plants
Glycogen(animal starch) –
glucose in animals and man
synthesized and stored in
the liver and muscles

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Table 3.Polysaccharides- complex form of carbohydrates that consist of 3 or more sugar units.
Type Composition Source Functions
starch Polymer of glucose containing a Main storage Storage of reserve
straight chain of glucose carbohydrate in plants food
molecules (amylose) and a
branched chain of glucose
molecules (amylopectin)
glycogen Glucose polymer Animals (equivalent to Storage of reserve
starch) food
inulin Fructose polymer Roots and tubers Storage of reserve
food
cellulose Glucose polymer Plant cell wall Cell wall matrix
pectin Galactose polymer and its Plant cell wall Cell wall matrix
derivatives
hemicellulose Pentose polymer and sugar acids Plant cell wall Cell wall matrix
lignin Glucose polymer Plant cell wall(dead Cell wall matrix
cells- sclerenchyma)
chitin Glucose polymer Body wall of Exoskeleton, support
arthropods, in some and protection,
fungi impermeable to water
murein Polysaccharide cross linked with Cell wall of Structural protection
amino acids prokaryotic cells
Hyaluronic acid Polymer of sugar acids Connective tissue Ground substance,
matrix, outer coat of protection
mammalian eggs
heparin Closely related to chondroitin Connective tissue cells anticoagulant
Gums and Polymers of sugars and sugar Gums – bark or trees Retain water in dry
mucilages acids Mucilages - flower season
Source: https://www.researchgate.net/publication/323551103_UNIT-I_Biomolecules

Derivatives of monosaccharides:
1. Amino sugars – replacement one or more hydroxyl groups by amino groups. Examples are : D-
glucosamine, D- galactosamine. They are present as hetero-poly saccharide constituents.
2. Deoxysugar – absence of oxygen in the sugar, eg. D-2_ Deoxyribose- most important
deoxysugar since it is a structural constituent of DNA(in contrast to D-ribose in RNA)
3. L- ascorbic ( vitamin C) – water soluble, closely resemble to monosaccharide

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II. PROTEINS (C,H,O,N)
The most abundant organic molecules of the living system occurring in every cell part and constitute
about 50% of cellular dry weight. It forms the fundamental basis of structure and function of life.
Large, N-containing biomolecules composed of long chains of amino acids (building blocks proteins)
- there are 20 common amino acids which feature different structural arrangements of C, H, O, N and S.
- amino acids combine to form a great variety of protein molecules can compose enzymes, hormones,
antibodies and structural components
The fundamental repeating units of proteins are the amino acids. Amino acids are consist of
amino group(NH2),carboxyl group or acid group(COOH) and body core known as the R group or side chain
which gives the identity of the amino acid.

Source: https://www.biologydiscussion.com/biomolecules/biomolecules-top-4-classes-of-biomolecules/11169
Figure 3. General Structure of an amino acid.

Importance of Proteins
1. They are essential in building and repairing body cells and tissues.
2. Enzymes which are proteins aid in hastening almost all bodily chemical reactions.
3. Proteins bring out the individual’s uniqueness. Each one is unique because of the varied proteins
in our genes.
4. It serves as transport molecules, food reserves, and provide protection as antibodies
Functions of Proteins:
1. Structural functions = primarily responsible for structure and body strength
Types: collagen and elastin in bone matrix, vascular system and keratin in epidermal tissues.
2. Dynamic functions= “work horse” of the cell
Types: enzymes, hormones, blood clotting factors, immunoglobulins, membrane receptors,
storage proteins, genetic control, muscle contraction respiration and antibodies.

Structures of proteins:

Source: https://sphweb.bumc.bu.edu/otlt/mph-modules/ph/ph709_basiccellbiology/ph709_basiccellbiology6.html
Figure 4. Four Levels of Protein Organization

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1. Primary Structure – linear sequence of amino acids. It forms the backbone of
proteins(polypeptides). The unique sequence of amino acids is determined by the genes in the
DNA. These are non-functional proteins.
Peptide bond – formed when the amino group of the amino acid links with the carboxyl group of
another amino acid, ten or more amino acids linked with each other forms a polypeptide.

