22BIO201: Intelligence of

Biological System-1

By
Dr. S. S. Kalaivani
Amrita School of AI
Google Scholar Link:
https://scholar.google.co.in/citations?user=4-
SwqD0AAAAJ&hl=en&oi=ao 1
 Objective
❖ Understanding the basic concepts about biomolecules, cell
division, central dogma of the cell, mutations and evolutionary
patterns.
❖ Knowledge about biological databases, bacterial genomes and its
hidden message.
❖ Understanding the mechanism of DNA methylation in circadian
rhythm.
❖ Application of statistical methods in sequence analysis and motif
finding.

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 Course Objective
CO1: Apply the cellular structure and biophysical process for creating
engineered models.
CO2: Incorporate the application of molecular mechanisms to build
advanced computational pipelines.
CO3: Apply statistical estimation and test of significance techniques for
Motifs and to learn python for using biological databases.
CO4: Apply chaos model to represent DNA Sequences.

L-T-P-C: 2- 0- 0- 2

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 Syllabus
Unit 1
Classification of Biomolecules Cell division: Mitosis and Meiosis;
Central Dogma of the cell: Replication, Transcription, Translation, Protein
Synthesis; Genetic Variants of Evolutionary Patterns: Mutations and
Polymorphisms.
Unit 2
Introduction to biological databases – Hidden messages in the genome –
Finding Replication Origins–Frequent words in Vibrio cholera – Encodings in DNA
to maintain circadian rhythm. Basics of Probability – Probability Distributions.
Unit 3
Statistics-Statistical Estimation and Inference of Sequence Analysis in
Matlab and Python. Simple values, names, expression, module, collection,
sequences, mapping and expression feature. Hunting for Regulatory Motifs –
Scoring Motifs - Motif Search – Greedy & Randomized Motif Search – Gibbs
Sampling – Chaos representation-DNA sequences comparison of related viruses.

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Evaluation Pattern

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 Introduction
Why we will learn Computational Biology?
Nowadays, biological data is being generated at an
unprecedented rate. In the era of data science, the data
science industry needs skilled employees to manage,
analyse, and interpret these vast datasets, enabling them to
gain insights into complex biological processes.
Data science

Domain
knowledge Statistics

Computer
Science

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Computational Biology Problems
1. Sequence Analysis - DNA/Protein Sequence Alignment, Genome Assembly, Motif Discovery
2. Structural Biology - Protein Structure Prediction, Molecular Docking.

3. Functional Genomics - Gene Expression Analysis, Gene Regulatory Networks

4. Systems Biology - Pathway Analysis, Metabolic Network Modeling

5. Evolutionary Biology - Phylogenetic Analysis, Comparative Genomics

6. Population Genetics - Genetic Variation Analysis, Genome-Wide Association Studies

7. Biomedical Informatics - Disease Gene Prediction, Drug Discovery

8. Imaging Informatics - Medical Image Analysis

9. Synthetic Biology - Gene Circuit Design
10. Single-Cell Analysis - Single-Cell RNA-seq Analysis

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Industry working on Life-Science data

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 Some Terminology

• Genome: An organism’s genetic material ( complete set of DNA)

– a bacteria contains about 600,000 DNA base pairs
– human and mouse genomes have some 3 billion
– consists of one of more chromosomes

• Gene: A discrete unit of hereditary information located on the chromosomes

and consisting of DNA bases (or nucleotides). It encodes instructions on how
to make proteins.

• Genotype: It is an organism and complete set of genetic material.

• Phenotype: It is individual’s observable physical properties of an organism,

such as, Height, Eye Colour and blood Type etc.,

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 All life depends on 3 critical molecules
• DNAs
– Hold information on how cell works
– Made of 4 types of nucleotides
• RNAs
– Act to transfer short pieces of information to different parts of cell
– Provide templates to synthesize into proteins
– Also made of 4 types of nucleotides
• Proteins
– Make up the cellular structure
– large, complex molecules made up of 20 types of smaller subunits called amino
acids
– Form enzymes that send signals to other cells and regulate gene activity
– Form body’s major components (e.g., hair, skin, etc.)

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Nitrogenous Bases

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 Double Helix of DNA
The double helix of DNA has these features:
➢ Concentration of adenine (A) is equal to thymine (T)
➢ Concentration of cytidine (C) is equal to guanine (G).
➢ Watson-Crick base-pairing A will only base-pair with T, and C
with G
▪ Base-pairs of G and C contain three H-bonds,
▪ Base-pairs of A and T contain two H-bonds.
▪ G-C base-pairs are more stable than A-T base-pairs
➢ Two polynucleotide strands wound around each other.
➢ The backbone of each consists of alternating deoxyribose and
phosphate groups

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