Foundation of Biochemistry Part 1 PDF

CHAPTER 1 – PART I FOUNDATION OF BIOCHEMISTRY CHAPTER OUTLINE: 1. Composition of Biomolecules 2. Molecular Organization of the Components of a Cell 3. Naming and Classification of Functional Groups Lesson 1.1 COMPOSITION OF BIOMOLECUL...

CHAPTER 1 – PART I FOUNDATION OF BIOCHEMISTRY CHAPTER OUTLINE: 1. Composition of Biomolecules 2. Molecular Organization of the Components of a Cell 3. Naming and Classification of Functional Groups Lesson 1.1 COMPOSITION OF BIOMOLECULES CHEMICAL MOLECULES OF LIFE The living matter is composed of mainly six elements — carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur (CHNOPS). These elements together constitute about 90% of the dry weight of the human body. Several other functionally important elements are also found in the cells. These include Ca, K, Na, Cl, Mg, Fe, Cu, Co, I, Zn, F, Mo and Se. Carbon is tetravalent and able to form bonds with itself and with many other elements, giving rise to different kinds of monomers, such as amino acids, nucleotides, and monosaccharides (sugar monomers). In present-day cells, amino acids (the monomers) combine by polymerization to form proteins, nucleotides (also monomers) combine to form nucleic acids, and the polymerization of sugar monomers produces polysaccharides. Proteins and nucleic acids play a key role in life processes. Amino Acids Nucleotides Sugar Monomers 1  The organic compounds such as amino acids, nucleotides and monosaccharides serve as the monomeric units or building blocks of complex biomolecules— proteins, nucleic acids (DNA and RNA) and polysaccharides, respectively. BUILDING BLOCK BIOMOLECULE MAJOR FUNCTIONS (REPEATING UNIT) Fundamental basis of structure and Protein Amino acids function of cell (static and dynamic functions). Deoxyribonucleic Deoxyribonucleotides Repository of hereditary information. acid (DNA) Ribonucleic acid Essentially required for protein Ribonucleotides (RNA) biosynthesis. Polysaccharide Monosaccharides Storage form of energy to meet short (glycogen) (glucose) term demands. Storage form of energy to meet long Lipid Fatty acids, glycerol term demands; structural components of membranes. STRUCTURAL HEIRARCHY OF AN ORGANISM The macromolecules (proteins, lipids, nucleic acids and polysaccharides) form supramolecular assemblies (e.g. membranes) which in turn organize into organelles, cells, tissues, organs and finally the whole organism. 2  BIOCHEMISTRY describes, in molecular terms, the structures, mechanisms, and chemical processes shared by all organisms, and provides organizing principles that underlie life in all its diverse forms. Lesson 1.2 MOLECULAR ORGANIZATION OF THE COMPONENTS OF A CELL THE CELL The cell is the structural and functional unit of life. It may be also regarded as the basic unit of biological activity. The concept of cell originated from the contributions of Schleiden and Schwann (1838). However, it was only after 1940, the complexities of cell structure were exposed. 3 PROKARYOTIC & EUKARYOTIC CELLS The cells of the living kingdom may be divided into two categories Prokaryotes (Greek: pro – before; karyon – nucleus) lack a well-defined nucleus and possess relatively simple structure. These include the various bacteria. Eukaryotes (Greek: eu – true; karyon – nucleus) possess a well-defined nucleus and are more complex in their structure and function. The higher organisms (animals and plants) are composed of eukaryotic cells. Characteristic Prokaryotic cell Eukaryotic cell Size Small (generally 1–10 μm) Large (generally 10–100 μm) Cell Cell is enveloped by a rigid cell Cell is enveloped by a flexible plasma membrane wall membrane Subcellular Distinct organelles are found (e.g. Absent organelles mitochondria, nucleus, lysosomes) Not well defined; DNA is found Nucleus is well defined, surrounded by Nucleus as nucleoid, histones are a membrane; DNA is associated with absent histones Mitochondria absent, enzymes Energy Enzymes of energy metabolism are of energy metabolism bound to metabolism located in mitochondria membrane Cell division Usually fission and no mitosis Mitosis Organelles and cytoskeleton Contains organelles and cytoskeleton Cytoplasm absent (a network of tubules and filaments) How is prokaryotic DNA organized without a nucleus? Although no well-defined nucleus is present in prokaryotes, the DNA of the cell is concentrated in one region called the nuclear region. This part of the cell directs the workings of the cell, much as the eukaryotic nucleus does. In general, there is only a single, closed, circular molecule of DNA in prokaryotes. This circle of DNA, which is the genome, is attached to the cell membrane. Before a prokaryotic cell divides, the DNA replicates itself, and both DNA circles are bound to the plasma membrane. The cell then divides, and each of the two daughter cells receives one copy of the DNA. 4  COMPONENTS OF A CELL NUCLEUS Nucleus is the largest cellular organelle, surrounded by a double membrane nuclear envelope. The outer membrane is continuous with the membranes of endoplasmic reticulum. At certain intervals, the two nuclear membranes have nuclear pores with a diameter of about 90 nm. These pores permit the free passage of the products synthesized in the nucleus into the surrounding cytoplasm. Nucleus contains DNA, the repository of genetic information. An assembly of nucleosomes constitutes chromatin fibers of chromosomes (Greek: chroma – color; soma – body). Thus, a single human chromosome is composed of about a million nucleosomes. The number of chromosomes is a characteristic feature of the species. Humans have 46 chromosomes, compactly packed in the nucleus. The nucleus of the eukaryotic cell contains a dense body known as nucleolus. It is rich in RNA, particularly the ribosomal RNA which enters the cytosol through nuclear pores. 