2. Secondary Structure – spatial arrangement of protein by twisting or folding of the polypeptide

chains. The amino acids are located close to each other in their sequence. Example: silk fiber
Types:
a. Alpha – helix- most common spiral structure of protein, has rigid arrangement of polypeptide
chain. This structure was proposed by Pauling and Corey (1951) and considered as one of the
milestone in Biochemistry research.
b. Beta- sheet- composed of two or more segments of fully extended peptide chains, the
hydrogen bonds are formed between the neighboring segments of the polypeptide chains,
also proposed by Pauling and Corey.
c. Tertiary structure – 3-Dimensional structure of a functional protein

*The stable, compact structure is due to the hydrophobic side chains held interior while the
hydrophilic groups are on the surface of the protein molecule. The bonds present in this structure
are H-bonds, disulfide bonds, ionic interactions(electrostatic bonds) and hydrophobic interactions
which contribute to tertiary structure of proteins.

d. Quaternary Structure – spatial arrangement of two or more identical or unrelated polypeptides

This structure is found in oligomers , proteins with two or more polypeptides. Examples are
hemoglobin and insulin.
Example:
Figure 5 (left photo) - The 3D shape of proteins and concept of specific binding site is important
not only in enzyme-substrate interaction but also for receptors which bind chemical signals in
specific way. Binding of histamine to corresponding receptors causes a change in the protein
conformation that triggers series of biochemical response within the cell- bronchial smooth
muscle cell contraction under asthma attack
Figure 5 (right photo)- Insulin hormone binding to specific insulin receptors embedded in the cell
membrane of fats and muscle cells. Binding of antibody would cause change in shape of the
receptor protein and trigger sequence of biochemical events

Source: https://sphweb.bumc.bu.edu/otlt/mph-modules/ph/ph709_basiccellbiology/ph709_basiccellbiology6.html

Figure 5. Quaternary structure of protein functioning in cell signaling.

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Table 4. Functional classification of proteins.
Protein Group Function
1. Structural proteins Keratin of hair and nails, bone collagen
2. Enzymes or catalytic proteins Hexokinase, pepsin
3. Transport proteins Hemoglobin, serum albumin
4. Hormonal proteins Insulin, growth hormones
5. Contractile proteins Actin, myosin
6. Storage proteins Ovalbumin, glutelin
7. Genetic proteins Nucleoproteins
8. Defense proteins immunoglobulins, snake venom, antibodies
9. Receptor proteins Hormones, viruses

Source: https://www.biologydiscussion.com/biomolecules/biomolecules-top-4-classes-of-biomolecules/11169
Figure 6. Summary of Protein Classification

1. Simple proteins: composed of only amino acid residues.

Globular – spherical in shape, soluble in water or other solvents and digestable
Scleroproteins – fibrous proteins, fiber like shape, insoluble in water and resistant to digestion
2. Conjugated proteins: contain a non-protein moiety(prosthetic or conjugating group
3. Derived proteins – denatured or degraded products of simple and conjugated proteins.
Primary derived proteins – produced by agents like heat, acids, alkali
Secondary derived proteins – hydrolytic products of protein

Organic compounds in Plants: Isoprenoid and Pigments

Isoprenoids or terpenoids or terpenes – found in turpentine oils in high concentrations, composed of a 5C
isoprene unit.

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Table 5. Terpene Classification

Pigments – colored organic compounds found in plants and animals. They have high molecular weight
composed of unsaturated hydrocarbons and cyclic structures.

Types:
1. Tetrapyrroles –
Chlorophyll - most abundant colored compound, the photosynthetic pigment, composed of
tetrapyrrole with nitrogen linked to magnesium
Examples:
a. Chlorophyll c, d,e,a with slight variation in colors, green, greenish blue, greenish yellow
b. Heme in certain proteins like hemoglobin, cytochromes, catalase and lycopene
2. Tetraterpenes – carotenoids
-variable color, generally yellow, orange or red
Examples : P-carotene, xanthophyll, lycopene
3. Anthocyanin – group of flavonoids which represent the natural phenolic products, these are
colored compounds found mostly in flowers and fruits. They contain a common ring structure
called anthocyanidin.
4. Quinoid pigments – present in trace amounts, do not significantly contribute to visible colors but
they are involved in electron transport chain, antioxidant functions.
Examples : benzoquinones, napthoquinones, anthraquinones, tannins and lignins

III. LIPIDS(C,H,O)

-Group of biochemical molecules that have high percentage of C & H atoms.

