Biology for Computer Engineers:Part 1(


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ubio is starting a series of biology tutorials aimed at introducing biology, biotechnology and bioinformatics to computer engineers. The first part of the presentation is essentially a biochemistry tutorial that introduces molecular biochemistry.

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  • A wonderful slideshow! I do agree with you that Biology and Computering is a perfect combination.
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Biology for Computer Engineers:Part 1(

  1. 1. <ul><li>Biology </li></ul><ul><li>For Computer Engineers </li></ul><ul><li>Part 1: Chemistry for Biology </li></ul>
  2. 2. <ul><li>Biological studies need computing </li></ul><ul><ul><li>Advanced imaging </li></ul></ul><ul><ul><li>Database technologies </li></ul></ul><ul><ul><li>Data mining </li></ul></ul><ul><ul><li>Graphical modeling </li></ul></ul><ul><ul><ul><li>DNA/Protein modeling </li></ul></ul></ul><ul><ul><li>Analysis software </li></ul></ul><ul><li>Advanced computing needs biological models </li></ul><ul><ul><li>Semantic systems </li></ul></ul><ul><ul><li>Machine learning </li></ul></ul><ul><ul><li>Robotics </li></ul></ul><ul><li>Why me, the computer geek? </li></ul>
  3. 3. <ul><li>Study of life </li></ul><ul><ul><li>Living things are all around us </li></ul></ul><ul><ul><ul><li>They are like complex software systems </li></ul></ul></ul><ul><ul><ul><li>Easy to see design patterns </li></ul></ul></ul><ul><ul><ul><ul><li>Composition </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Aggregation </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Events and signals </li></ul></ul></ul></ul><ul><ul><ul><ul><li>… and so on </li></ul></ul></ul></ul><ul><ul><ul><li>OOAD beginnings were based on biological models </li></ul></ul></ul><ul><li>What is Biology? </li></ul>
  4. 4. <ul><li>Top-down </li></ul><ul><ul><li>Study of living beings leads to study of cells and molecules </li></ul></ul><ul><ul><ul><li>historic evolution of biology </li></ul></ul></ul><ul><li>Bottom-up </li></ul><ul><ul><li>Study of how molecules and cells combine to form living beings </li></ul></ul><ul><ul><ul><li>Trend today – molecular biology </li></ul></ul></ul><ul><li>We follow the latter </li></ul><ul><li>Approaches to Biology </li></ul>
  5. 5. <ul><li>Composition </li></ul><ul><ul><li>All living beings are composed of cells </li></ul></ul><ul><ul><li>Cells are composed of molecules </li></ul></ul><ul><ul><li>Molecules are composed of atoms, and so on… </li></ul></ul><ul><li>Interactions between composed systems are predictable </li></ul><ul><ul><li>Individual outcomes are deterministic and repeatable </li></ul></ul><ul><ul><li>Higher order biological systems are very complex </li></ul></ul><ul><ul><ul><li>increased complexity reduces predictability </li></ul></ul></ul><ul><ul><li>Advances in science would bring more predicability </li></ul></ul><ul><ul><li>There is a role for heuristics </li></ul></ul><ul><li>Composition in Biology </li></ul>
  6. 6. <ul><li>All living beings are classified in a hierarchical tree </li></ul><ul><ul><li>Taxonomy </li></ul></ul><ul><li>Cells are of different types </li></ul><ul><ul><li>Each type of tissue is made of a different type of cell </li></ul></ul><ul><ul><ul><li>Nerve cells, different types of heart cells </li></ul></ul></ul><ul><li>Different types of complex molecules </li></ul><ul><ul><li>Carbohydrates, proteins, fats </li></ul></ul><ul><li>There are inheritance trees everywhere </li></ul><ul><li>Inheritance and Classification </li></ul>
