Chapter 1 Introduction to Biochemistry MC101 PDF

Batangas State University College of Health Sciences Chapter I INTRODUCTION BIOCHEMISTRY MC101 - BIOCHEMISTRY BRYLE A. ARMEZA, LPT  Content 01 Introduction 02 Objectives 03 Cell Structure 04 Water in the Cell Introduction 01 BIOCHEMISTRY The Study of Living Things Bi...

Batangas State University College of Health Sciences Chapter I INTRODUCTION BIOCHEMISTRY MC101 - BIOCHEMISTRY BRYLE A. ARMEZA, LPT  Content 01 Introduction 02 Objectives 03 Cell Structure 04 Water in the Cell Introduction 01 BIOCHEMISTRY The Study of Living Things Biochemistry is the systematic study of the chemical substances found in living organisms, their organization & chemical interactions with each other, 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. The Study of Living Things A biochemical substance is a chemical substance found within a living organism. Two types of biochemical substances: 1. Bioinorganic substances: water and inorganic salts. 2. Bioorganic substances: carbohydrates, lipids, proteins, and nucleic acids Biochemical substance As isolated compounds, bioinorganic and bioorganic substances have no life in and of themselves. Yet when these substances are gathered together in a cell, their chemical interactions are able to sustain life. 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.  Main classes of foodstuffs - Materials The bioorganic 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. Main classes of foodstuffs - Materials Lipids serve many purposes. They are used, both by plants and animals, as materials to make cell membranes and as sources of chemical energy. Main classes of foodstuffs - Materials 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. Information System 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. Thus the study of the enzyme makers, the nucleic acids, is included in any study of the molecular basis of life. Information System Hormones & neurotransmitters, two other components of cellular information, depend on the presence of right enzymes not only for their existence but for their functions. Biochemical substances To supply materials for any use parts, information, or energy - each organism has basic nutritional needs. These include not just bioorganic materials, including vitamins, but also bioinorganic materials including minerals, water, and oxygen. Thus, together with learning about the bioorganic materials of life and how they are processed and used, the need for vitamins, minerals, water, and oxygen will also be considered. Based on their cell structures, organisms are divided into two main groups: Prokaryotes Greek - meaning "before the nucleus"; single- celled organisms about 10 times smaller than eucaryotic cells A typical Escherichia coli cell is about 1 um wide and 2 to 3 um long Based on their cell structures, organisms are divided into two main groups: Eukaryote Greek - meaning "true nucleus". Most animal and plant cells are 10 to 30 um in diameter, about 10 times larger than most procaryotic cells. 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 Monera - prokaryotic organisms; includes bacteria and cyanobacteria Protista - unicellular eukaryotes: yeast, Euglena, Volvox, Amoeba, and Paramecium Fungi - molds and mushrooms Plantae Animalia Fungi, plants, and animals are multicellular eukaryotes (with few unicellular eukaryotes) The Study of Living Things - The CELL STRUCTURE 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. The Study of Living Things - The CELL STRUCTURE CELL 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. CELL MEMBRANE a lipid bilayer that mechanically holds cell together. component biomolecules: 1. Lipids: phospholipids, cholesterol 2. Proteins 3. Carbohydrates CELL MEMBRANE 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. CYTOPLASM structureless and highly viscous the aqueous phase of the cell in which many particulate constituents like mitochondria, ribosomes, etc. are suspended CYTOPLASM 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.) NUCLEUS The 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. NUCLEUS 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 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  MITOCHONDRIA MITOCHONDRIA the second largest organelle 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  MITOCHONDRIA MITOCHONDRIA MITOCHONDRIA MITOCHONDRIA site for cellular respiration The inner membrane, in which the enzymes of electron transport and energy conversion are located, is convoluted to form shelves termed cristae.  MITOCHONDRIA 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 numbe of small, spheric, electron- dense particles called ribosomes  MITOCHONDRIA ENDOPLASMIC RETICULUM -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 RIBOSOME 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 RIBOSOME they come together to form whole ribosomes when protein synthesis is initiated when not in use, the ribosomal subunits separate The 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 golgi apparatus / golgi complex he 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 LYSOSOMES An Overview The 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 LYSOSOMES LYSOSOMES 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 PEROXISOMES contains oxidative enzymes that oxidize amino acids, uric acid, and various 2- hydroxyamino acids using O2 with the formation of H2O2 H2O2 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 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 Biochemical reactions ionization is a prerequisite to many biochemical reactions and ionization takes place in water Physiologic regulation of body temperature high specific heat (amount of heat required to raise the temperature of 1g of H2O 1°C) 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  Characteristics of biochemical reactions Chemical reactions occurring in vivo have the following properties: 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 Mildness energy is taken up and released in a gentle way, not violently as those occurring in vitro (because of high specific heat of water which makes up a large proportion of the protoplasm) Characteristics of biochemical reactions Chemical reactions occurring in vivo have the following properties: Orderliness a high degree of orderliness is due to the existence of cell specialization within the different organs of the body