INTRODUCTION TO BIOCHEMISTRY

INTRODUCTION TO BIOCHEMISTRY The study of the chemical substances and vital processes occurring in living organisms. The chemical composition of a particular living system or biological substance. Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems. Biochemistry has become the foundation for understanding all biological processes. It has provided explanations for the causes of many diseases in humans, animals and plants. It can frequently suggest ways by which such diseases may be treated or cured. Biochemists study how living organisms extract food and energy from their environment and how they use the extracted molecules to make more of themselves. Buchner, by taking apart yeast cells, had opened the way to ask biochemical questions like: What kinds of molecules cause fermentation? How many different molecules are necessary? Why does the yeast cell do it? Why does it only happen if you keep oxygen out? These are questions that can be answered by separating the "dissolved substances" in the "juice" and asking what they are, how they interact with each other, and how their properties are related to their chemical nature.By using this approach, biochemists have succeeded in...Discovering that although too much cholesterol can cause heart disease, our bodies make cholesterol because it is an essential component of the membranes of our cells.Finding that cells distinctively mark themselves by putting specific groups of sugars, linked together in recognizable patterns, on their surfaces. Your body will reject transplanted tissue if the cells of that tissue have the wrong pattern of sugar groups on their surfaces.Learning that one of the reasons plants require the mineral nutrient magnesium is because it forms part of the structure of chlorophyll, the molecule plants use to trap solar energy.Exploring the way penicillin kills bacteria to discover that it prevents them from putting together the chemical structure of their cell walls. Biochemistry focuses on the study of life at molecular level - how genes and proteins regulate cells, tissues, organs and ultimately whole organisms like you. As you go about your daily life biochemistry is sure to be involved. It has a role in: understanding the causes of diseases; use of engineered therapeutic proteins in medicine; food production; understanding how cells function. This means you can see the effects of biochemistry all around you! It is central to all areas of the Biological or Life Sciences. The aim is to provide an understanding of every aspect of the structure and function of living things at the molecular level. It is a practical laboratory science that applies the molecular approaches of chemistry to the vast variety of biological systems.Biochemists work at all levels and with all types of biological organisms, ranging from biomolecules to man. There are close links with other specialist life sciences, such as Cell Biology, Genetics, Microbiology, Molecular Biology, Physiology and Pharmacology. In fact, in many cases the distinctions between these disciplines are becoming increasingly blurred. They use biochemical techniques and biochemists work in all these areas. Biochemistry offers the tremendous challenge of seeking to understand the most fundamental of life's processes at the molecular level, and to utilise this knowledge for the benefit of mankind. You will have read, for example, how biochemists, working with colleagues in other disciplines, have developed the new technologies of Molecular Biology and Genetic Engineering. These have enabled the production of therapeutically important human proteins such as insulin and blood clotting factors by cloning procedures, thus avoiding costly, time-consuming and inefficient isolation of these molecules from biological sources; the identification and possible remedying of genetic problems; and the use of DNA fingerprinting in forensic science. Biochemistry is the study of chemical processes associated with living organisms. Biochemists use concepts of biology, chemistry, physics, mathematics, microbiology, and genetics to unravel the complex puzzles of life. Biochemical techniques are used in clinical diagnosis of infectious diseases, genetic disorders, and cancer; as well as in many forms of research to improve the quality of our lives. Biochemists identify biological problems then develop and apply appropriate techniques to solve them at the molecular levelBiochemists study the most basic of life processes; for example, identifying the way in which DNA, which carries the genetic information, is transferred between cells and can be manipulated. This has led to the development of new technologies such as Molecular Biology and Genetic Engineering. The resulting recombinant DNA technology has formed the basis of modern biotechnology (e.g. production of human insulin), medical developments (e.g. prenatal diagnosis and genetic counselling) and forensic science (e.g. DNA fingerprinting).DNA directs the production of proteins. These have diverse functions, such as catalysing biological reactions (enzymes), carrying oxygen round the body (haemoglobin), protecting us from infection (antibodies) and holding us together (collagen). Using both simple and high-technology