Biochemistry and Cell Organization PDF

INTRODUCTION Biochemistry is the systematic study of the chemicals of the living systems, their organization, and the principles of their participation in the processes of life. Its importance is due to the increasing recognition that underlying...

INTRODUCTION Biochemistry is the systematic study of the chemicals of the living systems, their organization, and the principles of their participation in the processes of life. Its importance is due to the increasing recognition that underlying each and every biological function is a chemical reaction. Hundreds/thousands of chemical reactions are taking place in our cells every minute of our lives. Biochemical investigations have been directed towards the study of the chemical composition of cells and the chemical processes in which they participate. Several principles are central to the understanding of living organisms: 1) Cells, the basic structural units of all living things, are highly organized. 2) Living processes consist of hundreds of chemical reactions. 3) Certain fundamental reaction pathways are found in all living organisms. 4) All organisms use the same type of molecules. 5) The instructions for growth, development, and reproduction are encoded in an organism’s nucleic acids. The life of a cell requires materials, information, and energy: A cell in particular, and a whole organism in general, has three basic needs: materials, information, and energy. Without the daily satisfaction of these, human life would be severely constrained. The organic materials of life will be considered, starting with the three main classes of foodstuffs – carbohydrates, lipids, and proteins. Humans use these molecules to build and run their bodies and to try to stay in some state of repair. Plants rely heavily on carbohydrate for cell walls, and animals obtain considerable energy from carbohydrates made by plants. Lipids serve many purposes. They are used, both by plants and animals, as materials to make cell membranes and as sources of chemical energy. Proteins are particularly important in both the structures and functions of cells. Because of the catalytic role of proteins in regulating chemical events in cells, the study of proteins will be immediately followed with an examination of enzymes, which make up a particular family of proteins. Every cell has an information system – enzymes, hormones, and neurotransmitters are components of the intricate information system in the body. Without information, the materials and energy delivered to the body could produce only rubbish. Although enzymes are major players in the cells’ information system, they do not originate the cellular script. They only help to carry out directions that are encoded in the molecular structures of the nucleic acids, which are compounds that are able to direct the synthesis of enzymes. Hormones & neurotransmitters, two other components of cellular information, depend on the presence of right enzymes not only for their existence but for their functions. Thus the study of the enzyme makers, the nucleic acids, is included in any study of the molecular basis of life. All life processes consist of chemical reactions catalyzed by enzymes. The reactions of a living cell, which are known collectively as metabolism, result in highly coordinated and purposeful activity. Among the most frequent reactions encountered in biochemical processes are: 1) nucleophilic substitution 4) isomerization 2) elimination 5) oxidation – reduction 3) addition 6) hydrolysis To supply materials for any use – parts, information, or energy – each organism has basic nutritional needs. These include not just organic materials, including vitamins, but also mineral, water, and oxygen. Thus, together with learning about the materials of life and how they are processed and used, the need for vitamins, minerals, water, and oxygen will also be considered. 1  I. CELL STRUCTURE Based on their cell structures, organisms are divided into two main groups: 1) Prokaryote: Greek derivation meaning “before the nucleus”; single-celled organisms 2) Eukaryote: Greek derivation meaning “true nucleus”; contain a well-defined nucleus surrounded by a nuclear membrane; can be single celled, such as yeasts and Paramecium, or multicellular, such as animals and plants Five kingdoms: 1) Monera - only prokaryotic organisms; includes bacteria and cyanobacteria 2) Protista - includes unicellular eukaryotes: yeast, Euglena, Volvox, Amoeba, and Paramecium 3) Fungi - includes molds and mushrooms 4) Plantae Fungi, plants, and animals are multicellular eukaryotes 5) Animals (with few unicellular eukaryotes) The main difference between prokaryotic and eukaryotic cells is the existence of organelles, especially the nucleus, in eukaryotes. An organelle is a part of the cell that has a distinct function; it is surrounded by its own membrane within the cell. Or ganel l e Pr ok ar yotes Euk ar yotes Nucl eus No defi ni te nucl eus; DNA Pr esent pr esent but not separ ate fr om the r est of the cel l Cel l membr ane Pr esent Pr esent M i tochondr i a None; enzym es for oxi dati on Pr esent ar e on pl asma membr ane Endopl asmi c None Pr esent r eti cul um Ri bosomes Pr esent Pr esent Chl or opl asts None; photosyn thesi s Pr esent i n l ocal i zed i n chr omatophor es gr een pl ants 2  Organel l e Functi on Nucl eus Locati on of mai n genome & most DNA/RNA synthesi s Mi tochondri on Si te of energy-yi el di ng oxi dati on reacti ons; has i ts own DNA Chl oropl ast Si te of photosynthesi s i n green pl ants and al gae; has i ts own DNA Endopl asmi c Conti nuous membrane throughout the cel l , rough reti cul um part studded wi th ri bosomes; si tes of protei n synthesi s Gol gi Seri es of fl attened membranes; i nvol ved i n secreti on apparatus of protei ns from cel l s and i n reacti ons that l i nk sugars to other cel l ul ar components Lysosomes Membrane-bounded sacs contai ni ng hydrol yt i c enzym es Peroxi somes Sacs that contai n enzym es i nvol ved i n the metabol i sm of hydrogen peroxi de Cel l membrane Separates the cel l contents from the outsi de worl d Cel l wal l Ri gi d ext eri or l ayer of pl ant cel l s Central vacuol e Membrane-bound sac (pl ant cel l s) 1. Cell membrane / plasma membrane - a semi-permeable membrane surrounding the cell separating its internal environment from the external environment; permits and/or enhances the absorption of essential nutrients into the cell while preventing the diffusion of needed metabolites. - a lipid bilayer that mechanically holds cell together, composed of lipid and protein molecules. Lipids provide the