Complementary Lectures (1,2,3) PDF

‫اعداد وترتيب ‪:‬‬ ‫د‪.‬ريم الرحيمي‬ ‫‪1‬‬  Lecture 1: Themes in the Study of Life Biology is the scientific study of life. Biologists’ questions can be ambitious. They may ask how a single tiny cell becomes a tree or, how the human mind works, or how the different form...

‫اعداد وترتيب ‪:‬‬ ‫د‪.‬ريم الرحيمي‬ ‫‪1‬‬  Lecture 1: Themes in the Study of Life Biology is the scientific study of life. Biologists’ questions can be ambitious. They may ask how a single tiny cell becomes a tree or, how the human mind works, or how the different forms of life in a forest interact. At the most fundamental level, we may ask: What is life? Even a child realizes that a dog or a plant is alive, while a rock or a car is not. Yet the phenomenon we call life defies a simple, one-sentence definition. We recognize life by what living things do. THE PROPERTIES OF LIFE: 1-Order: This close-up of a sunflower illustrates the highly ordered structure that characterizes life. 2-Regulation: The regulation of blood flow through the blood vessels of this jackrabbit’s ears helps maintain a constant body temperature by adjusting heat exchange with the surrounding air. 3-Reproduction: Organisms (living things) reproduce their own kind. 4-Evolutionary adaptation: The appearance of this pygmy sea horse camouflages the animal in its environment. Such adaptations evolve over many generations by the reproductive success of those individuals with heritable traits that are best suited to their environments. 5-Energy processing: This butterfly obtains fuel in the form of nectar from flowers. The butterfly will use chemical energy stored in its food to power flight and other works. 6-Response to the environment: This Venus flytrap closed its trap rapidly in response to the environmental stimulus of a damselfly landing on the open trap. 7-Growth and development: Inherited information carried by genes controls the pattern of growth and development of organisms, such as this oak seedling (Figure 1) 2 The study of life can be divided into different levels of biological organization. Figure 1: Some properties of life. LEVELS OF BIOLOGICAL ORGANIZATION: 1-Biosphere: all of the environments on Earth that support life 2-Ecosystem: all the organisms living in a particular area and the physical components with which the organisms interact 3-Community: the entire array of organisms living in a particular ecosystem 4-Population: all the individuals of a species living in a specific area 5- Organisms: Individual living things are called organisms. Each of the maple trees and other plants in the forest is an organism. 6- Organs and Organ Systems: each a team of organs that cooperate in a larger function. Organs consist of multiple tissues. A maple leaf is an example of an organ, a body part that carries out a particular function in the body. Stems and roots are the other major organs of plants. The organs of complex animals and plants are organized into organ systems, 3 7- Tissues: Each tissue is a group of cells that work together, performing a specialized function. 8- Cells: The cell is life’s fundamental unit of structure and function. Some organisms are single cells, while others are multicellular. A single cell performs all the functions of life, while a multicellular organism has a division of labor among specialized cells. 9-Organelles: a membrane-enclosed structure that performs a specific function within a cell. Chloroplasts are examples of organelles. 10 -Molecules: A molecule is a chemical structure consisting of two or more units called atoms. Chlorophyll is the pigment molecule that makes a maple leaf green, and it absorbs sunlight during photosynthesis. Figure2:Levels of Biological Organization THEMES IN BIOLOGY: 5 unifying themes in Biology ✓ Life evolves. (e.g. Antibiotic resistance in bacteria evolves in response to the overuse of antibiotics.) ✓ Within biological systems, structure (the shape of something) and function (what it does) are often related. ✓ Life’s processes involve the expression and transmission of genetic information. - The unity of life is based on DNA and a common genetic code ✓ Life requires the transfer and transformation of energy and matter. ✓ 4  ✓ organisms interact with their environments - other organisms and physical factors Organizing The Diversity of Life: Approximately 1.8 million species have been identified and named to date, and thousands more are identified each year. Estimates of the total number of species that actually exist range from 10 million to over 100 million. Taxonomy is the branch of biology that names and classifies species into groups of increasing breadth Domains, followed by kingdoms, are the broadest units of classification Figure 3: Classifying life ❖ The three-domain system is currently used, and replaces the old five- kingdom system ❖ Domain Bacteria and domain Archaea comprise the prokaryotes ❖ Domain Eukarya includes all eukaryotic organisms. The domain Eukarya includes three multicellular kingdoms: ✓ Plantae ✓ Fungi 5  ✓ Animalia Other eukaryotic organisms were formerly grouped into a kingdom called Protista, though these are now often grouped into many separate kingdoms 6  Lecture 2: The Chemistry of Life Nature is not neatly packaged into individual sciences—biology, chemistry, physics, and so forth. Biologists specialize in the study of life, but organisms and their environments are natural systems to which the concepts of chemistry and physics apply. Biology is multidisciplinary. This lecture introduces some basic concepts of chemistry that apply to the study of life. We will cross the blurry boundary between nonlife and life somewhere in the transition