-Insoluble(fats and oils) in water but soluble in non-polar solvents
-have high energy content and are metabolized to release calories
-esters of fatty acids and are building blocks of biological membranes
-act as electrical insulators(insulate nerve axons)

Fats: contain saturated fatty acids, solid at room temperatures like animal fats, sparingly soluble in
water, soluble in in organic solvents like ether, acetone and benzene
Plant fats: unsaturated, liquid at room temperatures
Pure fats: colorless, bland in taste
- composed of polar head and nonpolar tail. It can be saturated or unsaturated.
- Example of lipids: oils, fats, phospholipids, glycolipids, etc.

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Functions of lipids:

1. -Source of energy and Energy storage

2. -Cell membrane/structural component- form barrier and control flows
3. of material in and out of the cell
4. -Protection and insulation
5. -Digestion and absorption
6. -Help in mediating communication between cells(hormones)
7. -concentrated fuel reserve of the body(triacyglycerols)
8. -constituents of membrane structure and regulate the membrane permeability (phospholipids
and cholesterol)
9. -source of fat soluble vitamins(A, D,E,K)
10. -important cellular metabolic regulator (steroid hormones and prostaglandins)
*Insulating capacity of fats – bad conductors of heat
*emulsification- conversion of lipid mass into small lipid droplets, process before fats can be absorbed
by intestinal wall
* saponification – hydrolysis of fats by alkali (lipases) to yield salts of fatty acids and glycerol –soaps
Hydrolytic rancidity- caused by the microorganisms which secrete enzymes like lipases splitting glycerol
and free fatty acids.

Lipid Classification:

Simple Lipids :
Classification of lipids
1. Simple lipids: Esters of fatty acids with various alcohols.
a. Fats and oils : Esters of fatty acids with glycerol. Oils are fats in the liquid state.
b. Waxes: Esters of fatty acids with higher molecular weight monohydric alcohols.
2. Complex lipids: Esters of fatty acids containing groups in addition to an alcohol and a fatty acid.
a. Phospholipids: Lipids containing, in addition to fatty acids and an alcohol, a phosphoric acid
residue. They frequently have nitrogen containing bases and other substituents, eg, in
glycerophospholipids the alcohol is glycerol and in sphingophospholipids the alcohol is sphingosine.
b. Glycolipids (glycosphingolipids): Lipids containing a fatty acid, sphingosine, and carbohydrate.
c. Other complex lipids: Lipids such as sulfolipids and aminolipids.
d. Lipoproteins macromolecular complexes of lipids with proteins.
3. Precursor and derived lipids: These include fatty acids, glycerol, steroids, other alcohols, fatty
aldehydes, and ketone bodies, hydrocarbons, lipid-soluble vitamins and hormones.
4. Miscellaneous lipids – include a large number of compounds possessing the characteristics of lipids
e.g.carotenoids, squalene, hydrocarbons like pentacosane in bees wax terpenes etc.
5. Neutral lipids – uncharged lipids including mono-,di-, and triacyglycerols, cholesterol and cholesteryl
esters.