5  The ground material of the nucleus is often referred to as nucleoplasm. It is rich in enzymes such as DNA polymerases and RNA polymerases. Hutchinson-Gilford progeria syndrome (HGPS) is a rare condition of aging beginning at birth (incidence 1 in 5 million births). HGPS occurs as a result of distortion of nuclear envelope due to accumulation of abnormal protein namely lamina A. MITOCHONDRIA The mitochondria (Greek: mitos – thread; chondros – granule) are the centers for the cellular respiration and energy metabolism. They are regarded as the power houses of the cell with variable size and shape. Mitochondria are rod-like or filamentous bodies, usually with dimensions of 1.0×3 μm. About 2,000 mitochondria, occupying about 1/5th of the total cell volume, are present in a typical cell. The mitochondria are composed of a double membrane system. The outer membrane is smooth and completely envelops the organelle. The inner membrane is folded to form cristae (Latin – crests) which occupy a larger surface area. The internal chamber of mitochondria is referred to as matrix or mitosol. 6 ENDOPLASMIC RETICULUM The network of membrane enclosed spaces that extends throughout the cytoplasm constitutes endoplasmic reticulum (ER). Some of these thread-like structures extend from the nuclear pores to the plasma membrane. A large portion of the ER is studded with ribosomes to give a granular appearance which is referred to as rough endoplasmic reticulum. Ribosomes are the factories of protein biosynthesis. During the process of cell fractionation, rough ER is disrupted to form small vesicles known as microsomes. The smooth endoplasmic reticulum does not contain ribosomes. It is involved in the synthesis of lipids (triacylglycerols, phospholipids, sterols) and metabolism of drugs, besides supplying Ca2+ for the cellular functions. GOLGI APPARATUS Eukaryotic cells contain a unique cluster of membrane vesicles known as dictyosomes which, in turn, constitute Golgi apparatus (or Golgi complex). The newly synthesized proteins are handed over to the Golgi apparatus which catalyze the addition of carbohydrates, lipids or sulfate moieties to the proteins. These chemical modifications are necessary for the transport of proteins across the plasma membrane. LYSOSOMES Lysosomes are spherical vesicles enveloped by a single membrane. Lysosomes are regarded as the digestive tract of the cell, since they are actively involved in digestion of cellular substances—namely proteins, lipids, carbohydrates and nucleic acids. 7  Lysosomal enzymes are categorized as hydrolases. These include the enzymes (with substrate in brackets)—α-glucosidase (glycogen), cathepsins (proteins), lipases (lipids), ribonucleases (RNA). Inclusion cell (I-cell) disease is a rare condition due to the absence of certain hydrolases in lysosomes. However, these enzymes are synthesized and found in the circulation. I-cell disease is due to a defect in protein targeting, as the enzymes cannot reach lysosomes. PEROXISOMES Peroxisomes, also known as microbodies, are single membrane cellular organelles. They are spherical or oval in shape and contain the enzyme catalase. Catalase protects the cell from the toxic effects of H2O2 by converting it to H2O and O2. Peroxisomes are also involved in the oxidation of long chain fatty acids (>C18), and synthesis of plasmalogens and glycolipids. Plants contain glyoxysomes, a specialized type of peroxisomes, which are involved in the glyoxylate pathway. 8  Peroxisome biogenesis disorders (PBDs), are a group of rare diseases involving the enzyme activities of peroxisomes. The biochemical abnormalities associated with PBDs include increased levels of very long chain fatty acids (C24 and C26) and decreased concentrations of plasmalogens. The most severe form of PBDs is Zellweger syndrome, a condition characterized by the absence of functional peroxisomes. The victims of this disease may die within one year after birth. CYTOSOL AND CYTOSKELETON The cellular matrix is collectively referred to as cytosol. Cytosol is basically a compartment containing several enzymes, metabolites and salts in an aqueous gel like medium. More recent studies however, indicate that the cytoplasm actually contains a complex network of protein filaments, spread throughout, that constitutes cytoskeleton. The cytoplasmic filaments are of three types – microtubules, actin filaments and intermediate filaments. PLANT CELL 9 CHLOROPLASTS Chloroplasts are important organelles found only in green plants and green algae. The photosynthetic apparatus is found in specialized structures called grana (singular granum), membranous bodies stacked within the chloroplast. Grana are easily seen through an electron microscope. Chloroplasts, like mitochondria, contain a characteristic DNA that is different from that found in the nucleus. Chloroplasts and mitochondria also contain ribosomes similar to those found in bacteria. CLASSIFICATIONS OF CELLS INTEGRATION OF CELLULAR FUNCTIONS The eukaryotic cells perform a wide range of complex reactions/functions to maintain tissues, and for the ultimate well-being of the whole organism. For this purpose, the various intracellular processes and biochemical reactions are tightly controlled and integrated. Division of a cell into two daughter cells is good example of the orderly occurrence of an integrated series of cellular reactions. 10  Apoptosis is the programmed cell death or cell suicide. This occurs when the cell has fulfilled its biological functions. Apoptosis may be regarded as a natural cell death and it differs from the cell death caused by injury due to radiation, anoxia etc. Programmed cell death is a highly regulated process. 11