Biological Chemistry

Chemical Biology research uses the tools of chemistry and synthesis to understand biology and disease pathways at the molecular level. Advanced Biological Chemistry interests include diverse topics such as nucleic acids, DNA repair, bioconjugate chemistry, peptides and peptidomimetics, glycoscience, biomolecular structure and function, imaging, and biological catalysis. Biophysical Chemistry represents the union of Chemistry, Physics, and Biology using a variety of experimental and theoretical approaches to understand the structure and function of biological systems. Advanced Biophysical Chemistry use different techniques such as nuclear magnetic resonance, electron paramagnetic resonance, x-ray crystallography, ultra-fast spectroscopy, as well as statistical and quantum mechanical theory to study the molecular details of important biological processes, such as: protein-protein and protein-nucleic acid interactions, protein structure and function, enzyme mechanisms, photosynthesis and neuronal transduction.

Carbohydrates

Carbohydrates, also known as sugars, are found in all living organisms. They are essential to the very source of life (ex. Ribose sugars in DNA and RNA) or sustaining life itself (ex. Metabolic conversion of carbohydrates into usable biochemical energy, ATP). Another important role of carbohydrates is structural (ex. Cellulose in plants).

• Carbohydrates
• Galactose
• Ribose
• Lactose
• Glucose
• Carbohydrate Isomers
• Fructose
• Glycogen
• Starch
• Carbohydrate Classification
• Sucrose
• Cellulose
• Case Studies 

Lipids

Lipids are biomolecules which are soluble in organic non-polar solvents. Consequently, fats and lipids are insoluble in water. Glycerides and waxes form a sub-group of compounds which have an ester as the major functional group and include: waxes, triglycerides, and phospholipids. Another diverse group of compounds which do not have any ester functional groups are also classified as lipids including: steroids, fatty acids, soaps, sphingolipids, and prostaglandins.

• Lipids
• DNA - Double Helix
• DNA - Replication
• DNA Structure
• Protein Synthesis
• RNA - Transcription
• Types of RNA
• Nucleotides

Proteins

Proteins are probably the most important class of biochemical molecules, although of course lipids and carbohydrates are also essential for life. Proteins are the basis for the major structural components of animal and human tissue. Proteins are natural polymer molecules consisting of amino acid units. The number of amino acids in proteins may range from two to several thousand.

• Proteins
• Amino Acid Reaction
• Protein Structure
• Case Studies
• Amino Acids
• Amino Acid Peptide Bonds

Enzymes

Enzymes are catalysts, most are proteins. Enzymes bind temporarily to one or more of the reactants of the reaction they catalyze. In doing so, they lower the amount of activation energy needed and thus speed up the reaction.

• Enzyme Basics
• General Enzymatic Kinetics
• Michaelis-Menten Kinetics and Briggs-Haldane Kinetics
• Sigmoid Kinetics
• Enzyme Inhibition
• Turnover Number
• Michaelis-Menten Kinetics
• The "Ping-Pong" Mechanism

Nucleic Acids

Deoxyribonucleic acid (DNA) is a macromolecule that consists of deoxyribonucleotide monomers linked to each other by phosphodiester bonds. The sequence of these nucleotides contains translates into a genetic blueprint by which a cell can synthesize proteins.

• Nucleic Acids 
• DNA - Double Helix 
• DNA - Replication 
• DNA Structure
• Protein Synthesis
• RNA - Transcription 
• Types of RNA
• Nucleotides

Biochemical Energy

1. Basics
2. ATP/ADP
3. Metabolism
4. Carbohydrates
1. Lipid
2. Proteins

Vitamins, Cofactors and Coenzymes

• Vitamins
• Vitamin A: Beta-Carotene
• FAD - Flavin Adenine Dinucleotide
• Nicotinamide Adenine Dinucleotide
• Cobalamin

Food Chemistry

• Food Energy Pyramids
• Mono sodium glutamate
• Sweetners
• Acesulfame-K
• Aspartame
• Cyclamate
• High Fructose Corn Syrup
• Saccharin
• Sucralose

Pharmaceutical Chemistry

A very broad definition of a drug would include "all chemicals other than food that affect living processes." If the affect helps the body, the drug is a medicine. However, if a drug causes a harmful effect on the body, the drug is a poison. The same chemical can be a medicine and a poison depending on conditions of use and the person using it. Another definition would be "medicinal agents used for diagnosis, prevention, treatment of symptoms, and cure of diseases."

• Drug Activity
• Anti-Cancer Drugs II
• Central Nervous System
• Antidepressants
• Drug Receptor Interactions
• Narcotic Analgesic Drugs
• Misc Antibiotics
• Anti-Cancer Drugs I
• Sulfa Drugs
• Hallucinogenic Drugs
• Barbiturates
• Penicillin
• Enzyme Inhibition
• Local Anesthetics

Photoactive Biology

Typically, both photo transduction and enzymatic activities occur with the aid of internal co-factors embedded in the protein scaffolding (e.g. chlorophyll in photosynthetic proteins, heme molecules in oxygen binding proteins and vitamins in enzymes). Since proteins are constructed from a combination of 20 naturally occurring amino acids, each with unique properties such as charge, polarity, polarizability and structure, a complex set of potential interactions can result between the protein environment and embedded cofactors. To ensure that biological functions occur efficiently, Nature has fine-tuned the properties of protein environments to optimize specific features of embedded reactions.

