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



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

 

 
 
Tags:  dna  biotechnology  biochemistry  biology  molecular biology  tutorial  presentation  protein  proteomics  genomics  medical biochemistry 
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Published:  March 27, 2008
 
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Slide 1: Biology For Computer Engineers Part 1: Chemistry for Biology © 2008 ubio. All rights reserved. 1
Slide 2: Why me, the computer geek?  Biological studies need computing Advanced imaging Database technologies Data mining Graphical modeling DNA/Protein modeling  Advanced computing needs biological  models Semantic systems Machine learning Robotics Analysis software © 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  Top­down Study of living beings leads to study of cells  and molecules historic evolution of biology Study of how molecules and cells combine to  form living beings Trend today – molecular biology  Bottom­up  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  Cells are of different types Each type of tissue is made of a different type of cell Taxonomy  Different types of complex molecules Carbohydrates, proteins, fats Nerve cells, different types of heart cells  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 Multi­branched, looks like a many­headed 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 9: Structure of Organic Molecules C O H Formaldehyde Cholesterol © 2008 ubio. All rights reserved. 9
Slide 10: Bio­Molecules  All organic molecules are not bio­ molecules Petrol is an organic molecule, but it has no role in  biology  Bio­molecules 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:  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 Amino Acids © 2008 ubio. All rights reserved. 11
Slide 12: Amino Acids Glycine – simplest amino  acid (NH2­CH2­COOH) Glucagon (polypeptide hormone) © 2008 ubio. All rights reserved. 12
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 Inter­cell and intra­cell signalling – hormones etc. Parts of proteins formed by certain types of peptide chains provide  these functions Called Domains No other bio­molecule has this versatility © 2008 ubio. All rights reserved. 13
Slide 14:  Polypeptides are amino acid chains These chains can fold in 3 dimensions Structure of Proteins  Proteins have secondary structure Lateral attraction between multiple polypeptide strands forming  sheets or helices These strands might be different parts of the same chain Sequence of sheets and helices fold in 3 dimensions They have only one strand  Proteins have tertiary structure  Proteins can have quaternary structure Not all proteins have quaternary structure © 2008 ubio. All rights reserved. Depends on attractive forces between different parts of the  sequence Multiple polypeptide chains with tertiary structure develop  attractions and align in a formation 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 16: Secondary Structure Sheet formation Helix formation Each strand in a  sheet is  represented by a  pointed ribbon 16 © 2008 ubio. All rights reserved.
Slide 17: Tertiary Structure A protein secondary structure  might be a sequence of sheets  and helices. The secondary structure folds in  3­d 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 thread­like 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  Amino­acid in position 6 of one of the  Cell Anaemia haemoglobin sub­units 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 de­oxygenated state, modified haemoglobin  molecules stick together to form long chain  polymers which then bundle together like a rigid  multi­strand 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 © 2008 ubio. All rights reserved. de­ oxygenated state de­ oxy ox y 19
Slide 20: Importance of Protein Structure  Protein denaturing,  misfolding, aggregation Loss of secondary, tertiary, quaternary  structures Does not affect primary structure Caused by Heat, Chemical /Biological  agents, Pressure Reversible in some cases Examples Egg white becomes white when  boiled Skin on curdled milk Denatured protein molecules  sometimes stick together Forms aggregates  Loss of structure and  disease Loss of structure renders proteins  dysfunctional Functions that depend on the  protein are affected Aggregates might be toxic or might  interrupt activity of cells Examples Alzheimer’s disease Parkinson’s disease Mad Cow disease This is a major research area © 2008 ubio. All rights reserved. 20
Slide 21: In Part 2… We open the door to molecular biology, and  meet… The Cell © 2008 ubio. All rights reserved. 21
Slide 22: ubiquitous . biology www.ubio.in © 2008 ubio. All rights reserved. 22

   
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