Classes of Lipids present in biological membranes:

1. Glycolipids – lipids whose head contains oligosaccharides with 1-15 saccharide residues
2. Phospholipids – contain positively charged head linked to negatively charged phosphate groups
3. Sterols – head contain steroid ring like the steroids

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Fatty acids
Made up of long hydrophobic, non-polar hydrocarbon tail and hydrophilic polar carboxylic acid
functional group at the head

Table 6. Natural fatty acids- Maybe saturated or unsaturated

COMMON FATTY ACIDS
Common Name No. of C atoms Formula
Saturated fatty acids: ( no C=C bonds)
Lauric acid 12 CH3(CH2)10COOH
Myristic acid 14 CH3(CH2)12COOH
Palmitic acid 16 CH3(CH2)14COOH most common
Stearic acid 18 CH3(CH2)16COOH most common
Arachidic acid 20 CH3(CH2)18COOH
Unsaturated:(1 or more double bonds in the hydrocarbon chain)
Palmitoleic acid 16 CH3(CH2)5CH = CH(CH2)7COOH
Oleic acid 18 CH3(CH2)7CH = CH(CH2)7COOH
Linoleic acid 18 CH3(CH2)4(CH = CHCH2)2(CH2)6COOH
Linolenic acid 18 CH3(CH2)2(CH = CHCH2)3(CH2)6COOH
Arachidonic acid 20 CH3(CH2)4(CH = CHCH2)4(CH2)6COOH
Source: https://www.academia.edu/34681920/Module_for_biomolecules

Figure 7. General structure of fatty acid.

Waxes
- lipids that are harder and less greasy compare to fats
- comprised of long fatty acids and monohydric alcohols

Phospholipids
-made up of two fatty acids, glycerol, phosphate and one simple organic molecules like choline
- fundamental building blocks of cellular membranes

Cholesterol
- Most abundant steroid in animal tissues
- Composed of four linked-hydrocarbons rings, with a hydroxyl group at one end and a branched
hydrocarbon chain at the other

Steroids family of lipids that have a backbone structure consisting of four fused C rings

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IV. Nucleic Acids (C, H, O, P, N)

Overview:
-hereditary information molecules of the cell
- direct the instruction of proteins genetic information an organism receives from its parents
- discovered in by Friedrich Miescher in 1869
- identified as genetic material by Oswald Avery, Colin McLeod and Maclyn McCarty in 1940.
- the elucidation of the DNA model were collaboration of the Xray diffraction work of Rosalind Franklin
and Erwin Chargaff, James Watson and Francis Crick in 1953.
- organic compounds with heterocyclic rings
-made up of polymer of nucleotides. Nucleotides are consist of nitrogenous base, pentose sugar and
phosphate group while nucleoside is made of nitrogenous base attached to the pentose sugar.
- carry genetic information in the cell, help synthesize proteins through process of translation and
transcription.

Examples: DNA and RNA which are polymerized nucleotides of the genetic material

Features of the DNA:

1. Double helix – made up of pair of two strand of bases joined by hydrogen bonds forming base
pairs
2. Complementary base pairing – a purine is paired with pyrimidine with corresponding hydrogen
bonds; adenine is doubly bonded with thymine, Cytosine is triply bonded with guanine
Hydrogen bonding between bases is responsible for stability of the molecule and specificity of
base pairing A:T, C:G.
3. Stable – due to hydrogen bonding between bases
4. Specificity of base pairing – most important feature of the Watson Crick model of DNA, provide
replicability of the genetic material and important role in gene function
5. Structurally variable – due to sequences of nitrogen bases in two strand of the DNA molecule.
Variety is supplied by varying order of bases on the lone molecule
6. Anti-parallelism- strands go in opposite directions, one end has free 5’ Phosphate and the other
has 3’hydroxyl group
7. Statistics: each base pair is 3.4Ao or 34nm apart, each turn/twist is 36o(360o involving 10 base
pairs, 34 Ao or 3.4nm, diameter is 20 Ao 0r 2nm, 34o helix pitch, -6 base pair tilt

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Chemical Composition of DNA

Nucleotide

phosphate group nucleoside

2-deoxy-D-ribose
Nitrogen bases
(sugar)

Purines Pyrimidines
Adenine Thymine
Guanine Cytosine

Figure 8. Composition of DNA (deoxyribonucleic Acid).

Source:
https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_an
d_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids
Figure 9. Molecular Structure of DNA

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Source:
https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_an
d_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids
Figure 10. Nucleotides, nucleosides and nitrogen bases of DNA

Source:
https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_an
d_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids
Figure 11. Anti-parallelism in DNA.

