MODULE 2.1 Introduction to Biochemistry PDF

MODULE 2.1 INTRODUCTION TO BIOCHEMISTRY Biochemistry is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. It seeks to describe the structure, organization, and functions of the living...

MODULE 2.1 INTRODUCTION TO BIOCHEMISTRY Biochemistry is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. It seeks to describe the structure, organization, and functions of the living organisms in molecular terms. It sought to answer particular kinds of questions such as: 1) What are the chemical structures of the components of living organisms? 2) How do the interactions of these components give rise to organized molecular structures, cells, multicellular tissues and organisms? 3) How are chemical reactions controlled inside living cells? Principal areas of Biochemistry: 1) Structural: concerned with the components of living matter, discusses the relationship of biological function to chemical structure 2) Metabolism: concerned with the total chemical reactions in living matter 3) Chemistry of processes and substances: store and transmit biological information related to molecular genetics that involves the heredity and genetic information Development of Biochemistry Biochemistry had its origins as a distinct field of study in the early nineteenth century, (1828) with the pioneering work of Friedrich Wohler who showed that urea, a substance of biological origin, could be synthesized in the laboratory from the inorganic compound ammonium cyanate. Prior to Wohler’s work, it was believed that the substances in living organisms was somehow qualitatively different from those in non- living organisms and did not behave according to known laws of physics and chemistry. To his colleagues, Wohler then wrote “I must tell you that I can prepare urea without requiring a kidney, or an animal, either man or dog.” This was a shocking statement in its time, for it breached the presumed barrier between the living and the non-living. Even after Wohler’s demonstration, a persuasive viewpoint called vitalism held that “if not the compounds, at least the reactions of living organisms could occur only in living cells. According to this view, biological reactions took place through the action of mysterious “life force” rather than physical and chemical processes. The vitalist dogma was shattered in 1897, when two German brothers – Edward and Hans Buchner found that extracts from dead, broken yeast cells could completely carry out the fermentation of sugar into ethanol. This discovery opened the door for the analysis of biochemical reactions and processes in vitro (Latin “in glass), meaning in a test tube, rather than in vivo (in living organism). In succeeding decades, many other metabolic reactions and reaction pathways were reproduced in vitro, allowing identification of reactants and products, and the biological catalysts (enzymes) that promote each biochemical reaction. In 1926, J.B. Sumner showed that the protein urease, an enzyme from jack beans, could be crystallized. This showed that although proteins have large and complex structures, their structures could be determined by the methods of chemistry like any other organic compound. This discovery marked the final fall of vitalism. Parallel with developments in biochemistry, cell biologists had been continually refining knowledge in cell structure and function. Robert Hooke first observed cells in the 19th Century. Steady improvements in microscopy led to the understanding that cells are complex compartmental structures. Walter Fleming discovered chromosomes in 1875 and identified and identified these as genetic elements in 1902. The development of the electron microscope between 1030 and 1950 led to the discovery of the mitochondria, chloroplast and other cell organelles. Chemical reactions and metabolic pathways associated with these cell structures were also studied. Gregor Mendel first proposed that genes are units of hereditary information in the mid-nineteenth Century. Experiments conducted in the 1940s to 1950s proved conclusively that the deoxyribonucleic acid is the bearer of the genetic information. In 1953, James Watson and Francis Crick described the double helical structure of the DNA. These and more advancements of knowledge in cell anatomy and physiology helped the full development of biochemistry. Biochemistry now is a field in which new discoveries are made almost daily about how cells manufacture the molecules needed for life and how the chemical reactions by which life is maintained occur. The knowledge explosion that has occurred in the field of Biochemistry during the last decades of the twentieth century and the beginning of the twenty-first is truly phenomenal. Table 1.1 Important scientists and their contribution to biochemistry and other related fields 1493- Theophrastus He held that illness was the result of external agents attacki 1541 Bombastus ng the body rather than imbalances within the body Paracelsus and advocated the use of chemicals against disease von Hohenheim causing agents 1837 Berzelius Postulated the catalytic nature of fermentation. He also identified lactic acid as a product of muscle activity 1838 Schleiden and Enunciated the cell theory Schwann 1854- Louis Pasteur Proved that fermentation is caused by microorganisms 1864 1869 Miescher Discovered DNA 1877 Kuhne Proposed the term ‘Enzyme’  1894 Emil Fischer Demonstrated the specificity of enzymes and the lock and key relationship between enzyme and substrate 1897 Buchner Discovered alcoholic fermentation in cell-free yeast extract 1902 Emil Fischer Demonstrated that proteins are polypeptides 1903- Neuberg First used the term ‘biochemistry’Proposed pathway for 1912 fermentation 1913 Michaelis and Developed kinetic theory of enzyme action Menten 1926 Sumner First crystallized an enzyme, urease and proved it to be a protein 1933 Embden Demonstrated crucial intermediates in the chemical Meyerhof and pathway of glycolysis and fermentation Parnas 1937 Krebs Discovered citric acid cycle 1940 Lipmann Role of ATP in biological systems 1950- Chargaff Discovered the base composition of DNA 1953 1953 Sanger and Determined the complete amino acid sequence of insulin Thompson 1953 Watson and Proposed the double-helical model for DNA structure Crick 1961- Nirenberg Identified the genetic code words for amino acids 1965 Khorana and Ochoa 1980 Snell Development of recombinant DNA research leading to genetic engineering 1988 Collin Pitchfork was the first person convicted of murder with DNA evidence, which led to growth of forensic science Branches of Biochemistry 1. Plant biochemistry - study of the biochemistry of autotrophic organisms such as photosynthesis and other plant specific biochemical processes 2. General biochemistry - encompasses both plant and animal biochemistry 3. Human/medical/medicinal biochemistry - focuses on the biochemistry of humans and medical illnesses 4. Cellular biochemistry - focuses on the chemical processes within cells - includes studying how cells produce energy, store and use nutrients, and how they produce and maintain their structure. 