Lecture-2

Biomolecules
 Goal

Goal of molecular cell biology - to understand the physiology

of living cells in terms of the information that is encoded in
the genome of the cell
How computer science can help
in achieving this goal?

 To identify where are the genes in the genome, which gene is

expressed when, where and how much, what factors affect its
expression, what’s its function, what happens in the disease
state, what are the genetic variations and how to identify
them, etc.
What kind of biological data analysis helped in combating
COVID-19 disease?
 What kind of analysis can we carry out to know about
the virus causing COVID-19?
• How to identify if a person is infected with SAR-COV-2?
• Is it the only known human coronavirus?
• Compare its genome with other viral genomes – to identify its
closest relative
• What proteins aid in its transmission and infection?
• Identify drug targets and develop vaccines
• What organs/tissues are affected by its infection?
• Its rate of propagation
• Is it mutating and becoming more virulent, or milder with
time, etc.
 Cells
All living things are made of cells: small, membrane-enclosed
units - have the ability to create copies of themselves by
growing and dividing in two - replication
E. B. Wilson: “the key to every biological problem must be
sought in the cell; for every living organism is, or at some time
has been, a cell.”
~ 1013 cells that form a human body, the whole organism has
been generated by cell divisions from a single cell
Cells are fundamental units of life
- the vehicle for all the hereditary
information that defines each species.

Study of the structure, function, and

behavior of cells is called Cell Biology
 Cells and Chromosomes
• All cells store their hereditary information in the same linear
chemical code: DNA (Deoxyribonucleic acid)
- organized in coiled structures called chromosomes.
• Chromosomes are physically separate molecules that range in
length from 50 - 250M base pairs.
• In most prokaryotes, each cell has a single chromosome.
• In eukaryotes, all cells contain same number of chromosomes,
8 in fruit flies, 46 in humans and bats, 84 in rhinoceros.
• In multi-cellular organisms, similar cells join together to form
tissues.
• Complete DNA content of an organism is
called the genome.
 Living organism divides into two major groups:
• Prokaryotes - cells with no nucleus, e.g., bacteria and
archaea
• Eukaryotes – cells with a nucleus, e.g., plants, animals
and protozoas. These maybe unicellular (e.g., Yeasts)
or multi-cellular (e.g., humans).
 Viruses
Viruses do not fall in either of the two divisions.
These are acellular entities with many of the properties
of other life forms but are genetically and structurally
too dissimilar to fit into the taxonomy scheme.
Viruses cannot be classified as living or non-living. They
can replicate & carry out their functions only in a host –
called obligate parasites.
May contain DNA or RNA as their nuclear material.
Viruses are acellular. So, if they do not have a cell, how
does their genetic material remain intact?
 DNA
DNA (Deoxyribonucleic acid):
Composed of four basic units - called nucleotides
Each nucleotide contains - a sugar, a phosphate and one of the
four bases:
Adenine (A), Thymine (T),
Guanine (G), Cytosine (C).
 DNA
Bases: are ring-shaped and come in four types which fit
together in pairs - this pairing forms the basis of information
carrying capacity of DNA.
These are categorized as:
Pyrimidines Purines

Base Pairing: C  G, A  T
 DNA
Backbone of a polynucleotide strand is made of linked sugar-
phosphate-sugar-phosphate, with one base joined to each
sugar molecule.

- built by creating a phosphodiester

bond that links 3′ carbon on the
sugar of growing chain with the
phosphate attached to 5′ carbon of
an incoming nucleotide.

DNA Strand
 DNA
Base Pairing: If two polynucleotide strands face each other, sugar-
phosphate backbone runs down each side, and complementary
pairs of bases in the middle spontaneously form hydrogen bonds:

Triple bond: C-G

Left Strand: 5’ to 3’:

phosphate connected to 5’ of
sugar which is connected at
3’ to the next phosphate Double bond:
A-T
What is the sequence on
both the strands?

Note: two strands are not mirror images

of each other - they run antiparallel
 DNA
Double-Stranded DNA: Nucleotides within each strand are
linked by strong (covalent) chemical bonds; complementary
nucleotides on opposite strands are held together by weak
hydrogen bonds:

Why does DNA form

a helical structure?

To minimize the
destabilizing effect
of water molecules
Double-Stranded DNA: If the sequence in the forward strand
in 5 to 3 direction is:
5 CATTGCCAGT 3
Then what would be the sequence on the reverse strand when
read in 5 to 3 orientation?
 DNA
If the sequence in the forward strand in 5 to 3 direction is:
5 CATTGCCAGT 3
Then what is the sequence on the reverse strand when read in
5 to 3 orientation?
First write its complement:
5 CATTGCCAGT 3
3 GTAACGGTCA 5
When read in 5 to 3 orientation, the sequence on the reverse
strand is:
5 ACTGGCAATG 3
 DNA Replication
In living cells DNA is not synthesized as a free strand in
isolation, but on a template formed by a pre-existing DNA
strand.