  7. 7. <ul><li>All biology starts from chemical reactions </li></ul><ul><ul><li>between organic molecules </li></ul></ul><ul><ul><li>that create organic molecules </li></ul></ul><ul><li>What are organic molecules? </li></ul><ul><ul><li>Molecules containing Carbon (C) </li></ul></ul><ul><ul><li>Combinations of C with H, O, N </li></ul></ul><ul><ul><li>Other elements present in small quantities </li></ul></ul><ul><ul><li>Sulphur, Phosphorous, Iron, Sodium etc. </li></ul></ul><ul><ul><li>These elements form organic building blocks using covalent bonds </li></ul></ul><ul><ul><ul><li>Hydroxyl – OH - </li></ul></ul></ul><ul><ul><ul><li>Acid - COOH </li></ul></ul></ul><ul><ul><ul><li>Amine – NH 2 + , and so on… </li></ul></ul></ul><ul><li>Organic Chemistry for Biology </li></ul>
  8. 8. <ul><li>Organic building blocks form chains </li></ul><ul><ul><li>Bonds between building blocks </li></ul></ul><ul><ul><li>Long or short chains, three dimensional growth </li></ul></ul><ul><ul><li>Multi-branched, looks like a many-headed hydra </li></ul></ul><ul><ul><li>Growth controlled by weak molecular forces </li></ul></ul><ul><ul><ul><li>Electrostatic attraction between groups with opposite charge </li></ul></ul></ul><ul><ul><ul><li>Hydrogen bonds </li></ul></ul></ul><ul><ul><ul><ul><li>Attraction between an O or N atom in a molecule with an H atom in another molecule </li></ul></ul></ul></ul><ul><ul><ul><li>Van der Waal’s bonds, hydrophobic bonds etc. </li></ul></ul></ul><ul><ul><li>Environmental factors can control growth of organic molecules </li></ul></ul><ul><ul><ul><li>In solution, Temperature, Pressure, Electric fields etc. </li></ul></ul></ul><ul><ul><ul><li>These factors can overcome weak forces </li></ul></ul></ul><ul><li>Organic Molecules </li></ul>
  9. 9. <ul><li>Structure of Organic Molecules </li></ul><ul><li>Formaldehyde Cholesterol </li></ul>C O H
  10. 10. <ul><li>All organic molecules are not bio-molecules </li></ul><ul><ul><li>Petrol is an organic molecule, but it has no role in biology </li></ul></ul><ul><li>Bio-molecules are those that participate in the process of life </li></ul><ul><ul><li>Fats (lipids) </li></ul></ul><ul><ul><li>Carbohydrates </li></ul></ul><ul><ul><li>Amino Acids, Proteins </li></ul></ul><ul><ul><li>Nucleic Acid (DNA, RNA) </li></ul></ul><ul><ul><li>… </li></ul></ul><ul><li>Now, we are at the gates of molecular biology </li></ul><ul><li>Bio-Molecules </li></ul>
  11. 11. <ul><li>Two organic building blocks at ends </li></ul><ul><ul><li>An Amine (NH2+) </li></ul></ul><ul><ul><li>An Acid (COOH-) </li></ul></ul><ul><ul><li>Can string together easily to form chains </li></ul></ul><ul><ul><ul><li>Peptide link </li></ul></ul></ul><ul><ul><ul><ul><li>NH2+ on one amino acid binds with COOH- on another </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Generally stable, breaks slowly in the presence of water </li></ul></ul></ul></ul><ul><ul><ul><li>Peptides can chain together to form polypeptides </li></ul></ul></ul><ul><ul><ul><li>Polypeptides chain to form Proteins </li></ul></ul></ul><ul><ul><li>Amino acids are monomers, (poly)peptides are polymers </li></ul></ul><ul><ul><ul><li>Monomers have a single molecular structure </li></ul></ul></ul><ul><ul><ul><li>Polymers are made of repeated monomers </li></ul></ul></ul><ul><li>Amino Acids </li></ul>
  12. 12. <ul><li>Amino Acids </li></ul><ul><li>Glucagon </li></ul><ul><li>(polypeptide hormone) </li></ul>Glycine – simplest amino acid (NH2-CH2-COOH)
  13. 13. <ul><li>Proteins are the most important bio-molecules </li></ul><ul><ul><li>Arguably – perhaps, DNA and RNA are the most important </li></ul></ul><ul><ul><li>Complex, very large organic molecules </li></ul></ul><ul><ul><li>Formed from 20 different amino acids </li></ul></ul><ul><li>Multiple functions that are important for cells </li></ul><ul><ul><li>Assistance to metabolism – enzymes etc. </li></ul></ul><ul><ul><li>Maintaining cell shape </li></ul></ul><ul><ul><li>Inter-cell and intra-cell signalling – hormones etc. </li></ul></ul><ul><ul><li>Parts of proteins formed by certain types of peptide chains provide these functions </li></ul></ul><ul><ul><ul><li>Called Domains </li></ul></ul></ul><ul><ul><li>No other bio-molecule has this versatility </li></ul></ul><ul><li>Proteins </li></ul>