5. Molecular biochemistry - looks at the structure and function of biomolecules, such as proteins, DNA, and carbohydrates - includes understanding how these molecules carry out biochemical reactions and how they interact. 6. Metabolic biochemistry - focuses on the chemical reactions in the body to maintain life - includes studying energy production, nutrient metabolism, and detoxification 7. Biochemical genetics - investigates the role of genes in biochemical processes - includes understanding how genes are involved in synthesizing proteins and other biomolecules and how they function 8. Enzymology - studies the behavior of biological catalysts or enzymes, such as certain proteins or specific catalytic RNA, and coenzymes and cofactors such as metals and vitamins 9. Neurochemistry - study of organic molecules involved in neuronal activity - frequently referred to as neurotransmitters and other molecules such as neuro-active drugs influencing neuronal function 10. Comparative Biochemistry - deals with the relations between different life forms and how they evolved from original chemical structure 11. Microbial Biochemistry - deals with the metabolism of bacteria and other microorganisms 12. Pathological Biochemistry - concerned with the abnormalities of metabolism found in diseases. - Genetics has been receiving attention because metabolic abnormalities are inherited Importance of Biochemistry 1) Biochemistry has become the basic language of all biologic sciences. It is concerned with the molecules present in living organisms, the chemical reactions with their corresponding catalysts and the regulation of each metabolic process. 2) Biochemistry provides basic information in health care. Health depends on harmonious balance of chemical reactions in the body. Diseases, on the other hand, reflect abnormalities in biomolecules, biochemical reactions or biochemical reactions or biochemical processes. 3) Researches in biochemistry provide insights into understanding nutrition, and medical sciences, among many other fields. 4) Biochemical approaches are fundamental in illuminating the causes of diseases and in designing appropriate therapy. 5) Biochemical laboratory tools are integral components of diagnosis and monitoring of treatment. Liver disease, for example, is now routinely diagnosed and monitored by measurement of the levels of transaminases and bilirubin in the blood. 6) A sound knowledge of biochemistry and of other related basic disciplines is essential for the rational practice of medicine and related health sciences. Biochemistry as a Chemical Science Biochemistry is often described as a life science but it remains first and foremost a chemical science. In order to understand the impact of biochemistry in the life sciences, one must first be familiar with the chemical composition of living organisms. Primarily, living organisms contain the chemical elements: 1) carbon, hydrogen, oxygen and nitrogen (C, H, O, N) which are very important to life because of their strong tendencies to form covalent bonds. The stability of carbon-to-carbon bonds and the possibility of forming single, double, or triple bonds give carbon the versatility to be a part of diverse chemical compounds. The abundance of oxygen and hydrogen is explained by the major role of water in living organisms. 2) sulfur (S) which is an important constituent of proteins 3) phosphorous (P) which plays essential roles in energy metabolism and in the structure of nucleic acids 4) sodium (Na), potassium (K), magnesium (Mg), calcium (Ca) and chlorine (Cl) ions which form inorganic salts in living organisms 5) cobalt (Co), copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn) are metals present in all organisms in small amounts but are essential to life 6) other elements such as aluminum (Al), boron (B), bromine (Br), etc which are found in or required by some living organisms in trace amounts.  These elements bond together in several ways to form biochemical substances which are chemical substances found within living organisms. Biochemical substances are divided into two groups: 1) Bioinorganic substances – chemical substances in living organisms which do not contain the element carbon. These include: a) water – its solvent properties are indispensable in biochemical properties, hence, the human body is 70% water. b) inorganic salts – used by cells to transmit electrical impulses across membranes, maintain normal osmotic pressure and acid-base balance in the body; constitutes 4% to 5% of the body mass.  Sodium Chloride (NaCl) – for maintaining fluid balance, regulating blood pressure, transmitting nerve impulses, and muscle function.  Potassium Chloride (KCl) – for nerve function, muscle contraction, and maintaining proper heart rhythm.  Calcium Phosphate (Ca3(PO4)2) – major components of bones and teeth, providing structural support. Calcium is also involved in muscle contraction, blood clotting, and nerve transmission.  Magnesium Sulfate (MgSO4) – for muscle and nerve function, blood glucose control, and bone health.  Iron (Fe) – for the formation of hemoglobin in red blood cells, which carries oxygen to tissues throughout the body. 2) Bioorganic substances - chemical substances in living organisms which contain the element carbon. These represent 25% of the total body mass and include: a) Carbohydrates - generally consist of the elements carbon, hydrogen and oxygen in 1:2:1 ratio; constitute about 2% of total body mass. They are essential components of nucleic acids, act as storehouses of chemical energy, and are important structural components of living organisms. b) Lipids – primarily composed of the elements carbon, hydrogen and oxygen and compose about 8% of total body mass. They are insoluble in water but soluble in non-polar solvents and in solvents with low polarity. They serve for energy storage, form parts of cell membranes and act as chemical messengers. c) Proteins – structurally made of the elements carbon, hydrogen, oxygen, nitrogen and phosphorous; constitute about 15 % of the total body mass. Proteins are considered the most important biological compounds. Enormous types of proteins exist and they perform variety of functions. d) Nucleic acids – constitute about 2% of the total body mass and are made of chains of nucleotides. Two kinds of nucleic acids are found in cells, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is found in chromosomes while RNA could be found in the nucleus and in the cytoplasm of cells. Each has its own role in the transmission of hereditary information.