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CSE 516/CSE 446 Introduction To Bioinformatics: Presented by Dr. Shazzad Hosain Asst. Prof. EECS, NSU

This document provides an overview of the course CSE 516/CSE 446 Introduction to Bioinformatics. It discusses key textbooks, the mark distribution, and covers topics like the molecular biology of the cell, how the first cell may have come into existence from organic molecules on early Earth, the development of self-replicating RNA molecules, the emergence of the first protocells defined by membranes, and how DNA eventually became the primary hereditary material in cells while RNA and proteins took on other roles.

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Alimushwan Adnan
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49 views

CSE 516/CSE 446 Introduction To Bioinformatics: Presented by Dr. Shazzad Hosain Asst. Prof. EECS, NSU

This document provides an overview of the course CSE 516/CSE 446 Introduction to Bioinformatics. It discusses key textbooks, the mark distribution, and covers topics like the molecular biology of the cell, how the first cell may have come into existence from organic molecules on early Earth, the development of self-replicating RNA molecules, the emergence of the first protocells defined by membranes, and how DNA eventually became the primary hereditary material in cells while RNA and proteins took on other roles.

Uploaded by

Alimushwan Adnan
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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CSE 516/CSE 446

Introduction to Bioinformatics
Presented By
Dr. Shazzad Hosain
Asst. Prof. EECS, NSU
Books
• Molecular Biology of the Cell – by Bruce
Alberts, Alexander Johnson
• Algorithms on Strings, Trees and Sequences –
by Dan Gausfield
• An Introduction to Bioinformatics Algorithms
- by Neil C. Jones, Pavel A. Pevzner
Mark Distribution
Items Percentage
Attendance 5%
Quizzes 20% Best 4 out of 5
Assignments 15%
Mid Term 20%
Final Project 10%
Final 30%

There will be no makeup for quizzes or exams.


Chapter 1: Molecular Biology of the Cell

• What is cell?
• Why so many species?
• Evolution of the Cell by natural selection
– Random variation in the genetic information
– Selection in favor of genetic information.
• How the first cell comes into existence?
From molecules to the first cell
• Condition of earth billions of years before?
– Was the surface initially molten?
– The atmosphere contains ammonia or methane?
– We do not know exactly
• But everyone seems to agree
– Earth was a place of volcanic eruptions, lightning,
torrential rains
– Little free oxygen or no ozone layer to absorb
ultraviolet rays from sun
From molecules to the first cell, cont.
• Organic molecules were likely produced under
such condition

HCHO Formaldehyde
HCOOH Formic acid
HCN Hydrogen cyanide

Undergo further reactions


From molecules to the first cell, cont.

• Major classes of molecules such as amino


acids, sugars and the purines and pyrimidines
required to make nucleotides can be produced
• Over tens to hundreds of millions of years, at
some point of time and place very likely to
form simple organic molecules
Developing Complex Chemical Systems
• Amino acids and nucleotides can associate to
form polymers
– Amino acid + amino acid forms peptide bond
– Nucleotide + nucleotide by phosphodiester bond
• Repetition of these reactions lead to
– Polypeptide, known as proteins
• Only 20 different amino acids join to form proteins
– Polynucleotide, known as DNA and RNA
• Only 4 types of nucleotides form DNA / RNA
– Adenine (A), Cytosine (C), Guanine (G)
– Uracil (U) for RNA or Thymine (T) for DNA
Developing Complex Chemical Systems
What is Life?
• The Crucial Property: Ability to reproduce itself
– In other way: Ability to catalyze reactions that
directly / indirectly reproduce the catalyst itself
• What is Catalyst?
– That promotes/helps other reactions
• Life has autocatalytic property
• Polymers acts as catalyst, can replicate
themselves
Life as replication
• What molecules have autocatalytic property?
– Polypeptides are versatile catalysts in present cells
– But no known protein that directly replicates itself
• Poly-nucleotides contrast with polypeptides
– Limited capabilities as catalysts
– But exactly copies itself
Replication of Poly-nucleotides
Replication of Poly-nucleotides, cont.
Structure of RNA Molecules
The structure determines
• Its own stability
• Personality, i.e. actions on other
molecules
• Ability to replicate and so on
RNA possess two properties
• Genotype
– The hereditary information
• Phenotype
– The expression of the genetic information
Natural Selection
• Depends on the environment
• Presence of other RNA molecules
• Some RNA molecule splice other RNA
molecules
• Self splicing RNA molecule
• Reaction depends on specific arrangement of
molecules (ribosome) that forms on the
surface of RNA
The Cooperative System

• Consider an RNA molecule that


catalyze any RNA replication
• It can catalyze to replicate itself, fig. a
• Also catalyze other RNA, fig. b
• The cooperative system then replicates with great efficiency
• It will compete with other systems
Self Replication is conditioned
• Replication requires some catalyst
• Known as enzymes, mostly proteins
Membranes Defined the First Cell
Head hydrophilic
Tail hydrophobic
DNA as the hereditary material
• This is speculative evolutionary process
– No fossil record, but evidence shows the feasibility
• Present day simplest cell is mycoplasma
• First cell is more primitive than mycoplasma
• Today DNA is the hereditary info repository
• RNA played this role in early cells
DNA the double helix form
• Double helix is more stable
– Replication is easy
– Repair mechanism is easy
– Guides synthesis of RNA (two types)
• Messenger RNA or mRNA, which synthesize protein
• Ribosomal RNA or non-mRNA works as catalyst
• Suggests that
– RNA DNA evolution
– DNA took the responsibility of hereditary info
– Protein remains the major catalyst
– RNA as the intermediary
– RNA DNA evolution
– DNA took the
responsibility of
hereditary info
– Protein remains the
major catalyst
– RNA as the
intermediary
End of Chapter 1

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