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Forms of DNA

Source:
https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_an
d_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids
Figure 12. Forms of DNA – A, B, Z(left to right)

Different forms of DNA exist due to its variability and depends on the sequence as well as the
environment.
1. B- form – right handed double helical Watson-Crick model is the most common in nature and
well known DNA structure
2. A -form - The major difference between A-form and B-form nucleic acid is in the confirmation of
the deoxyribose sugar ring. It is in the C2′ endoconformation for B-form, whereas it is in the C3′
endoconformation in A-form.
** A second major difference between A-form and B-form nucleic acid is the placement of base-
pairs within the duplex. In B-form, the base-pairs are almost centered over the helical axis but in A-
form, they are displaced away from the central axis and closer to the major groove. The result is a
ribbon-like helix with a more open cylindrical core in A-form.
** Right-handed helix
** 11 bp per turn; 0.26 nm axial rise; 28o helix pitch; 20o base-pair tilt
** 33o twist angle; 2.3nm helix diameter
3. Z-form - Z-DNA is a radically different duplex structure, with the two strands coiling in left-
handed helices and a pronounced zig-zag (hence the name) pattern in the phosphodiester
backbone.
 Z-DNA can form when the DNA is in an alternating purine-pyrimidine sequence such as GCGCGC,
and indeed the G and C nucleotides are in different conformations, leading to the zig-zag
pattern.
 The big difference is at the G nucleotide.
 It has the sugar in the C3′ endoconformation (like A-form nucleic acid, and in contrast to B-form
DNA) and the guanine base is in the synconformation.
 This places the guanine back over the sugar ring, in contrast to the usual anticonformation seen
in A- and B-form nucleic acid. Note that having the base in the anticonformation places it in the
position where it can readily form H-bonds with the complementary base on the opposite
strand.

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 The duplex in Z-DNA has to accommodate the distortion of this G nucleotide in the
synconformation. The cytosine in the adjacent nucleotide of Z-DNA is in the “normal” C2′ endo,
anticonformation.
 Discovered by Rich, Nordheim &Wang in 1984.
 It has antiparallel strands as B-DNA.
 It is long and thin as compared to B-DNA.
 12 bp per turn; 0.45 nm axial rise; 45o helix pitch; 7o base-pair tilt
 -30o twist angle; 1.8 nm helix diameter

Conditions favoring different Forms of DNA

1. ionic or hydration environment, which can facilitate conversion between different helical forms.
A-DNA is favored by low hydration, whereas Z-DNA can be favored by high salt.
2. DNA sequence: A-DNA is favored by certain stretches of purines (or pyrimidines), whereas Z-DNA
can be most readily formed by alternating purine-pyrimidine steps.
3. presence of proteins that can bind to DNA in one helical conformation and force the DNA to adopt
a different conformation, such as proteins which bind to B-DNA and can drive it to either A-or Z
forms.
4. In living cells, most of the DNA is in a mixture of Aand B-DNA conformations, with a few small
regions capable of forming Z-DNA

Rare forms of DNA

Table 7. Rare Forms of DNA
Forms Description
of DNA
C-DNA Formed at 66% relative humidity and in presence of Li+ and Mg2+ ions.
Right-handed with the axial rise of 3.32A° per base pair
33 base pairs per turn
Helical pitch 3.32A°×9.33°A=30.97A°.
Base pair rotation=38.58°.
Has a diameter of 19 A°, smaller than that of A-&B- DNA.
The tilt of base is 7.8°
D-DNA Rare variant with 8 base pairs per helical turn
These forms of DNA found in some DNA molecules devoid of guanine.
The axial rise of 3.03A°per base pairs
The tilt of 16.7° from the axis of the helix
E-DNA Extended or eccentric DNA.
E-DNA has a long helical axis rise and base perpendicular to the helical axis.
Deep major groove and the shallow minor groove.
E-DNA allowed to crystallize for a period time longer, the methylated
sequence forms standard A-DNA.
E-DNA is the intermediate in the crystallographic pathway from B-DNA to A-DNA.