from molecules to cells. This chapter focuses on the chemical components that make up all matter. Organisms are composed of matter, which is anything that takes up space and has mass. Matter exists in many forms. Rocks, metals, oils, gases, and living organisms are a few examples of what seems to be an endless assortment of matter. Elements and Compounds Matter is made up of elements. An element is a substance that cannot be broken down to other substances by chemical reactions. Today, chemists recognize 92 elements occurring in nature; gold, copper, carbon, and oxygen are examples. Each element has a symbol, usually the first letter or two of its name. Some symbols are derived from Latin or German; for instance, the symbol for sodium is Na, from the Latin word natrium. A compound is a substance consisting of two or more different elements combined in a fixed ratio. Table salt, for example, is sodium chloride (NaCl), a compound composed of the elements sodium (Na) and chlorine (Cl) in a 1:1 ratio. Pure sodium is a metal, and pure chlorine is a poisonous gas. When chemically combined, however, sodium and chlorine form an edible compound. Water (H2O), another compound, consists of the elements hydrogen (H) and oxygen (O) in a 2:1 ratio. These are simple examples of organized matter having emergent properties: A compound has characteristics different from those of its elements. The Elements of Life Of the 92 natural elements, about 20–25% are essential elements that an organism needs to live a healthy life and reproduce. The essential elements are similar among organisms, but there is some variation—for example, humans need 25 elements, but plants need only 17. Just four elements—oxygen (O), carbon (C), hydrogen (H), and nitrogen (N)—make up 96% of living matter. Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), and a few other elements account for most 7 of the remaining 4% of an organism’s mass. All the elements needed by the human body are listed in Table 1 Table 1: The elements Each element consists of a certain type of atom that is different from the atoms of any other element. An atom is the smallest unit of matter that still retains the properties of an element. Atoms are so small that it would take about a million of them to stretch across the period printed at the end of this sentence. We symbolize atoms with the same abbreviation used for the element that is made up of those atoms. For example, the symbol C stands for both the element carbon and a single carbon atom. three kinds of particles are relevant here: neutrons, protons, and electrons. Protons and electrons are electrically charged. Each proton has one unit of positive charge, and each electron has one unit of negative charge. These interactions usually result in atoms staying close together, held by Figure 4 : Simplified models of a helium (He) atom 8 WATER AND LIFE: Water is the substance that makes possible life as we know it here on Earth. All organisms familiar to us are made mostly of water and live in an environment dominated by water. Water is the biological medium here on Earth, and possibly on other planets as well. Three-quarters of Earth’s surface is covered by water. Although most of this water is in liquid form, water is also present on Earth as a solid (ice) and a gas (water vapor). Studied on its own, the water molecule is deceptively simple. It is shaped like a wide V, with its two hydrogen atoms joined to the oxygen atom by single covalent bonds( fig.5). Figure 5: A hydrogen bond. WATER’S LIFE-SUPPORTING PROPERTIES: We will examine four emergent properties of water that contribute to Earth’s suitability as an environment for life: 1-Cohesion of Water: Water molecules stay close to each other because of hydrogen bonding. Although the arrangement of molecules in a sample of liquid water is constantly changing, at any given moment many of the molecules are linked by multiple hydrogen bonds. These linkages make water more structured than most other liquids. Collectively, the hydrogen bonds hold the substance together, a phenomenon called cohesion. Cohesion is the attraction between molecules of the same kind. Cohesion due to hydrogen bonding contributes to the transport of water and dissolved nutrients against 9 gravity in plants (fig.6). Water from the roots reaches the leaves through a network of water-conducting cells. Adhesion, the clinging of one substance to another. Adhesion is an attraction between different substances, for example, between water and plant cell walls. Related to cohesion is surface tension, a measure of how difficult it is to stretch or break the surface of a liquid. At the interface between water and air is an ordered arrangement of water molecules, hydrogen-bonded to one another and to the water below. This gives water an unusually high surface tension, making it behave as though it were coated with an invisible film. Figure 6: Water transport in plants. 