methods, biochemists work out how these proteins function. Biochemists also develop methods for making use of proteins, such as enzymes in biotechnology and antibodies in hormone analysis.With knowledge of the basic molecular mechanisms, biochemists study how life processes are integrated to allow individual cells to function and interact to form complex organisms. They work with all sorts of organisms, from viruses and bacteria to plants and man.These are just a few of the areas. It would take a whole book, in fact many books, to do justice to the multitude of roles of biochemists. Biochemists work in many walks of life - in industry, hospitals, agriculture, research institutes, education and associated areas. There are many areas of everyday life as diverse as medical products and diagnostics, new food and its safety, crop improvement, cosmetics and forensic science that owe their development or even existence to biochemists IndustryPharmaceutical, food, brewing, biotechnology and agrochemical companies all need and employ biochemists to develop new products and to monitor the production, quality control and safety of existing ones. MedicineHospitals, public health laboratories and medical research institutes, as well as the pharmaceutical industry, all require biochemists. Here they provide a diagnostic service, carrying out tests on blood, urine and other body fluids, alongside researching the underlying causes of disease and the methods of treatment. Agriculture and the EnvironmentBiochemists and biotechnologists, who often have a biochemistry degree, working in agriculture have been responsible for many developments, such as pest-resistant crops, improvements in crop yields and tomatoes that keep better. They also monitor the environment. Employers include seed companies, local government, the Civil Service and water authorities. EducationAll levels of education offer prospects for biochemists. The combination of biology and chemistry, along with the training in numerical and analytical skills that is given in any area of science, makes biochemistry ideal for teaching throughout the school age range. There are also opportunities for more advanced teaching, usually associated with research, in universities and colleges, and medical, dental and veterinary schools. Away from ScienceA science background can be an excellent starting point for many other careers. Biochemistry is a numerate subject that develops analytical thinking, creativity in problem solving, and the ability to handle large amounts of complex information - skills required in jobs in all walks of life including, for example, sales and marketing, accountancy and finance, journalism, and patent work. Biochemists have become successful popular authors and even a national president! Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Wöhler published a paper about the synthesis of urea, proving that organic compounds can be created artificially. The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to have been first used in 1881, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuber, a German chemist. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle). Today, the findings of biochemistry are used in many areas, from genetics to molecular biology and from agriculture to medicine macromolecule is a large molecule with a large molecular mass, but generally the use of the term is restricted to polymers and molecules which structurally include polymers. [1] Illustration of a polypeptide macromolecule Many examples come from biology and in particular biochemistry. In case of "biomacromolecules" or biopolymers, there are proteins, carbohydrates and nucleic acids (such as DNA). Lipids (fat) are not considered true macromolecules by most biologists as they are not covalently bonded, and so are not true polymers. Synthetic examples include plastics. The integral domains of crystals and metals, while composed of very large numbers of atoms joined by molecule-like bonds, are rarely referred to as "macromolecules." The term macromolecule is also sometimes used to refer to aggregates of two or more macromolecules held together by intermolecular forces rather than by chemical "bonds". This usage is common in particular when the individual macromolecules involved aggregate or "assemble" spontaneously and rarely exist in isolation. Such an aggregate is more properly called a macromolecular complex. In such a context, individual macromolecules are often referred to as subunits (see e.g. protein subunit). Substances that are composed of macromolecules often have unusual physical properties. The properties of liquid crystals and such elastomers as rubber are examples. Although too small to see, individual pieces of DNA in solution can be broken in two simply by suctioning the solution through an ordinary straw. This is not true of smaller molecules. The 1964 edition of Linus Pauling's College Chemistry asserted that DNA in nature is never longer than about 5000 base pairs. This is because biochemists were inadvertently and with perfect consistency breaking their samples into pieces. In fact, the DNA of chromosomes can be tens of millions of base pairs long. Another common macromolecular property that does not characterize smaller