Copying of genetic information

by DNA replication

templated polymerization
 Central Dogma of Molecular Biology
All cells transcribe portions of their hereditary information
into the same intermediary form: Ribonucleic acid (RNA).

DNA expresses its information, by

letting the information guide the
synthesis of other molecules in the
cell: RNAs and Proteins
Process begins with a templated
polymerization called transcription,
for the synthesis of RNA.
In the more complex process of
translation, these RNA molecules
direct the synthesis of proteins
Ribonucleic Acid (RNA):
It is single-stranded molecule
Composed of four basic units - called nucleotides:
Each nucleotide contains - a sugar (ribose), a phosphate and
one of the four bases: Adenine (A), Uracil (U), Guanine (G),
Cytosine (C)
RNA polynucleotide strand is built by creating a
phosphodiester bond between nucleotides.
Intra-strand base pairing is a characteristic feature of RNA
Base Pairing – formed by weak H-bonds and follows the
following complementarity rule:
G C, A U, and G U
 Ring Structure of Nucleic Acid bases
Adenine (A) Guanine (G)

H H O
N
N H
N Purines N
N
N H
N N N N
H H H

Cytosine (C)
Uracil (U)
H H
N
Pyridimines
N

N O
H
 RNA
Nucleotide pairing between different regions of the RNA
polymer chain causes the molecule to adopt a distinctive shape.
sugar-phosphate
backbone

Base pairing:
G-C, A-U, G-U

Distinct shapes of RNA molecules resulting from such internal

associations enable it to recognize other molecules by binding to them
selectively, or, in certain cases, catalyze chemical changes in the
molecules that are bound.
RNA Synthesis:
RNA is also read in the 5 to 3 orientation.

RNA molecules that are copied from the genes (which

ultimately direct the synthesis of proteins) are called
messenger RNA (mRNA) molecules.
 RNA Synthesis

1. For the following DNA sequence in the forward strand:

5 CATTGCCAGT 3
What will be the sequence of the RNA strand synthesized?

2. If the following DNA sequence is used as template for RNA

synthesis:
5 CATTGCCAGT 3
Give the sequence of the RNA strand read in 5 to 3
orientation.
 RNA Synthesis
1. If the DNA sequence in the forward strand is given as:
5 CATTGCCAGT 3
Template sequence used for RNA synthesis is its complement:
5 CATTGCCAGT 3
3 GTAACGGTCA 5 template

The synthesized RNA sequence is the reverse complement of

the template:
3 GTAACGGTCA 5 template
5 CAUUGCCAGU 3 RNA

- i.e., synthesized RNA sequence is basically the DNA sequence

in the forward strand with T replaced by U
 RNA Synthesis
If the template DNA sequence for RNA synthesis is given:
5 CATTGCCAGT 3
First write its complement:
5 CATTGCCAGT 3
3 GUAACGGUCA 5 complement
Then the synthesized RNA sequence in 5 to 3 orientation is:
5 ACUGGCAAUG 3 RNA

- i.e., synthesized RNA sequence is basically the complement of

the template DNA sequence with T replaced by U, when read in
the 5 to 3 orientation
RNA Synthesis:
There are other RNA molecules also obtained from genes.
The final product in such cases is RNA.
These RNAs are known as noncoding RNAs because they do
not code for protein.
e.g., in yeast Saccharomyces cerevisiae, over 1200 genes
(~15%) produce RNA as their final product; Humans may
produce on the order of 10,000 noncoding RNAs.
These RNAs, like proteins, serve as enzymatic, structural,
and regulatory components for a wide variety of processes in
the cell.
Note: rRNA, tRNA and snRNA play an important role in protein synthesis
 Protein Synthesis
Proteins are synthesized from DNA in a two-step process:

Each chromosome has several genes

that code for various traits in the body.
RNA molecules direct synthesis of
proteins in a process called translation
- information in mRNA is read out in
groups of three nucleotides, called
codons.
 The Genetic Code

Start
codon

The genetic code is degenerate

 Protein Synthesis
Using the genetic code, obtain the amino acid sequence
synthesized from the following mRNA sequence:
5 ACU GGC AAU 3
Thr Gly Asn
This genetic code is read out by a class of small RNA
molecules, called transfer RNAs (tRNAs).
- each type of tRNA attaches at one end a specific amino acid
and at its other end has a specific sequence of 3 nucleotides
- an anticodon that enables it to recognize, through base-
pairing, a particular codon in the mRNA sequence.
- This process occurs on ribosome, a large multi-molecular
machine composed of both proteins and ribosomal RNA.
 Proteins
Like DNA and RNA, Proteins carry information in linear
sequence on a 20-letter alphabet, called amino acids:

