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 ItemsPercentage Attendance5% Quizzes20% Assignments15% Mid Term20% Final Project10% Final30% For other details visit: and follow the corresponding link. There will be no makeup for quizzes or exams. Best 4 out of 5

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 The cooperative system then replicates with great efficiency It will compete with other systems Consider an RNA molecule that catalyze any RNA replication It can catalyze to replicate itself, fig. a Also catalyze other RNA, fig. b

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