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EXTRACHROMOSOMAL OR ORGANELLE DNA

The DNA is present in a cell nucleus known as the genome of an organism, but DNA is also present in
membrane bound organelles specifically mitochondria and chloroplast and these DNA type are called
extrachromosomal or cytoplasmic DNA. This type of DNA is for the synthesis of their own protein
molecules to perform different biological functions.

1. Chloroplast DNA
Chloroplast is the site of photosynthesis. Photosynthesis provides energy source to all living
organisms as the animal cannot produce their own food. The chloroplast pigment, chlorophyll is significant
in the photosynthesis process and energy production by the systemic reaction of photosystem I and II.
Carl Correns first discovered non Mendelian inheritance in Mirabilis jalapa where color
difference in this plant is due to cytoplasmic DNA, located in the chloroplast. The color difference or
variegation is the different colored patches on the leaves where the chloroplast DNA or plastid controls
the color. In addition, chloroplast can synthesized protein in the presence of light or ATP together with
Chlorophylls, cytochrome a and b and other molecules.
Chloroplast has multiple copies of DNA molecules(ranging from 40-60 copies per chloroplast and
differs in different species of plants. Based on the research of Ruth Sager, drug resistant genes are found
on the chloroplast DNA(10% of antibiotic resistance genes in Chlamydomonas algae). In higher plants,
cpDNA ranges from 120-160 kb in size, which could be circular or linear in form.

2 Categories of Chloroplast DNA (cpDNA)

a. Genes that encode for protein synthesis machinery since chloroplast has its own genome and
central dogma machinery. Present genes in the chloroplast are for RNA polymerase subunits,
tRNA and ribosomes.
b. Genes that encode for a specific protein component of the photosystems (I an II) and the gene
encoding for chlor0phyll.

The presence of the fore-mentioned components of the chloroplast (protein synthesis machinery and
genes), can imply the food making process on their own. In animals, food generation is mediated by
symbiotic photosynthetic bacteria in plant cells.

2. Mitochondrial DNA
Mitochondria is a membrane bound organelle, symbiotically situated in the cytoplasm of
eukaryotic cells. This organelle provides energy (ATP) to both plant and animals. ATP, main energy
form for all biological reactions, is produced during the oxidative phosphorylation and fatty acid
synthesis
The mitochondria contain unique circular DNA molecules which code for small number of protein,
having its own protein machinery, specific tRNA, aminoacyl tRNA synthetases, ribosomes and mRNA are
present. If mutational changes happen in the mitochondria it leads to heritable alterations in the
organism, in humans, some of the complex genetic disorders are due to mtDNA mutations. Such genetic
disorders are muscle weakness and muscle discoordination, poor growth, visual and hearing loss, autism
spectrum disorders, heart, liver and kidney problems, learning and developmental disability, neurological
defect and adrenal and thyroid gland defects. In addition, major disorders in mtDNA are congenital
hearing loss, cytochrome C oxidase deficiency, ataxia, Leigh syndrome, Pearson syndrome and creatinine
deficiency syndrome.

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The genome of the mitochondria is smaller and circular and contains only a few genes
(ranging from 16kb-100kb in multiple copies) and perceived as similar to bacteria. The mitochondrial DNA
(mtDNA) is highly conserved or unchanged in higher animals from evolution. It has a single promoter site
(transcribed as one single unit just like bacterial DNA) and has endonuclease cleaving the giant transcribed
DNA into segments of RNA types (tRNA, rRNA and mRNA) . The rRNa size in mitochondria is similar to
bacterial rRNA but smaller than eukaryotic rRNA. Mitochondria has its own membrane like bacterial cell
membrane and is able to synthesize ATP. The protein involved in ATP production is not all encoded by
mtDNA, some are encoded by nuclear DNA just like cytochrome oxidase enzyme(for oxidative
phosphorylation in mitochondria. Synthesis of molecules in mitochondria are governed by mtDNA and
nuclear DNA leading to Non-Mendelian pattern of inheritance and complex in understanding. The
inheritance of mtDNA is only possible for female individuals in the population.