ATRVGTCWPRA
Protein structure is divided in 4 hierarchical levels:
• Primary structure - represented by AA sequences

• Secondary structure - -helices & -sheets

peptide bond
• Tertiary and Quaternary structures
- represented by 3D structures

Backbone - N-C-C sequence

Primary Structure: ATRVGTCWPRA

-helix

Secondary
Structures
-sheets

Tertiary Structure Quaternary Structure

 Function of Proteins
• Proteins make up much of the cellular structure – hair, skin,
fingernails, etc.
• Enzymes – catalyze chemical reactions within the cell
• Transcription factors – regulate the manner in which genes
direct production of other proteins
• Receptors – proteins on the surface of cells act as receptors
for hormones and other signaling molecules
• Recognize and bind to Nucleic acids (DNA, RNA) and other
Proteins – to carry out their functions in the cell
 Genes
Special sequences in the DNA code for genes:
• Protein-coding genes, for which the final product is a
protein.
- Same gene may give rise to more than one protein (~ 6
per gene in humans).
• Non-coding RNA genes - for which the final product is
RNA
Genotype – An organism's genotype is the set of genes that it
carries.

Phenotype – An organism's phenotype is all of its observable

characteristics which are influenced both by its genotype and
by the environment e.g., height, hair colour, levels of
hormones, etc.
Differences in the genotypes can produce different phenotypes

Genes for ear form are

different, causing one of the
cats to have normal ears and
the other to have curled ears

A change in environment also

can affect the phenotype.
Pinkness is not encoded in the
genotype of flamingos – but the
food they eat – brine shrimp and
blue-green algae from which
they obtain a natural pink dye,
canthaxanthin.
 Analyze Network of Networks

Types of interactions:
(1)enzyme catalysis,
(2)posttranscriptional control of gene
expression by proteins
(3)effect of metabolite on gene
transcription mediated by protein
(4)protein-protein interaction
(5)effect of a downstream metabolite
on transcription through binding
by protein
(6)Feedback inhibition/activation of
an enzyme by a metabolite
(7)exchange of a metabolite with
outside of the system (eg ,cell)

Complexity and interdependency of biochemical networks

 Genes
The biological function of a gene is to preserve and express
the genetic information encoded within it
Genes are normally very stable entities
Genetic stability is not absolute, however.
Genes may occasionally become altered; these changes called
mutations create new alleles.
Mutant genes are also stable entities and are inherited in the
same way as normal, wild-type genes.
 Genes
Normal diploid cells of humans contain two sets of genes –
one set inherited from each parent.
- corresponding genes derived from each parent are called
alleles.
Together the two alleles govern the phenotype of an
organism.
What is the percentage of genes in a genome?
 Genes
Gene-fraction varies from ~70% in prokaryotes to ~2 - 3% in
humans
- does that imply prokaryotes have more gene content than
eukaryotes?
- Size of a prokaryotic genome? Eukaryotic genome?
What is the function of the remaining ~97-98% of H. genome?
Major part of the genome is repetitive (~50%), and the
remaining part consists of noncoding regions, whose functions
may include providing chromosomal structural integrity and
regulating where, when, and in what quantity proteins are
made.
 Mutations
Mutations - are local changes in the
DNA content, caused by inexact
replication and are of various kinds:
• Substitution - a base is replaced by
another - may or may not alter the
protein sequence depending on the
place it occurs.
• Insertion/Deletion – addition/removal
of one or more bases – results in a
frame-shift in coding regions.
• Rearrangement - a change in the
order of complete segments along a
chromosome – large scale variation
 Mutations
Role of Mutations:
• Mutations are the source of phenotypic variation on which
natural selection acts, creating species & changing them.
Without mutations there wouldn’t be any evolution!
• They are responsible for inherited disorders and diseases,
which involve alterations in gene.
• Large scale rearrangements are responsible for creating new
species, e.g., the human and mouse genome are very similar –
major difference being the internal order of DNA segments.
Chromosomal rearrangements
occur both within and between
chromosomes during evolution

The colors on the mouse

chromosomes and the numbers
alongside indicate the human
chromosomes containing
homologous segments.
Steps Leading from Gene to Protein