basic structure of biological membranes. Proteins are embedded in the membranes and provide channels/carriers for the transport of ions and nutrients. Other membrane proteins act as receptors that bind certain cellular constituents, particularly enzymes in a location apparently most advantageous for the performance of their specific biochemical functions. Receptors also bind hormones on the external surface of the cell which interaction initiates a programmed response by the cell. For example, binding of the hormone insulin to insulin receptors results in a series of changes in the cell’s activity, 2. Nucleus - the “information center” of the cell; enclosed by a nuclear membrane and contains the cell’s genetic information and the machinery for converting that information into protein molecules. - site of DNA and RNA synthesis - contains a comparatively large amount of nucleoprotein (50% DNA and 50% proteins, histones and prolamines located in the chromosomes, and a small amount of RNA; >95% of nucleic acids of the cell is in the nucleus Nucleolus - small, round dense body present within the nucleus; not surrounded by a membrane; essentially a cluster of looped chromosomal segments; contains 10-20% of the total RNA of the cell, chiefly mRNA - serve as a storehouse for mRNA prior to its movement into the cytoplasm by way of the nuclear pores 3. Cytoplasm - structureless and highly viscous; the aqueous phase of the cell in which many particulate constituents like mitochondria, ribosomes, etc. are suspended. - contains a wide variety of solutes including proteins, enzymes, nucleic acids (RNA), a number of electrolytes, metabolites for cellular utilization (e.g., glucose), and waste products of cellular activity (e.g., urea, creatinine, uric acid, etc.) 3  4. Mitochondria - the second largest organelle; usually ellipsoidal in shape; the powerhouse of the cell where carbohydrates, lipids, and amino acids are oxidized to CO2 and H2O by molecular O2 and the energy set free is converted into the energy of ATP - has a double-membrane structure, an outer membrane and an inner membrane. The inner membrane, in which the enzymes of electron transport and energy conversion are located, is convoluted to form shelves termed cristae; site for cellular respiration. 5. Endoplasmic reticulum - appears to be a system of interconnected tubules or canaliculi extending throughout the cell cytoplasm and is continuous with the outer nuclear membrane; two types: rough and smooth er - rough er is lined with a number of small, spheric, electron-dense particles called ribosomes; primarily involved in synthesis of membrane proteins and proteins for export from the cell - smooth er lacks ribosomes; appears to be involved in the biosynthesis of steroids, phospholipids, and complex polysaccharides; functions also include biotransformation, a process in which water-soluble organic molecules are prepared for excretion 6. Ribosomes - consist of ~50% RNA (rRNA) and 50% protein; involved in protein synthesis in the cell and are sometimes referred to as the “workbench” for protein synthesis - complex structures containing two irregularly shaped subunits of unequal size; they come together to form whole ribosomes when protein synthesis is initiated, when not in use, the ribosomal subunits separate 7. Golgi apparatus (Golgi complex) - structures composed of flattened sacs with vesicles, located near the nucleus, probably continuous with er - the organelles to which synthesized proteins are transported and temporarily stored before release from the cell - the “packaging stations” of the cell, the primary site for packaging and distribution of cell products to internal and external compartments - there is a continuous flow of substances through the Golgi apparatus - responsible for sorting and packaging several types of proteins, small molecules, and new membrane components 8. Lysosomes - membrane-bound organelles containing a variety of hydrolytic and degradative enzymes and having an optimum pH of 5.0 - has regulatory and defense function; function in the digestion of materials brought into the cell by phagocytosis and pinocytosis; also serve to digest cell components after cell death; the “suicide bags” of the cell - upon death of the cell or its exposure to environmental conditions, the lysosomal membrane disintegrates, releasing its contents, which cause the self-digestion or autolysis of the cell constituents 9. Peroxisomes - contains oxidative enzymes that oxidize amino acids, uric acid, and various 2-hydroxyamino acids using O2 with the formation of H2O2, which is then converted to H2O and O2 by the enzyme catalase also present in the peroxisomes – thus the cell protects itself from the toxicity of H2O2 The study of the composition of the living matter is necessary for the intelligent understanding of the chemical processes taking place in the body. The protoplasm, the living matter, is composed of: a) bioinorganic substances that include water (70-90%) and inorganic salts (chloride, sulfate, phosphate, carbonate, etc. salts of Na, K, Ca, Mg, NH4) and b) bioorganic compounds that include proteins, lipids, carbohydrates, and nucleic acids. 4 Some importance of water in the cell: 1. the solvent - the agency that enables water-soluble, water-miscible, or emulsifiable substances to be transferred in the body not only in the blood but also intercellularly and intracellularly 2. in biochemical reactions - ionization is a prerequisite to many biochemical reactions and ionization takes place in water 3. in physiologic regulation of body temperature - high specific heat (amount of heat required to raise the temperature of 1g of H2O 1oC) enables the body to store heat effectively without greatly raising its temperature - high heat conductivity permits heat to be transferred readily from the interior of the body to the surface - high latent heat of evaporation causes a great deal of heat to be used in its evaporation and thus cools the surface of the body Chemical reactions occurring in vivo have the following properties: 1. mildness - energy is taken up and released in a gentle way, nor violently as those occurring in vitro (because of high specific heat of water which makes up a large proportion of the protoplasm) 2. speed - glucose, for instance, is oxidized in the body with surprising speed, while in vitro, the same reaction is quite a long and tedious process. This is due to the presence of enzymes, without which life as we know it would not be possible 3. orderliness - a high degree of orderliness is due to the existence of cell specialization within the different organs of the body 5