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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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© 2008 ubio. All rights reserved. 1
Biology
For Computer EngineersPart 1: Chemistry for Biology
© 2008 ubio. All rights reserved. 2
Biological studies need computingAdvanced imagingDatabase technologiesData miningGraphical modeling
DNA/Protein modeling
Analysis softwareAdvanced computing needs biological models
Semantic systemsMachine learningRobotics
Why me, the computer geek?
© 2008 ubio. All rights reserved. 3
Study of lifeLiving things are all around us
They are like complex software systemsEasy to see design patterns
CompositionAggregationEvents and signals…and so on
OOAD beginnings were based on biological models
What is Biology?
© 2008 ubio. All rights reserved. 4
Top-downStudy of living beings leads to study of cells and molecules
historic evolution of biologyBottom-up
Study of how molecules and cells combine to form living beings
Trend today – molecular biologyWe follow the latter
Approaches to Biology
© 2008 ubio. All rights reserved. 5
CompositionAll living beings are composed of cellsCells are composed of moleculesMolecules are composed of atoms, and so on…
Interactions between composed systems are predictable
Individual outcomes are deterministic and repeatableHigher order biological systems are very complex
increased complexity reduces predictabilityAdvances in science would bring more predicabilityThere is a role for heuristics
Composition in Biology
© 2008 ubio. All rights reserved. 6
All living beings are classified in a hierarchical treeTaxonomy
Cells are of different typesEach 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
Inheritance and Classification
© 2008 ubio. All rights reserved. 7
All biology starts from chemical reactionsbetween 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…
Organic Chemistry for Biology
© 2008 ubio. All rights reserved. 8
Organic building blocks form chainsBonds 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
Organic Molecules
© 2008 ubio. All rights reserved. 9
Structure of Organic Molecules
Formaldehyde Cholesterol
COH
© 2008 ubio. All rights reserved. 10
All organic molecules are not bio-moleculesPetrol is an organic molecule, but it has no role in biology
Bio-molecules are those that participate in the process of life
Fats (lipids)CarbohydratesAmino Acids, ProteinsNucleic Acid (DNA, RNA)…
Now, we are at the gates of molecular biology
Bio-Molecules
© 2008 ubio. All rights reserved. 11
Two organic building blocks at endsAn 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. 12
Amino Acids
Glucagon(polypeptide hormone)
Glycine – simplest amino acid(NH2-CH2-COOH)
© 2008 ubio. All rights reserved. 13
Proteins are the most important bio-moleculesArguably – 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
Proteins
© 2008 ubio. All rights reserved. 14
Polypeptides are amino acid chainsThese 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 structureMultiple polypeptide chains with tertiary structure develop attractions and align in a formation
Not all proteins have quaternary structure
Structure of Proteins
© 2008 ubio. All rights reserved. 15
Primary StructureEach 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/hydrophilicAcidic/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. 16
Secondary Structure
Sheet formation
Helix formation
Each strand in a sheet is represented by a pointed ribbon
© 2008 ubio. All rights reserved. 17
Tertiary StructureA 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. 18
Quaternary StructureCollagen 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. 19
Importance of Protein StructureImpact 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-oxygenatedstate
© 2008 ubio. All rights reserved. 20
Importance of Protein Structure Protein denaturing,
misfolding, aggregationLoss 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. 21
We open the door to molecular biology, and meet…
The Cell
In Part 2…
© 2008 ubio. All rights reserved. 22
ubiquitous . biologywww.ubio.in
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