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

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

Published on March 27, 2008

Author: bishorvi

Source: slideshare.net

Description

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.

Biology For Computer Engineers Part 1: Chemistry for Biology

Biology

For Computer Engineers

Part 1: Chemistry for Biology

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 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

Why me, the computer geek?

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 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

What is 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 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

Approaches to 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 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

Composition in Biology

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 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

Inheritance and Classification

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 – NH 2 + , and so on… 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 – NH 2 + , and so on…

Organic Chemistry for Biology

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 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

Organic Molecules

Structure of Organic Molecules Formaldehyde Cholesterol C O H

Structure of Organic Molecules

Formaldehyde Cholesterol

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 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

Bio-Molecules

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

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

Amino Acids Glucagon (polypeptide hormone) Glycine – simplest amino acid (NH2-CH2-COOH)

Amino Acids

Glucagon

(polypeptide hormone)

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 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

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 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

Structure of Proteins

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.

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.

Secondary Structure Sheet formation Helix formation Each strand in a sheet is represented by a pointed ribbon

Secondary Structure

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.

Tertiary Structure

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)

Quaternary Structure

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. 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

Importance of Protein Structure

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

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

We open the door to molecular biology, and meet… The Cell In Part 2…

We open the door to molecular biology, and meet…

The Cell

In Part 2…

ubiquitous . biology www.ubio.in

ubiquitous . biology

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