Prokaryotes

Eukaryotes
 Gene Structure

TAG/TGA

UTR: Untranslated region

 Eukaryote Gene Structure
Start codon: ATG Stop Codon: TAA/TAG/TGA

Splice sites: GT/AG

Primary RNA transcript

Transcription is initiated only at certain specific positions in the

sequence, signaling the beginning of genes, called promoters.
 Alternative Splicing
• In many cases, the pattern of splicing can vary depending on
the tissue in which the transcription occurs.
e.g., an exon maybe spliced in the gene transcribed in liver,
but retained when transcribed in the brain.
• This variation called alternative splicing, contributes to the
overall protein diversity in the organism
 Alternative Initiation
• Another type of variation that contributes to protein diversity
is alternative initiation

• Alternative translation is an important mechanism of post-

transcriptional gene regulation leading to the expression of
different protein isoforms originating from the same mRNA
 Data Representation
DNA - a complex, dynamic, three-dimensional molecule
represented as a string of alphabets

- a perfect representation for computer analysis

 Data Representation
For all computational purposes, a DNA sequence is
considered to be a string on a 4-letter alphabet: A, T, G, C
ACGCTGAATAGC
Aim: to find grammar & syntax rules of DNA language based
on this 4-letter alphabet
- similar to English Grammar to form meaningful sentences
Similarly, RNA sequence is represented as a string of 4
alphabets and protein sequence a string of 20 alphabets
 Biological Sequence Analysis

Pattern Recognition:
Assumption in biological sequence analysis:
- strings carrying information will be different from
random strings
If a hidden pattern can be identified in a string, it must
be carrying some functional information
 Biological Sequence Analysis
Order of occurrence of bases:
not completely random

- Different regions of the genome exhibit different patterns of

the four bases, A, T, G, C
e.g., protein coding regions, regulatory regions, intron/exon
boundaries, repeat regions, etc.

Aim: Identify various patterns to infer their functional roles

 Example
⬧ ⬧  ⚫⧫◆ ◼
◼⧫⬧

⬧ ⚫⚫  ⬧⧫

◼❖ ◼⬧◆

This is a lecture on bioinformatics

asjd lkjfl jdjd sjftye nvcrow nzcdjhspu

 Frequency of letters
A. 7.3% N. 7.8%
B. 0.9% O. 7.4%
C. 3.0% P. 2.7%
D. 4.4% Q. 0.3%
E. 13.0% R. 7.7%
F. 2.8% S. 6.3%
G. 1.6% T. 9.3%
H. 3.5% U. 2.7%
I. 7.4% V. 1.3%
J. 0.2% W. 1.6%
K. 0.3% X. 0.5%
L. 3.5% Y. 1.9%
M. 2.5% Z. 0.1%
 Other statistics
Frequencies of the most common first letter of a word, last
letter of a word, doublets, triplets, etc.

20 most used words in written English

- the of to in and a for was is that on at he with by be it an
as his
20 most used words in spoken English
- the and I to of a you that in it is yes was this but on well
he have for
 Parallels in DNA language
ATGGTGGTCATGGCGCCCCGAACCCTCTTCCTGCTG
CTCTCGGGGGCCCTGACCCTGACCGAGACCTGGGCG
GGTGAGTGCGGGGTCAGGAGGGAAACAGCCCCTGC
GCGGAGGAGGGAGGGGCCGGCCCGGCGGG

GTCTCAACCCCTCCTCGCCCCCAGGCTCCCACTCCA
TGAGGTATTTCAGCGCCGCCGTGTCCCGGCCCGGCC
GCGGGGAGCCCCGCTTCATCGCCATGGGCTACGTGG
ACGACACGCAGTTCGTGCGGTTC
 Parallels in DNA language
ATG GTG GTC ATG GCG CCC CGA ACC CTC TTC
CTG CTG CTC TCG GGG GCC CTG ACC CTG ACC
GAG ACC TGG GCG GGT GAG TGC GGG GTC AGG
AGG GAA ACA GCC CCT GCG CGG AGG AGG GAG
GGG CCG GCC CGG CGG…

GTC TCA ACC CCT CCT CGC CCC CAG GCT CCC ACT
CCA TGA GGT ATT TCA GCG CCG CCG TGT CCC
GGC CCG GCC GCG GGG AGC CCC GCT TCA TCG
CCA TGG GCT ACG TGG ACG ACA CGC AGT TCG
TGC GGT TC…

1st exon and 1st intron of Human HLA gene

This task needs to be automated because of the large genome
sizes:

Smallest genome:
Mycoplasma genitalium 0.5 x 106 bp

Human genome: 3 x 109 bp – not the largest!

~ 10-100 times the Britannica Encyclopedia
Plant genomes are even larger.
 DNA Sequence Analysis
– Evolution has operated on every sequence that we see today
- genes and sequences involved in gene regulation are
conserved.
– these are transferred, like code modules, from one organism
to another.
– Because of evolution, similar sequences have similar
functions.
– Algorithms for comparing sequences and finding similar
regions are at the heart of computational biology.