  14. 14. <ul><li>Polypeptides are amino acid chains </li></ul><ul><ul><li>These chains can fold in 3 dimensions </li></ul></ul><ul><ul><li>They have only one strand </li></ul></ul><ul><li>Proteins have secondary structure </li></ul><ul><ul><li>Lateral attraction between multiple polypeptide strands forming sheets or helices </li></ul></ul><ul><ul><li>These strands might be different parts of the same chain </li></ul></ul><ul><li>Proteins have tertiary structure </li></ul><ul><ul><li>Sequence of sheets and helices fold in 3 dimensions </li></ul></ul><ul><ul><ul><li>Depends on attractive forces between different parts of the sequence </li></ul></ul></ul><ul><li>Proteins can have quaternary structure </li></ul><ul><ul><li>Multiple polypeptide chains with tertiary structure develop attractions and align in a formation </li></ul></ul><ul><ul><li>Not all proteins have quaternary structure </li></ul></ul><ul><li>Structure of Proteins </li></ul>
  15. 15. <ul><li>Primary Structure </li></ul><ul><li>Each bead in the chain is an amino acid. </li></ul><ul><li>Amino Acids are represented by 3-letter abbreviations. Upto 20 amino acids are used to make proteins. </li></ul><ul><li>Each Amino Acid has unique chemical properties: </li></ul><ul><ul><li>Hydrophobic/hydrophilic </li></ul></ul><ul><ul><li>Acidic/Basic, etc. </li></ul></ul><ul><li>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. </li></ul>
  16. 16. <ul><li>Secondary Structure </li></ul>Sheet formation Helix formation Each strand in a sheet is represented by a pointed ribbon
  17. 17. <ul><li>Tertiary Structure </li></ul>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.
  18. 18. <ul><li>Quaternary Structure </li></ul>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)
  19. 19. <ul><li>Importance of Protein Structure </li></ul>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. In de-oxygenated state, modified haemoglobin molecules stick together to form long chain polymers which then bundle together like a rigid multi-strand braid. The braid causes affected RBCs to bend like a sickle. They become normal again upon oxygenation. Repeated change in structure causes rupture and destruction of RBCs de-oxy oxy de-oxygenated state
  20. 20. <ul><li>Importance of Protein Structure </li></ul><ul><li>Protein denaturing, misfolding, aggregation </li></ul><ul><ul><li>Loss of secondary, tertiary, quaternary structures </li></ul></ul><ul><ul><li>Does not affect primary structure </li></ul></ul><ul><ul><li>Caused by Heat, Chemical /Biological agents, Pressure </li></ul></ul><ul><ul><li>Reversible in some cases </li></ul></ul><ul><ul><li>Examples </li></ul></ul><ul><ul><ul><li>Egg white becomes white when boiled </li></ul></ul></ul><ul><ul><ul><li>Skin on curdled milk </li></ul></ul></ul><ul><ul><li>Denatured protein molecules sometimes stick together </li></ul></ul><ul><ul><ul><li>Forms aggregates </li></ul></ul></ul><ul><li>Loss of structure and disease </li></ul><ul><ul><li>Loss of structure renders proteins dysfunctional </li></ul></ul><ul><ul><ul><li>Functions that depend on the protein are affected </li></ul></ul></ul><ul><ul><li>Aggregates might be toxic or might interrupt activity of cells </li></ul></ul><ul><ul><li>Examples </li></ul></ul><ul><ul><ul><li>Alzheimer’s disease </li></ul></ul></ul><ul><ul><ul><li>Parkinson’s disease </li></ul></ul></ul><ul><ul><ul><li>Mad Cow disease </li></ul></ul></ul><ul><ul><li>This is a major research area </li></ul></ul>
  21. 21. <ul><li>We open the door to molecular biology, and meet… </li></ul><ul><li>The Cell </li></ul><ul><li>In Part 2… </li></ul>
  22. 22. <ul><li>ubiquitous . biology </li></ul>