2-Moderation of Temperature by Water : Water moderates air temperature by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler. Water is effective as a heat bank because it can absorb or release a relatively large amount of heat with only a slight change in its own temperature. Water has a stronger resistance to temperature change than most other substances. When water is heated, the heat is first used to break hydrogen bonds rather than raise the temperature. When water cools, hydrogen bonds form, releasing a considerable amount of heat. Evaporative cooling of water helps stabilize temperatures. For example sweating helps dissipate our excess body heat. 3-Floating of Ice on Liquid Water : 10 Water is one of the few substances that are less dense as a solid than as a liquid. In other words, ice floats on liquid water. The ability of ice to float due to its lower density is an important factor in the suitability of the environment for life (fig 8). If ice sank, then eventually all ponds, lakes, and even oceans would freeze solid, making life as we know it impossible on Earth. Figure 8: ice: crystalline structure and floating barrier 4-The Solvent of Life: A sugar cube placed in a glass of water will dissolve with a little stirring. The glass will then contain a uniform mixture of sugar and water; the concentration of dissolved sugar will be the same everywhere in the mixture. A liquid that is a completely homogeneous mixture of two or more substances is called a solution. The dissolving agent of a solution is the solvent, and the substance that is dissolved is the solute. In this case, water is the solvent and sugar is the solute. An aqueous solution is one in which the solute is dissolved in water; water is the solvent. Water can dissolve an enormous variety of solutes necessary for life, providing a medium for chemical reactions. ACIDS AND BASES What would cause an aqueous solution to have an imbalance in H+ and OH- concentrations? When acids dissolve in water, they donate additional H+ to the solution. An acid is a substance that increases the hydrogen ion concentration of a solution. For example, hydrochloric acid (HCl). Bases is A substance that reduces the hydrogen ion concentration of a solution is called a bas. The pH scale is a measure of the hydrogen ion (H+) concentration in a solution. Each pH unit represents a 10-fold change in the concentration of H+. 11 The chemistry of life is sensitive to acidic and basic conditions Even a slight change in pH can be harmful to an organism because the molecules in cells are extremely sensitive to H+ and OH - concentration. Biological fluids contain buffers, substances that minimize changes in pH by: accepting H+ when it is in excess OR donating H+ when it is depleted. ORGANIC COMPOUNDS Living organisms are made up of chemicals based mostly on the element carbon. For example, a cell is mostly water, and the rest of the cell consists mainly of carbon-based molecules (organic compounds). compounds containing carbon are said to be organic, and their study is called organic chemistry. Living matter is made mostly of carbon, oxygen, hydrogen, and nitrogen. Biological diversity results from carbon’s ability to form a huge number of molecules with shapes and properties. Carbon, with a valence of 4, can bond to various other atoms, including O, H, and N. Carbon can also bond to other carbon. atoms, forming the carbon skeletons of organic compounds. These skeletons vary in length and shape and have bonding sites for atoms of other elements. THE STRUCTURE AND FUNCTION OF BIOLOGICAL MOLECULES: Given the rich complexity of life on Earth, it might surprise you that the most important large molecules found in all living things—from bacteria to elephants—can be sorted into just four main classes: carbohydrates, lipids, proteins, and nucleic acids. On the molecular scale, members of three of these classes—carbohydrates, proteins, and nucleic acids—are huge and are therefore called macromolecules. The macromolecules in three of the four classes of life’s organic compounds—carbohydrates, proteins, and nucleic acids, all except lipids—are chain-like molecules called polymers (from the Greek polys, many, and meros, part). A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a 12 train consists of a chain of cars. The repeating units that serve as the building blocks of a polymer are smaller molecules called monomers (from the Greek monos, single). Some monomers also have other functions of their own. " Macromolecules are polymers, built from monomers " MAKING POLYMERS & BREAKING POLYMERS: The Synthesis and Breakdown of Polymers Although each class of polymer is made up of a different type of monomer, the chemical mechanisms by which cells make and break down polymers are basically the same in all cases. In cells, these processes are facilitated by enzymes, specialized macromolecules that speed up chemical reactions. Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule; this is known as a dehydration reaction. When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction: One monomer provides a hydroxyl group (¬OH), while the other provides a hydrogen (¬H). This reaction is repeated as monomers are added to the chain one by one, making a polymer. Polymers are disassembled to monomers by hydrolysis, a process that is essentially the reverse of the dehydration reaction (Fig 9). Hydrolysis means water breakage (from the Greek hydro, water, and lysis, break). The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water (Fig. 10) attaching to one monomer and the hydroxyl group attaching to the other. An example of hydrolysis within our bodies is the process of digestion. The bulk of the organic material in our food is in the form of polymers that are much too large to enter our cells. Within the digestive tract, various enzymes attack the polymers, speeding up hydrolysis. Released monomers are then absorbed into the bloodstream for distribution to all body cells. 13  Figure 9: The synthesis and breakdown of polymers. LARGE BIOLOGICAL MOLECULES : There are four categories of large biological molecules found in all living creatures: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids Carbohydrates Carbohydrates include sugars and polymers of sugars. The simplest carbohydrates are the : 1-monosaccharides, or simple sugars; these are the monomers from which more complex carbohydrates are built. Glucose (C6H12O6), the most common monosaccharide, is of central importance in the chemistry of life. Monosaccharides serve as a major fuel for cells and as raw material for building molecules. 