Introduction to Biochemistry

*What is Biochemistry?* * Biochemistry also known as Chemistry of life is the study of chemical substances and vital processes occurring in living organism. Biochemistry governs all living organisms and living processes. * Study of chemical processes in living organisms, including, but not limited to, living matter. * Biochemistry is the science dealing with the chemical composition and chemical reactions happening within, and between the living cells of all organisms.

→ The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.
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Biochemists focus heavily on the role, function, and structure of biomolecules

*Goals of Biochemistry* * . It seeks to describe the structure, organization, and functions of living matter in molecular terms. * Is to understand the structure and behavior of biomolecules. * Biochemistry can be divided into three principal areas:

1. The structural chemistry of the components of living matter and the relationship of biological function to chemical structure.

2. Metabolism - the totality of chemical reactions that occur in living matter.

3. The chemistry of processes and substances that store and transmit biological information.

*Roots of biochemistry*
Biochemistry had its origins as a distinct field of study in the early nineteenth century with the pioneering work of Friedrich Wohler. Prior to Wohler’s time it was believed that substances or the composition of the living matters are different from non-living.
In1828, Wohler showed that urea can be produced in the laboratory without using biological sources like urine instead he used Ammonium cyanate, an inorganic compound.
After Wohler demonstrate that experiment, a persuasive viewpoint called Vitalism held that, if not the compounds at least the reaction of living matter could occur only in living organism. But later on, this viewpoint was shattered in the year 1897 when the Buchner brothers discovered that sugar could be fermented from yeast extract. This discovery opened the door to analysis of biochemical reactions and processes in Vitro (Latin word which means “in a glass/ in test tube”)
In 1926, J.B Sumner showed that the protein urease could be crystallized like any organic compound and their structures can be determined by the methods of chemistry.
In parallel with developments in biochemistry, cell biologist had been continually refining knowledge of cellular structure.
In 1875, Chromosomes were discovered by Walter Flemming and identified as genetic elements by 1902.
The idea of gene, a unit of hereditary information, was first proposed by Gregor Mendel in mid-nineteenth century. At first, the early scientist believed that only proteins were structurally complex enough to carry genetic information but of course that belief was definitely wrong it is the Deoxyribonucleic acid (DNA) that carries the genetic information of one organism.
After many decades, the three disciplines, Biochemistry, cell biology, and Genetics became inextricably interwoven and the new science of Molecular biology emerges.

*Biochemistry as a discipline and an interdisciplinary science*
Biochemistry draws its major themes from

1. Organic chemistry, which describes the properties of biomolecules

2. Biophysics, which applies the techniques of physics to study the structures of biomolecules

3. Medical research, which increasingly seeks to understand disease states in molecular terms

4. Nutrition, which has illuminated metabolism by describing the dietary requirements for maintenance of health;

5. Microbiology, which has shown that single-celled organisms and viruses are ideally suited for the elucidation of many metabolic pathways and regulatory mechanisms

6. Physiology investigates life processes at the tissue and organism levels

7. Cell biology, which describes the biochemical division of labor within a cell
8. Genetics, which describes mechanisms that give a particular cell or organism its biochemical identity.

It is truly an interdisciplinary science.

Biochemistry is also a distinct discipline, with its own identity. It is distinctive in its emphasis on the structures and reactions of biomolecules, particularly on enzymes and biological catalysis.

*Biochemistry as a chemical science*

Though we often describe biochemistry as a life science and relate its developments to the history of biology, it remains first and foremost a chemical science. In order for us to understand biochemistry, we must first study basic chemistry. * *The chemical elements of living organism*
Life depends primarily on a few elements (C, H, O, N), although many others are used to a lesser extent.
The very early universe was made almost entirely of Hydrogen and Helium, for these simplest elements was produced in the condensation of matter following the primeval explosion, or the “Big bang theory”. Although almost the entire world is made up of these 2 elements, this 2 are still not essential for life because it require large and complex molecular structure to bring life.
In other books/research materials there are 6 instead of 4 major elements that composed a living matter.
Hydrogen, Oxygen, Carbon, Calcium, Phosphorus, and Nitrogen * Biological molecules
The complexity of life processes requires that many of the molecules that participate in these processes be enormous. The most extreme example is DNA or the Deoxyribonucleic acid.
Protein molecule— A molecule serves as an antibody in the immune reaction. DNA molecules in a human cell would reach a length of about 2 meters if stretched end to end.
Polymers—
Made by joining monomers
Polymerized—
The monomers of a given type of macromolecule are of limited diversity and are linked together.
Biomolecules—
is any molecule that is produced by a living organism, including large macromolecules such as proteins, polysaccharides, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites, and natural products. * Macromolecules— These giant molecules constitute a large fraction of the mass of any cells. * Proteins— Any of a class of highly complex organic compounds, composed principally of amino acids that occur in all living things and form an essential part of animal food requirements.