• Photosynthesis
• Photoreceptors
• Vision

Quantitative structure-activity Relationships

Metabolism

• Kreb's Cycle
• Caffeine
• Gluconeogenesis
• Calvin-Benson-Bassham Cycle
• Electron Transport Chain
• Pentose Phosphate Pathway
• Glycolysis
• Beta-Oxidation
• Pyruvate Dehydrogenase Complex
• Nutrition

Introduction to MATLAB -Yossi Farjoun

Resource Description

This course was offered as a non-credit program during the Independent Activities Period (IAP), which is a special 4-week term at MIT that runs from the first week of January until the end of the month.

The course, intended for students with no programming experience, provides the foundations of programming in MATLAB®. Variables, arrays, conditional statements, loops, functions, and plots are explained. At the end of the course, students should be able to use MATLAB in their own work, and be prepared to deepen their MATLAB programming skills and tackle other languages for computing, such as Java, C++, or Python.

The course mostly follows the official MATLAB Manual, available from The MathWorks. We will cover material from chapters 2-5.

Lecture Notes

LECTURE NOTES CONTENTS	FILES
Lecture 1: Introduction to MATLAB Basics ·         Getting MATLAB to Run ·         Programming ·         The Command Prompt ·         Simple Expressions ·         Variables ·         Referencing Matrix Elements	Lecture 1 Notes and Exercises (HTML)
Lecture 2: Matrices ·         Accessing Matrix Elements ·         Assigning into Submatrices	Lecture 2 Notes and Exercises (HTML)
Lecture 3: Basic Tools ·         Matrix Concatenations ·         More Expressions ·         Plotting ·         Logical Constructs ·         Formatting Text	Lecture 3 Notes and Exercises (HTML)
Lecture 4: Flow Control ·         "if" Statement ·         "for" Loops	Lecture 4 Notes and Exercises (HTML)
Lecture 5: Defining Functions ·         "while" Statements ·         Variable Scope	Lecture 5 Notes and Exercises (HTML)
Lecture 6: Functions and Logic ·         Multiple Input Functions ·         More on Logic	Lecture 6 Notes and Exercises (HTML)

In silico Approaches for Designing Bioactive Peptides A National Workshop (18th – 21st October, 2011)

BIC is organizing a workshop with theme revolving around bioactive peptides. Bioactive peptides are likely to have applications as antimicrobials, antivirals, pharmaceuticals, antiinflammatories, anticancers etc. A few research groups at IMTECH are currently engaged in research on such properties of peptides. Peptides certianly have advantage as drugs of choice for treament of various diseases. Computational approaches can offer a platform for quick and easy way to design and model peptides, thus, reducing time and resources before approaching bench.

The aim of this workshop is to familiarize participants with experimental as well as in silico approaches including prediction, modeling and molecular simulations, designing of peptides etc. The workshop will also include exploitation of properties of unusual amino acids and their retro-inverso nature.

Registration Fees

M.Sc. Students – Rs. 2000/- Ph.D Students – Rs. 3000/- Univ. Faculty/ Scientist– Rs. 4000/- Industry Person- Rs. 5000/- Accomodation fee extra*. *Applicants requiring accommodation must indicate in the registration form.Such applicants need to pay Rs 500 in addition to registration fee. How to apply The filled up registration form (hand written/typed) should be sent along with demand draft in favor of Director, IMTECH on any Nationalized Bank payable at Chandigarh, latest by 30th September, 2011. The registration form of M.Sc. and Ph.D. students must be forwarded by their respective head of the department of university/institute. Pamphlet of the Workshop Registration Form Contact : Dr. Balvinder Singh, Convenor, Bioinformatics Centre, Institute of Microbial Technology, Sector 39-A, Chandigarh—160036 Phone: 0172-6665452,2690557 Fax No. 0172-2690585, 2690632 E-mail: bvs@imtech.res.in

Introduction to MATLAB (MIT)

Course Description

This course provides an aggressively gentle introduction to MATLAB®. It is designed to give students fluency in MATLAB, including popular toolboxes. The course consists of interactive lectures with students doing sample MATLAB problems in real time. Problem-based MATLAB assignments are given which require significant time on MATLAB.

This course is offered during the Independent Activities Period (IAP), which is a special 4-week term at MIT that runs from the first week of January until the end of the month.

LEC #	TOPICS	FILES
1	Variables, scripts, and operations	(PDF)
2	Visualization and programming	(PDF)
3	Solving equations and curve fitting	(PDF)
4	Advanced methods	(PDF)
5	Symbolics, Simulink®, file I/O, building GUIs	(PDF)

Assignments

ASSN #	DESCRIPTIONS	ASSIGNMENTS	SUPPORTING FILES
1	This assignment focuses on vector/matrix variables and learning new functions by using help.	(PDF)	classGrades.mat (MAT)
2	This assignment focuses on writing functions and visualizing data.	(PDF)	noisyData.mat (MAT) optionalData.mat (MAT) googlePrices.mat (MAT)
3	This assignment focuses on solving problems and has a very cool optional problem which is actually pretty easy.	(PDF)	HH.zip (ZIP) (This ZIP file contains: 6 .m files.) randomData.mat (MAT)
4	This assignment focuses on more advanced concepts like random number generation, advanced data structures, images, and animation.	(PDF)