2-Disaccharides are double sugars, consisting of two monosaccharides joined by a covalent bond between two monosaccharides by a dehydration reaction.This covalent bond is called a glycosidic linkage. For example, maltose is a disaccharide formed by the linking of two molecules of glucose. 14  3-Carbohydrate macromolecules are polymers called polysaccharides, composed of many sugars building blocks. Both plants and animals store sugars for later use in the form of storage polysaccharides. Plants store starch, a polymer of glucose monomers. Glycogen is a storage polysaccharide in animals. Figure 10: Carbohydrates Lipids Lipids are the one class of large biological molecules that does not include true polymers. ▪Lipids are hydrophobic (“water-fearing”), unable to mix with water. ▪Lipids are a diverse group of molecules made from different molecular building blocks. (Lipids are not polymers.) we will focus on the types of lipids that are most biologically important: fats, phospholipids, and steroids. A fat is consists of a glycerol molecule joined with three fatty acid molecules via a dehydration ( fig 11). Glycerol is an alcohol; each of its three carbons bears a hydroxyl group. A fatty acid has a long carbon skeleton, usually 16 or 18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group. 15 The major function of fats is energy storage. The terms saturated fats and unsaturated fats are commonly used in the context of nutrition. These terms refer to the structure of the hydrocarbon chains of the fatty acids. If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton. Such a structure is said to be saturated with hydrogen, and the resulting fatty acid is therefore called a saturated fatty acid. An unsaturated fatty acid has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. A diet rich in saturated fats is one of several factors that may contribute to the cardiovascular disease known as atherosclerosis. The major function of fats is energy storage. Figure 11: The structure of Fat Phospholipids Cells as we know them could not exist without another type of lipid—phospholipids. Phospholipids are essential for cells because they are major constituents of cell membranes. Their structure provides a classic example of how form fits function at the molecular level. A phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. A phospholipid has a hydrophilic (polar) head and two hydrophobic (nonpolar) tails (fig.12) 16  Figure 12: The structure of a phospholipid Steroids are lipids characterized by a carbon skeleton consisting of four fused rings. Different steroids are distinguished by the particular chemical groups attached to this ensemble of rings. Cholesterol, a type of steroid, is a crucial molecule in animals. It is a common component of animal cell membranes and is also the precursor from which other steroids, such as the vertebrate sex hormones, are synthesized. In vertebrates, cholesterol is synthesized in the liver and is also obtained from the diet. A high level of cholesterol in the blood may contribute to atherosclerosis. Proteins: Proteins account for more than 50% of the dry mass of most cells, and they are instrumental in almost everything organisms do. Some proteins speed up chemical reactions, while others play a role in defense, storage, transport, cellular communication, movement, or structural support. Fig.14 shows examples of proteins with these functions. Life would not be possible without enzymes, most of which are proteins. Enzymatic proteins regulate metabolism by acting as catalysts. Diverse as proteins are, they are all constructed from the same set of 20 amino acids, linked in unbranched polymers. The bond between amino 17 acids is called a peptide bond, so a polymer of amino acids is called a polypeptide. A protein is a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three dimensional structure. All amino acids share a common structure. An amino acid is an organic molecule with both an amino group and a carboxyl group (fig13). Figure 13: the structure of protein Figure 14: proteins function 18  Nucleic Acids Genes consist of DNA, which belongs to the class of compounds called nucleic acids. Nucleic acids are polymers made of monomers called nucleotides. The two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next. Unique among molecules, DNA provides directions for its own replication. DNA also directs RNA synthesis and, through RNA, controls protein synthesis; this entire process is called gene expression. A nucleotide, in general, is composed of three parts: a five-carbon sugar (a pentose), a nitrogen-containing (nitrogenous) base, and one or more phosphate groups (Fig 16) There are two families of nitrogenous bases: pyrimidines and purines. A pyrimidine has one six-membered ring of carbon and nitrogen atoms. The members of the pyrimidine family are cytosine (C), thymine (T), and uracil (U). Purines are larger, with a six-membered ring fused to a five-membered ring. The purines are adenine (A) and guanine (G). The specific pyrimidines and purines differ in the chemical groups attached to the rings. Adenine, guanine, and cytosine are found in both DNA and RNA; thymine is found only in DNA and uracil only in RNA. Now let’s add the sugar to which the nitrogenous base is attached. In DNA the sugar is deoxyribose; in RNA it is ribose. Figure 16: the Structure of DNA & RNA. 19  : Campbell Biology 10th Edition by Jane B. Reece, Lisa A. Urry Michael L. Cain Steven A. Wasserman Peter V. Minorsky , Robert B. Jackson 20