Protein chains are called “Polypeptides”

Amino acids— Any of a large number of compounds found in living cells that contain carbon, oxygen, hydrogen, and nitrogen and join together to form proteins. * Carbohydrates— Any of a group of compounds, including sugar, starches, and cellulose, that contain carbon combined with hydrogen and oxygen, essential in the metabolism of plants and animals. * Lipids— An organic compound consisting fats, oils, and related substances along with proteins and carbohydrates, are the structural components of living cells.
Cellulose—
A simple example of carbohydrates, made by joining thousands of molecules of sugar(glucose), a major constituent of the cell walls of plants. * Nucleic acid— A complex compound found in a living cells and viruses. Nucleic acids in the form of DNA and RNA control cellular function and heredity.
DNA or Deoxyribonucleic acid— Chemical in the human cell that controls body development. DNA molecules in a human cell would reach a length of about 2 meters if stretched end to end.

*Biochemistry as a biological science* → Biochemistry is a biological science. It is the chemistry of life. It is the study of the structure, composition and chemical reactions of substances in living system.

* Distinguishing characteristic of a living matter
The attributes that distinguishes living matter from nonliving matter are the following: 1. Complexity 2. Motility 3. Renewal 4. Self-replicating
Complexity—interconnected whole. Living creatures are complex but many things in the universe are complex but non-living.
Motility—it is the ability to move independently. Living creatures have the ability to move independently but there are nonliving things that are very much alive, an example of this is mushrooms.
Renewal— It is the major quality that distinguishes life. Organisms create an elegant molecular order within them and pass a pattern of that order on to descendant organisms.
Self-replicating— Living organism replicates. The reproductive process has become exceeding complex through evolution, but its basis remains the same: information describing the structure of an organism is passed from one generation to the next.

* The unit of biological organization : The cell
Cells are the smallest unit and building block of all living things. It contains all parts necessary to survive in a changing world.
The word cells come from the Latin word “cella” meaning “small room”.
“2 great classes of organisms” 1. Prokaryotic 2. Eukaryotic
Prokaryotic—the prokaryotic cell is simpler and therefore smaller than a eukaryote cell; - it lacks a nucleus and most of the other organelles of eukaryotes.
Eukaryotic—Eukaryotes include multicellular plants and animals and also some unicellular p. Their cells contain membrane and organelles; each performs specific functions increases efficiency: a. Nucleus—Membrane have storage site of genetic information that determines heredity and averts the activities of a cell. b. Mitochondria—Double-membrane power plants of the cell the cell and the location of aerobic respiration. c. Smooth/rough endoplasmic reticulum—Network of membranes were lipids and proteins are synthesized. Rough ER is covered with ribosomes. d. Golgi apparatus—Organelle that packages and exports protein and lipids produced in ER. e. Vesicles—Sacs in which substances are transported or stored. f. Lysosome—Vesicle of digestive enzymes that degraded old cellular components. g. Plant cells—contains several additional components: 1. Chloroplast—Sites of photosynthesis that contains chlorophyll (green pigment) and have a double membrane. 2. Vacuole—Vesicle used to store water, proteins and wastes. 3. Cell wall—rigid cellulose layer around the cell wall.

* “Windows on cellular function : The virus”
Virus is a small infection agent that can replicate only inside the living cells of an organism. It can infect all types of organisms.
Examples of viruses: 1. Influenza virus—a vital disease caring fevers, muscular pain, and Catarrh (inflammation of mucous membrane esp. the nose and with a watery discharge). 2. Adenovirus—any of a family of double stranded DNA viruses that cause infections of the respiratory system. 3. Bacteriophage Lambda—is a bacterial virus or Bacteriophage that infects the bacterial species Escherichia coli.

* “New tools in the Biological Revolution”
Biochemistry has been such more an experimental science than a theoretical one. The experimental nature of biochemistry has two important corollaries. First, in order to understand biochemistry, you must understand the critical experiments and experimental techniques on which our common understanding rests. Second, the spectacular growth of biochemical knowledge over the past four decades is due to development of many powerful research methodologies.
Gene cloning dates from about 1973. It is the replicator of DNA fragments by the use of a self-replicating genetic material. Unlike reproductive cloning, which replicates an entire organism, gene cloning duplicates only individual gene of an organism’s DNA.

* “The use of Biochemistry”
Biochemistry is a research discipline but the result of biochemical research are used extensively in the world outside the laboratory--- in agriculture, medical sciences, food sciences, clinical chemistry, pharmacology, toxicology and so on.
In agriculture, biochemistry studies the interaction of herbicides with plants. Herbicides are substances used to destroy plants. In Medical Science, utilizing biochemistry in medicine opens a window of cure for diseases and vaccines. In Food science, biochemist study such topics as how living things obtain energy from food, ways to develop abundant and inexpensive sources of nutritious foods, determines the chemical composition of foods, develop methods to extract nutrients from waste products or invest ways to prolong the shelf life food products. In clinical chemistry, biochemical measurements on people help diagnose illness and monitor responses to treatment. In Pharmacology, biochemist investigate the mechanism of a dry action in the body as in Toxicology, biochemist does research to understand ways in which organic compound in the body are changed by enzymes into toxic metabolites.