Biology for Computer Engineers:Part 1(www.ubio.in)

Slide 2: Why me, the computer geek?  Biological studies need computing Advanced imaging Database technologies Data mining Graphical modeling DNA/Protein modeling Analysis software  Advanced computing needs biological models Semantic systems Machine learning Robotics © 2008 ubio. All rights reserved. 2

Slide 3: What is Biology?  Study of life Living things are all around us They are like complex software systems Easy to see design patterns Composition Aggregation Events and signals …and so on OOAD beginnings were based on biological models © 2008 ubio. All rights reserved. 3

Slide 4: Approaches to Biology  Top-down Study of living beings leads to study of cells and molecules historic evolution of biology  Bottom-up Study of how molecules and cells combine to form living beings Trend today – molecular biology  We follow the latter © 2008 ubio. All rights reserved. 4

Slide 5: Composition in Biology  Composition All living beings are composed of cells Cells are composed of molecules Molecules are composed of atoms, and so on…  Interactions between composed systems are predictable Individual outcomes are deterministic and repeatable Higher order biological systems are very complex increased complexity reduces predictability Advances in science would bring more predicability There is a role for heuristics © 2008 ubio. All rights reserved. 5

Slide 6: Inheritance and Classification  All living beings are classified in a hierarchical tree Taxonomy  Cells are of different types Each type of tissue is made of a different type of cell Nerve cells, different types of heart cells  Different types of complex molecules Carbohydrates, proteins, fats  There are inheritance trees everywhere © 2008 ubio. All rights reserved. 6

Slide 7: Organic Chemistry for Biology  All biology starts from chemical reactions between organic molecules that create organic molecules  What are organic molecules? Molecules containing Carbon (C) Combinations of C with H, O, N Other elements present in small quantities Sulphur, Phosphorous, Iron, Sodium etc. These elements form organic building blocks using covalent bonds Hydroxyl – OH- Acid - COOH Amine – NH2+, and so on… © 2008 ubio. All rights reserved. 7

Slide 8: Organic Molecules  Organic building blocks form chains Bonds between building blocks Long or short chains, three dimensional growth Multi-branched, looks like a many-headed hydra Growth controlled by weak molecular forces Electrostatic attraction between groups with opposite charge Hydrogen bonds Attraction between an O or N atom in a molecule with an H atom in another molecule Van der Waal’s bonds, hydrophobic bonds etc. Environmental factors can control growth of organic molecules In solution, Temperature, Pressure, Electric fields etc. These factors can overcome weak forces © 2008 ubio. All rights reserved. 8

Slide 10: Bio-Molecules  All organic molecules are not bio-molecules Petrol is an organic molecule, but it has no role in biology  Bio-molecules are those that participate in the process of life Fats (lipids) Carbohydrates Amino Acids, Proteins Nucleic Acid (DNA, RNA) …  Now, we are at the gates of molecular biology © 2008 ubio. All rights reserved. 10

Slide 11: Amino Acids  Two organic building blocks at ends An Amine (NH2+) An Acid (COOH-) Can string together easily to form chains Peptide link NH2+ on one amino acid binds with COOH- on another Generally stable, breaks slowly in the presence of water Peptides can chain together to form polypeptides Polypeptides chain to form Proteins Amino acids are monomers, (poly)peptides are polymers Monomers have a single molecular structure Polymers are made of repeated monomers © 2008 ubio. All rights reserved. 11

Slide 13: Proteins  Proteins are the most important bio-molecules Arguably – perhaps, DNA and RNA are the most important Complex, very large organic molecules Formed from 20 different amino acids  Multiple functions that are important for cells Assistance to metabolism – enzymes etc. Maintaining cell shape Inter-cell and intra-cell signalling – hormones etc. Parts of proteins formed by certain types of peptide chains provide these functions Called Domains No other bio-molecule has this versatility © 2008 ubio. All rights reserved. 13

Slide 14: Structure of Proteins  Polypeptides are amino acid chains These chains can fold in 3 dimensions They have only one strand  Proteins have secondary structure Lateral attraction between multiple polypeptide strands forming sheets or helices These strands might be different parts of the same chain  Proteins have tertiary structure Sequence of sheets and helices fold in 3 dimensions Depends on attractive forces between different parts of the sequence  Proteins can have quaternary structure Multiple polypeptide chains with tertiary structure develop attractions and align in a formation Not all proteins have quaternary structure © 2008 ubio. All rights reserved. 14

Slide 15: Primary Structure Each bead in the chain is an amino acid. Amino Acids are represented by 3-letter abbreviations. Upto 20 amino acids are used to make proteins. Each Amino Acid has unique chemical properties: Hydrophobic/hydrophilic Acidic/Basic, etc. Some Amino Acids can be manufactured by the body. Amino Acids that are not manufactured have to be taken through food. These are Essential Amino Acids. © 2008 ubio. All rights reserved. 15

Slide 17: Tertiary Structure A protein secondary structure might be a sequence of sheets and helices. The secondary structure folds in 3-d space due to attractive forces. This creates the tertiary structure. © 2008 ubio. All rights reserved. 17

Slide 18: Quaternary Structure Collagen triple helix: There are three polypeptide chains intertwined with each other to form the thread-like collagen structure. Collagen is used to make long muscular tissue like ligaments Haemoglobin consists of 4 polypeptide chains, each containing a heme group (that contains iron, shown in green) © 2008 ubio. All rights reserved. 18

Slide 19: Importance of Protein Structure Impact of Primary Structure modification: the curious case of Sickle Cell Anaemia Amino-acid in position 6 of one of the haemoglobin sub-units is different in people with Sickle Cell Anaemia. Haemoglobin molecules float around in red blood cells (RBCs). Oxygen binds to them in lungs and unbinds in tissues. This is how tissues receive Oxygen. de-oxygenated state In de-oxygenated state, modified haemoglobin molecules stick together to form long chain polymers which then bundle together like a rigid multi-strand braid. de-oxy The braid causes affected RBCs to bend like a sickle. They become normal again upon oxygenation. Repeated change in structure causes rupture and oxy destruction of RBCs © 2008 ubio. All rights reserved. 19

Slide 20: Importance of Protein Structure  Protein denaturing,  Loss of structure and misfolding, aggregation disease Loss of secondary, tertiary, quaternary Loss of structure renders proteins structures dysfunctional Does not affect primary structure Functions that depend on the protein are affected Caused by Heat, Chemical /Biological agents, Pressure Aggregates might be toxic or might interrupt activity of cells Reversible in some cases Examples Examples Alzheimer’s disease Egg white becomes white when boiled Parkinson’s disease Skin on curdled milk Mad Cow disease Denatured protein molecules sometimes stick together This is a major research area Forms aggregates © 2008 ubio. All rights reserved. 20

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