Table 8. Comparison of Extrachromosomal DNA with Nuclear DNA.

Property Nuclear DNA mtDNA cpDNA
arrangement Double helix and non-circular circular Circular or linear
copy 2 copies, one on each 10 to 100 copies per 40to 60 copies per
chromosome mitochondria chloroplast
Inheritance Mendelian Non-Mendelian/Maternal Non-Mendelian
Nuclear envelope present Absent, bounded in absent
mitochondrial membrane
DNA Location Located on chromosomes and Circular and don not Circular or linear
packed into chromatins arrange chromatin and do not arrange
in chromatin
size More than 3 billion base pairs 16 to 100kb 120to 160 kb

RNA- Ribonucleic acids

- Single stranded
- Functions in cellular protein synthesis
- Carrier of genetic codes in viruses
- Composed of ribose nucleotides- nitrogenous bases attached to a ribose sugar
- The nitrogenous bases in RNA are adenine, guanine, cytosine and uracil

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Source: https://www.technologynetworks.com/genomics/lists/what-are-the-key-differences-between-dna-and-rna-296719
Figure 13. Differences between DNA and RNA

Table 9. Differences between DNA and RNA:

Feature DNA RNA
sugar deoxyribose ribose
Number of strands Double stranded Single stranded
Nitrogenous bases Adenine, thymine, cytosine, and Adenine, thymine, cytosine and uracil
guanine
Location Found in nucleus( in chromosome Forms in the nucleolus and moves to
form), and small amount in specialized regions of the cytoplasm
mitochondria and chloroplast depending on the type of RNA formed
Base pairs A-T, C-G A-U, C-G
Length Longer polymer Variable, shorter that long polymer
Reactivity Due to its deoxyribose sugar, which RNA, containing a ribose sugar, is
contains one less oxygen containing more reactive than DNA and is not
hydroxyl group, DNA is more stable stable in alkaline conditions. RNA’s
than RNA, which is useful for a larger helical grooves mean it is more
molecule which has the task of easily subject to attack by enzymes.
keeping genetic information safe
UV sensitivity DNA is vulnerable to damage by UV RNA is resistant to damage from UV
light
Function Encodes all genetic information, Reader that decodes the genetic
blueprint of life, storage device which information
allows to pass these information
between generations

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Types and functions of RNA
 Messenger RNA(mRNA) – copies portion of the genetic code via the process of
transcription, transports the copies to ribosomes(cellular protein factories), found in the
nucleus
 Transfer RNA (tRNA) – responsible for carrying the amino acids, basic protein building
blocks to the ribosomes via translation, free roaming molecule in the cytoplasm
 Ribosomal RNA (rRNA) – component of the ribosome factory for without it no protein
synthesis., found as part of ribosomes.
 Coding RNA(cRNA)
 Non coding RNA (ncRNA):
a. Housekeeping ncRNA- tRNA and rRNA
b. Regulatory ncRNA – classified according to their size
i. Long ncRNA- at least 200 nucletofdes
ii. Small ncRNA – fewere than 200 nucleotides

 Subdivision of small ncRNA

a. microRNA (miRNA)- about 22 nucleotides long and function in gene regulation in most
eukaryotes, can silence(inhibit) gene expression by dinging to target mRNA and inhibiting
translation, thus preventing functional proteins from being produced. Also play significant roles
in cancer and other diseases examples: tumor suppressor and oncogenic (cancer0-initiating)
miRNAs can regulate unique target genes, leading to tumorigenesis and tumor progression
b. small nucleolar RNA (snoRNA)
c. small nuclear RNA (snRNA)
d. small-interfering RNA (siRNA)
e. PIWI-interacting RNA (piRNA)- about 26-31 nucleotides long and exist in most animals,
functions as regulator of expression of transposons (jumping genes) by keeping the genes from
being transcribed in the germ cells (sperm and eggs), complementary to different transposons
and can specifically target those transposons.
f. circular RNA (circ RNA) - unique from other RNA types because its 5’ and 3’ ends are bonded
together, creating a loop. They are generated from many protein-encoding genes and can serve
templates for protein synthesis similar to mRNA. They can bind miRNA, acting as “sponges” that
prevent miRNA molecules from binding to their targets. They also play an important role in
regulating transcription and alternative splicing of the genes from which circ RNAs were derived.

