Restriction Endonucleases

The Restriction endonucleases recognizes a specific base sequence of four to eight bases in double-stranded DNA and cleaves both strands of the duplex.

There are known type of restriction endonucleases : type I,II and III. Type II enzymes are frequently used in the rDNA technology. Type I and type III are not use because these type enzymes cleaves the DNA far from the recognition sites.

The Restriction endonuclease recognizes particular specific sequences are 4 to 6 nucleotides recognize by the type II enzymes because these enzymes only cleave at this site. The palindrome sequence is “Two-fold symmetry” as shown above video.

Restriction Endonuclease

Lecture Video : Metabolism Part III

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur.

Intermediary Metabolism III

See this links:

Metabolism Part I

Metabolism Part II

(Links will update soon)

Lecture Video Metabolism II

Intermediary Metabolism II

Lecture Video Intermediary Metabolism

Metabolism (pronounced: muh-tah-buh-lih-zum) is a collection of chemical reactions that takes place in the body's cells. Metabolism converts the fuel in the food we eat into the energy needed to power everything we do, from moving to thinking to growing. Specific proteins in the body control the chemical reactions of metabolism, and each chemical reaction is coordinated with other body functions. In fact, thousands of metabolic reactions happen at the same time — all regulated by the body — to keep our cells healthy and working.

Metabolism is a constant process that begins when we're conceived and ends when we die. It is a vital process for all life forms — not just humans. If metabolism stops, living things die.

Here's an example of how the process of metabolism works in humans — and it begins with plants. First, a green plant takes in energy from sunlight. The plant uses this energy and a molecule called chlorophyll (which gives plants their green colour) to build sugars from water and carbon dioxide. This process is called photosynthesis, and you probably learned about it in biology class.

When people and animals eat the plants (or, if they're carnivores, they eat animals that have eaten the plants), they take in this energy (in the form of sugar), along with other vital cell-building chemicals. The body's next step is to break the sugar down so that the energy released can be distributed to, and used as fuel by, the body's cells.

After food is eaten, molecules in the digestive system called enzymes break proteins down into amino acids, fats into fatty acids, and carbohydrates into simple sugars (e.g., glucose). In addition to sugar, both amino acids and fatty acids can be used as energy sources by the body when needed. These compounds are absorbed into the blood, which transports them to the cells. After they enter the cells, other enzymes act to speed up or regulate the chemical reactions involved with "metabolizing" these compounds. During these processes, the energy from these compounds can be released for use by the body or stored in body tissues, especially the liver, muscles, and body fat.

See the Lecture Video

 

Intermediary Metabolism

 

 

 

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur.

List of Biomolecules video lectures

A biomolecule is a chemical molecule that naturally occurs in living organisms. Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur. Other elements sometimes are incorporated but are much less common.

This is very useful videos.

1. Amino Acids

Amino acids part I

Amino acids Part II

2. Proteins

Proteins Part I

Protein Part II

Protein Part III

Protein Part IV

3. Nucleic Acids

Nucleic Acids Part I

Nucleic Acids Part II

Nucleic Acids Part III

4. Carbohydrates

Carbohydrates Part I

Carbohydrates Part II

5. Enzymology

Enzymes I : Basics

Enzymes II

Enzymes III : Enzymes as Biocatalysts

          6.Lipids and Membranes
          Lipids and Membranes 1
          Lipids and Membranes II
          Membrane Transport


         7. Vitamins and Coenzyme

            Vitamins and Coenzymes 1
            Vitamins and Coenzymes II

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Video lecture : Lipids and Membranes 1

The lipids are important constituents of the diet because of their high energy value and also because of the fat-soluble vitamins and the essential fatty acids found with the fat of the natural foodstuffs. In the body, the fats serve as efficient source of energy which is stored in the adipose tissues.

Lipids are not generally classed as macromolecules, even though they share some of their features: for example, most are synthesized as linear polymers of a smaller molecule (the acetyl group on acetyl-CoA), and they self-assemble into larger structures (membranes).

Definition:

The lipids are a heterogeneous group of compounds related to fatty acids and include fats, oils, waxes and other related substances. These are oily or greasy organic substances, relatively insoluble in water and considerably soluble in organic solvents like ether, chloroform and benzene.

They are, thus, hydrophobic in nature. These are variously called as lipins or lipoids. The latter term is, however, sometimes used to refer “fat-like” substances which may not actually be related to the fatty acids. The term ‘lipid’ was first used by the German biochemist Bloor in 1943 for a major class of tissue components and foodstuffs.

lipids are molecular organic compounds, composed largely of carbon and hydrogen, that are essential for cell growth. Lipids are non-soluble in water and combine with carbohydrates and proteins to form the majority of all plant and animal cells. Lipids are more commonly synonymous with the word "fats" when speaking in terms of personal health, and though all fats are lipids, not all lipids are fats.