molecules is the need for assistance in dissolving into solution. Many require salts or particular ions to dissolve in water. Proteins will denature if the solute concentration of their solution is too high or too low. According to IUPAC recommendations the term macromolecule is reserved for an individual molecule, and the term polymer is used as to denote a substance composed of macromolecules. Polymer may also be employed unambiguously as an adjective, according to accepted usage, e.g. polymer blend, polymer molecule. [2] [edit] External links Major categories of bio-compounds: Carbohydrates : sugar -- disaccharide -- polysaccharide -- cholesterol -- starch -- glycogen Lipids : fatty acid -- fats -- essential oils -- oils -- waxes Nucleic acids : DNA -- RNA -- mRNA -- tRNA -- rRNA -- codon -- adenosine -- cytosine -- guanine -- thymine -- uracil Proteins : amino acid -- glycine -- arginine -- lysine peptide -- primary structure -- secondary structure -- tertiary structure -- conformation -- protein folding Chemical properties: molecular bond -- covalent bond -- ionic bond -- hydrogen bond -- ester -- ethyl molecular charge -- hydrophilic -- hydrophobic -- polar pH -- acid -- alkaline -- base oxidation -- reduction -- hydrolysis Structural compounds: In cells: flagellin -- peptidoglycan -- myelin -- actin -- myosin In animals: chitin -- keratin -- collagen -- silk In plants: cellulose -- lignin -- cell wall Enzymes and enzyme activity: enzyme kinetics -- enzyme inhibition proteolysis -- ubiquitin -- proteasome kinase -- dehydrogenase Membranes : fluid mosaic model -- diffusion -- osmosis phospholipids -- glycolipid -- glycocalyx -- antigen -- isoprene ion channel -- proton pump -- electron transport -- ion gradient -- antiporter -- symporter -- quinone -- riboflavin Energy pathways : pigments : chlorophyll -- carotenoids -- xanthophyll -- cytochrome -- phycobilin -- bacteriorhodopsin -- hemoglobin -- myoglobin -- absorption spectrum -- action spectrum -- fluorescence Photosynthesis : light reaction -- dark reaction Fermentation : Acetyl-CoA -- lactic acid Cellular respiration : Adenosine triphosphate (ATP) -- NADH -- pyruvate -- oxalate -- citrate Chemosynthesis Regulation hormones : auxin signal transduction -- growth factor -- transcription factor -- protein kinase -- SH3 domain Malfunctions : tumor -- oncogene -- tumor suppressor gene Receptors : Integrin -- transmembrane receptor -- ion channel Techniques : electrophoresis -- chromatography -- mass spectrometry -- x-ray diffraction -- Southern blot -- fractionation -- Gram stain Objective To describe functional groups of organic compounds of biological interest and provide some examples of chemical reactions and interconversions among these. Reference: Stryer, 4th edition, 1994, Chapter 1, pp. 3-16 I. Some Examples of Chemical Reactions I. Functional Groups a. Alcohols R-CH2-OH(primary); R2-CH-OH (secondary); R3-C-OH (tertiary) Sustitution on the Carbon atom defines whether the alcohol is primary, secondary or tertiary. Carbon atom in these cases is in sp3 hybrid state. b. Aldehydes and Ketones R-CHO; R2-C=O Carbon atom is double bonded to oxygen in both cases. The difference is in substitutions. Aldehyde has an R group and a H atom whereas in a ketone both substituents are R groups. Carbon atom in these cases is in sp2 hybrid state. c. Acids R-C=O Acids are able to dissociate into H+ and anions ! OH d. Acid Anhydrides (R-CO)2O Acid anhydrides are formed from molecules of same or different acids with the elimination of a molecule of water. An example would the formation of pyrophosphate from two molecules of phosphoric acid. e. Esters RCH2-O-COCH3 An ester is formed from an alcohol and an acid with the elimination of a molecule of water.Physiological examples include formation of triacyl glycerols from fatty acids and glycerol. f. Unsaturated Compounds Unsaturated compouds like R-CH=CH---- are formed either by the elimination of water fron a hydroxy compund like R-CHOH-CH2---- or by dehydrogenation of compunds like R-CH2-CH2---. The double bond may be cis or trans depending on the positions of hydrogen atoms in space. In cis configuration, H atoms would lie in a plane perpendicular to the plane of the double bond whereas iin trans configuration H atoms lie in the same plane as the double bond. g. Amines and Amides II. Reaction Types A. Oxidation/Reduction (removal of electron or reaction with O2) B. Esterification (carboxylic acid plus alcohol) C. Hydrolysis (cleavage of a bond by water) D. Phosphorolysis (cleavage of a bond by inorganic phosphate) E. Decarboxylation F. Deamination G. Transamination (amino group transfer) H. Phosphorylation (ester bond on sugars, some amino acids, bases) I. Dehydration J. Phosphorylation (transfer of a phosphate group) K. Transmethylation L. Condensation III. Coupled Reactions Decarboxylation and oxidation/reduction Study Assignment I Draw the structures of molecules that have the functional groups listed above and identify the functional groups. Some molecules will have several functional groups. Study Assignment II For reaction types listed in IIA-L, above, write out the entire reaction, including molecular structure. Use material presented to you in Biochemistry lectures to complete the assignment.