RNA in Diseases:
 miRNA capable of regulating cancer- associated genes which facilitate in tumor
development
 miRNA metabolism dysregulation linked to neurodegenerative diseases like Alzheimer
disease

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 tRNA bound to specialized proteins known as caspases(involved in apoptosis -
programmed cell death) would inhibit apoptosis, escaping apoptosis s ignaling is an
assurance of cancer
 tRNA derived fragments (tRFs)- play a role in cancer
 identification of novel classes of tumor-specific RNA transcripts- MALAT1 (metastasis
associated lung adenocarcinoma transcript), associated with the proliferation and
metastasis(spread) or tumor cells
 RNA class containing repeat sequences that sequester RNA binding proteins(RBPs) result
to aggregates in neural tissue and these aggregates play in the development of
neurological diseases such as amyotrophic lateral sclerosis(ALS) and myotonic dystrophy
 The discovery of additional links between RNA and disease is expected. Increased understanding
of RNA and its functions, combined with the continued development of sequencing technologies
and efforts to screen RNA and RBPs as therapeutic targets, are likely to facilitate such discoveries.

Functions:
a. Primarily carry out biochemical reactions similar to enzymes
b. Complex regulatory functions cells
c. Play important roles in both normal cellular processes and disease

 Summary:
 Biomolecules, also, are fundamental building blocks of living organisms, and therefore,
the presence and appropriate concentrations of biomolecules are vital for the structure
and proper function of living cells.
 Biomolecules are composed of macromolecules such as carbohydrates, proteins, lipids
and nucleic acids.
 Carbohydrates are classified into monosaccharides, disaccharides and polysaccharides.
Among the carbohydrates, glucose is the most important source of energy.
 Proteins are polymers of different amino acids, 20 of which are essential. Proteins have
its own unique sequence and shape held together by chemical interactions. Proteins
structure may change without losing its primary sequence through the process of
denaturation. Denaturation is affected by changes in temperature, pH or chemical
exposure. Protein folding is critical to its function.
 Lipids make up the building blocks of the structure and function of living cells. Lipids
include fats, oils, waxes and steroids including vitamins and hormones.
 Nucleic acids are important molecules in storing and transmitting hereditary
information through generations. These molecules are represented by DNA and RNA.
DNA is the genetic material of most eukaryotic organisms and RNA is the genetic
material of some viruses.

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References:

Book/s:
Karp G. 2005. Cell and Molecular Biology: Concepts and Experiments. 4th ed. John Wiley and Sons, Inc.
pp. 32-85.

e-Book:
Karp, G. 2020. Cell and Molecular Biology: Concepts and Experiments. Retrieved from: epdf.pub_cell-
and-molecular-biology-concepts-and-experiments.pdf

Online Resources:

Notes of Molecular Biology of the Cell by Alberts. 2019. Biolympiads. Retrieved from:
https://biolympiads.com/notes-of-molecular-biology-of-the-cell-by-alberts/

Biomolecules. 2020. Ncert. Retrieved from : http://ncert.nic.in/textbook/pdf/lech205.pdf

UNIT I – Biomolecules. 2018. Research Gate. Retrieved from:
https://www.researchgate.net/publication/323551103_UNIT-I_Biomolecules

https://www.duncanvilleisd.org/cms/lib6/TX01917816/Centricity/Domain/592/Test%20Summary%20Sh
eet.15.16.Unit%203.pdf

Different forms of DNA-A form, B-Form, Z-form. 2019. Microbe Notes. Retrieved from:
https://microbenotes.com/different-forms-of-dna-b-form-a-form-z-form/

RNA-Definition, Structure, Types and Functions. Retrieved from:

https://www.britannica.com/science/RNA

DNA: Definition, Structure, Function, Evidence and Types. 2018. Retrieved from:
https://geneticeducation.co.in/dna-definition-structure-function-evidence-and-types/

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