The three major purposes of lipids are energy storage, cell membrane development, and serving as a component of hormones and vitamins in the body. In healthcare, physicians order lipid tests or lipid profiles to measure cholesterol and triglycerides in a person's blood. Lipoprotein is the medical term used to define a combination of fat and protein.

Cholesterol is a naturally occurring substance in the body and is comprised of lipids. Cholesterol is separated into two types, high-density lipoprotein (HDL) and low-density lipoprotein (LDL). In a lipid test, the lipoproteins are separated so the level of each can be measured. Lipid tests are often part of preventative routine care, as they help determine whether there is significant risk for atherosclerosis, a hardening of the arteries that interferes with or interrupts blood flow. Lipoprotein levels are measured and dietary changes are usually in order when total cholesterol levels approach or rise above 200 milligrams per decilitre in the blood.

Fatty acids, also comprised of lipids, are an important dietary concern. Some fatty acids are essential and others are harmful. Fatty acids are categorized as mono-saturated, mono-unsaturated, and poly-unsaturated. Some essential fatty acids cannot be created by the body, and must be consumed in the diet. These include linoleic acid and alpha-linolenic acid.

 

Lipids & membranes 1

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur.

Nucleic Acids Lecture III

Nucleic Acids Lecture III

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. For more details on NPTEl visit http://nptel.iitm.ac.in

Nucleic Acids Lecture II

Nucleic acids Lecture II

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. For more details on NPTEl visit http://nptel.iitm.ac.in

Nucleic Acids Lecture I

Nucleic acids Lecture I

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. For more details on NPTEl visit http://nptel.iitm.ac.in

Carbohydrate Lecture II

Carbohydrate lecture II

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. For more details on NPTEl visit http://nptel.iitm.ac.in

Carbohydrates lecture I

Carbohydrates lecture I

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. For more details on NPTEl visit http://nptel.iitm.ac.in

Lecture Video - 3 Enzymes as Biocatalysts

Lecture Video Enzymes II

What is Enzymes?

Enzymes are biological catalysts: this means that they speed up the chemical reactions in living things. Without enzymes, our guts would take weeks and weeks to digest our food, our muscles, nerves and bones would not work properly and so on - we would not be living!

A catalyst is any substance which makes a chemical reaction go faster, without itself being changed. A catalyst can be used over and over again in a chemical reaction: it does not get used up. Enzymes are very much the same except that they are easily denatured (destroyed: but do NOT use this word since the protein molecule is not broken down into amino-acids, it just loses it shape and will not work any more) by heat. Our enzymes work best at body temperature. Our enzymes also have to have the correct pH.

All enzymes are made of protein; that is why they are sensitive to heat, pH and heavy metal ions. Unlike ordinary catalysts, they are specific to one chemical reaction. An ordinary catalyst may be used for several different chemical reactions, but an enzyme only works for one specific reaction.

Human saliva contains an enzyme called amylase. This enzyme helps to turn starch into a sugar called maltose. When you swallow a mouthful of food, the amylase stops working because it is much too acid in the stomach pH 2. Amyalse works best in neutral or slightly alkaline conditions, i.e. at about pH 7. When your food gets into the small intestine, more amylase is made by the pancreas and this turns the remaining starch into maltose. Another enzyme (maltase) turns all this maltose into glucose. Glucose is then absorbed into the blood.

Enzymes in the human alimentary canal and what they digest:

 

Enzyme            Substrate

Amylase                          Starch

Maltase                            Maltose

Sucrase                          Sucrose

Lipase                             Fats

Pepsin                           Proteins

 

All animals, green plants, fungi and bacteria produce enzymes: so enzymes are not just about digesting food. The enzymes which we use to digest our food are extra-cellular, that means they are found outside cells. We also have enzymes inside our cells; these are intra-cellular enzymes. Enzymes are used in ALL chemical reactions in living things; this includes respiration, photosynthesis, movement growth, getting rid of toxic chemicals in the liver and so on.

Viruses are rather different, but you do not need to know much about them for GCSE, so just make sure that you don't catch any!

Enzymes must have the correct shape to do their job. They are made of proteins, and proteins are very easily affected by heat, pH and heavy metal ions. Some people say that enzymes work like a key in a lock. If the key has been twisted by heat, or dissolved in acid or stuck up with chewing gum it will not work. Enzymes change their shape if the temperature or pH changes, so they have to have the right conditions. Copper ions are poisonous: if you get copper ions in your blood they will block up some of the important enzymes in red and white blood cells.

 

See the Video Lectures on Enzymes

Enzymes part I

Enzymes Part II

Enzymes Part III : Enzymes as Biocatalysts

Enzymes Part IV

Enzyme Part V : Specificity of Enzyme Action

Enzyme Part VI : Kinetics of Enzyme Catalysed Reactions

Enzyme Part VII

Enzyme Part VIII

Lecture Video Enzymes I

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. For more details on NPTEl visit http://nptel.iitm.ac.in

Video Lecture : Protein Structure–I

Protein Structure Video lecture I

Video Lecture : Protein Structure 4

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur.

Protein Lecture IV

Video Lecture : Protein structure II

Video Lecture : Protein Structure III

Protein Structure III

Protein is an essential nutrient

Protein is one of the nutrients along with carbohydrate, fat, vitamins, minerals, and water. The source of all of these nutrients is good. Some foods contain much higher amounts of specific nutrients than others and sometimes we refer to certain foods as “protein foods”.

It is important to realize that all goods contain more than one nutrient and most foods contain substantial amounts of several nutrients. For example, meat, which is a good source of protein, carbohydrate, fat, riboflavin and calcium.

Protein is an essential nutrient. There is no life without protein. Protein is contained in every part of your body, the skin, muscles, hair, blood, body organs, eyes, even fingernails and bone. Next to water, protein is the most plentiful substance in your body.

Structure of Proteins

Proteins are composed of small units. These units are the amino acids which are called the building blocks of protein. There are about 20 different amino acids which are commonly known.

Each different protein is composed of various amino acids put together in varying order with almost limitless combinations. Most proteins are large molecules that may contain
several hundred amino acids arranged in branches and chains.

Functions
Protein has a critical physiological function. Protein is primarily used in the body to build, maintain, and repair body tissues. In the event that protein intake is greater than that required by the body for this primary function, excessive protein is converted to energy for immediate use or stored in the body as fat. Protein energy will be used only after other energy sources (carbohydrate and fat) are exhausted or unavailable.

See the Video, given by

Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur.

Lecture Video I

Lecture Video II

Lecture Video III

Lecture Video IV

Lecture - 2 Amino Acids II

Amino Acids Notes part1

Amino acids are monomeric units of proteins. Proteins are high molecular weight organic polymer. Although about 200 to 300 amino acids occur in nature, only 20 of them are seen in human body.

Amino acids are relatively simple molecules containing both an amine group and an acid group. The biologically important amino acids are the alpha-amino acids that have the amine and acid groups attached to the same carbon atom. There are more than 300 known natural amino acids; however, only 20 of them are used in protein synthesis. Francis Crick (who with James Watson determined the structure of DNA) labeled this set of amino acids the magic 20. Other amino acids are found in certain proteins, but in almost all cases these additional amino acids result from the modification of one of the magic 20 after the protein formed.

Definition:

“A substance which has both carboxyl and amino group in the same molecule is called ‘amino acid’. The amino group is basic while the carboxyl group (-COOH) is acidic in nature”.

General Structure:

Amino acids are a group of organic compounds containing two functional groups – amino and carboxyl. The amino group (-NH2) is basic while the carboxyl group (-COOH) is acidic in nature.

All proteins are polymers of amino acids and all these acids except two have an amino group attached to the carbon atom next to the carboxyl group. The general formula of the amino acid is ..

Rules to write the Amino acids:

We should write the general formula by using the given points:

• We should write the Carboxyl group on Top side of the center  carbon (asymmetric carbon)

• We should write the Amino group on Left side of the centre carbon (asymmetric carbon).
• We should write the hydrogen atom on Right side of the centre carbon (asymmetric carbon).
• We should write the ‘R’ side chain at the Bottom of the centre carbon (asymmetric carbon).

The amino acids are termed as α-amino acids, if both the carboxyl and amino groups are attached to the same carbon atom. The amino acids mostly exist in the ionized form in the biological system.

Stereochemistry:

Carbon atom is attached to four different groups, which is simply called “asymmetric” and therefore exhibits optical isomerism. All amino acids contain asymmetric carbon, except Glycine. (Glycine is Optically inactive compound).

D & L Forms:

Amino acids can be shown in two different forms depends on the position of amino group on the asymmetric carbon atom. When the amino group situated on the left side, which is L-form. When the amino group situated on the sight side, which is D-form. All naturally occurring amino acids are in L-configuration.

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Lecture Series on BioChemistry I by Prof.S.Dasgupta, Dept of Chemistry, IIT Kharagpur. 

Lecture - 1 Amino Acids I

Next Amino Acid lecture part II

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