Fluent Essays

It will be a 50 question multiple choice test.  You will have 75 minutes to complete it.  This test will cover the following study guides:  Introduction to Biology, Chemical Background for Biology, The Importance of Water in Biology, and Organic Molecules and their Importance in Living Things.    There should be only one correct answer for each question. ORGANIC MOLECULES AND THEIR IMPORTANCE IN LIVING THINGS Organic molecules – molecules which contain carbon. We will consider four classes of organic molecules that are important is living things: Carbohydrates, lipids, proteins, and nucleic acids. The central role of carbon The element carbon forms the backbone of organic molecules. A carbon atom has six protons and six electrons, two electrons in its first energy level and four in its second energy level. Thus carbon can form four covalent bonds with four other atoms. For example, Carbon joined to four hydrogen atoms forms Methane (CH4), which is natural gas. Carbon can also form bonds with other carbon atoms forming chains. Ethane (C2H6), for example, contains two carbons; propane, three; and butane (C4H10), four. Ethane C2H6 Propane C3H8 Butane C4H10 In the examples shown above including methane (CH4), ethane (C2H6), and butane (C4H10) the carbon atoms are joined either to each other or to hydrogen atoms. Such compounds, consisting of only carbon and hydrogen, are known as hydrocarbons. A hydrocarbon is an organic molecule that is composed of only carbon and hydrogen. Hydrocarbons are important because they form fuels, including gasoline, diesel fuel, and heating oil, that are burned to produce energy. Covalent Bonds The molecules shown above have atoms that are joined by covalent bonds. A covalent bond is the sharing of a pair of valence electrons by two atoms. This is also considered a single covalent bond. The bonds in the molecules above, for example, between the carbons and the hydrogens are examples of single covalent bonds. They are represented by drawing a single line between the two atoms. Atoms may also be joined by double covalent bonds. A double covalent bond is the sharing of two pairs of valence electrons by two atoms. An example of a molecule containing a double covalent bond, ethene, is shown below. Ethene C2H4 Functional groups In addition to bonding to other carbon atoms or hydrogen atoms, carbon atoms can also join to groups of atoms known as functional groups. Functional groups determine the specific chemical properties of an organic molecule. Hydroxyl Group A hydroxyl group (―OH), consists of a hydrogen atom bonded to an oxygen atom. Do not confuse this functional group with the hydroxide ion, (OH−). Hydroxyl groups are found in alcohols. Some examples are methanol, or wood alcohol (CH3OH), and ethanol, or grain alcohol (C2H5OH), which is present in all alcoholic beverages. Hydroxyl groups are found in Glycerol, C3H5(OH)3, which forms the backbone of triglycerides (fats and oils). Hydroxyl groups are also common in sugars. Carbonyl Groups “The carbonyl group (CO) consists of a carbon atom joined to an oxygen atom by a double bond (Campbell, 2009).” Carbonyl groups include aldehyde groups and ketone groups. Aldehyde Groups An aldehyde group is a carbonyl group that is located at the end of the organic molecule. Ketone Groups A ketone group is a carbonyl group that is located in the interior of the organic molecule. Aldehyde and ketone groups are commonly found in sugars. The aldehyde group is found in glucose and galactose, for example. The ketone group is found in fructose. Carboxyl Group The carboxyl group, ―COOH, consists of a carbon atom double bonded to an oxygen atom and single bonded to a hydroxyl group. Carboxyl groups are found in organic acids. The carboxyl group can release a hydrogen ion from the hydroxyl group into the solution. In this way it acts as an acid. The carboxyl group (-COOH), is a functional group that gives a molecule the properties of an acid. An example of an acid that contains a carboxyl group is acetic acid. Amino Groups The amino group (−NH2) consists of a nitrogen atom joined to two hydrogen atoms. The amino group is found in amino acids and proteins. Sulfhydryl Groups The sulfhydryl group (―SH) consists of a sulfur atom joined to a hydrogen atom. Sulfhydryl groups are found in certain amino acids such as cysteine. It is also found in proteins. In proteins, sulfhydryl groups can join together to link chains of the protein. This is important in bending the protein into a particular shape that is important in enabling the protein to perform its function. Phosphate Groups Phosphate groups (PO4−) a phosphorus atom is bonded to four oxygen atoms. Two oxygens carry negative charges. Phosphate groups are found in high-energy molecules such as ATP (adenosine triphosphate). Methyl Groups A methyl group consists of a carbon atom joined to three hydrogen atoms. Methyl groups are structural components of many organic molecules. “Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes (Campbell, 2009).” Macromolecules such as polysaccharides, fats, or proteins are composed of subunits or monomers. The monomers are linked together by a reaction known as dehydration synthesis or condensation. In this process a molecule of water is removed between the monomers and a chemical bond is formed between the two molecules. Macromolecules are broken down in the reaction known as hydrolysis. Hydrolysis is the breaking down of a large molecule into smaller ones through the addition of a molecule of water. A hydrogen is attached to one subunit and a hydroxyl to the other, breaking the covalent bond. CARBOHYDRATES Carbohydrates – organic molecules that contain carbon, hydrogen, and oxygen. In a carbohydrate, the hydrogen and oxygen are found in a 2:1 ratio. Their empirical formula (a list of the atoms in a molecule with a subscript to indicate how many of each) is (CH2O)n, where n is the number of carbon atoms. In this type of formula we can see that a carbohydrate consists of carbon combined with two hydrogens and oxygen (H2O) or water, forming a molecule with the formula C(H2O)n. Therefore carbohydrates are “hydrates of carbon”. Carbohydrates are the primary energy-storage molecules in most living things. Carbohydrates also serve as structural elements. Because they contain many carbon-hydrogen (C-H) bonds, which release energy when they are broken, carbohydrates are well suited for energy storage. There are three kinds of carbohydrates, including 1. Monosaccharides (simple sugars) such as ribose, glucose, and fructose, contain only one sugar molecule. 2. Disaccharides (double sugars) consist of two sugar molecules joined together. Some examples are sucrose (table sugar), maltose (malt sugar), and lactose (milk sugar). 3. Polysaccharides are made up of many sugar molecules (monosaccharides) linked together. Examples are cellulose and starch. Monosaccharides Monosaccharides or simple sugars can be described by the formula (CH2O)n, where n may be as small as 3, as in C3H6O3, or as large as 8, as in C8H16O8. Importance Monosaccharides are metabolized to release energy. The primary energy source of cells is glucose, a six-carbon sugar. The 5-carbon sugars ribose and deoxyribose are units used to build the structure of nucleic acids. Ribose found in RNA; deoxyribose is found in DNA. Hydroxyl groups and an aldehyde or ketone group characterize monosaccharides. Monosaccharides also contain hydroxyl groups. Examples of Monosaccharides Glucose Glucose has the formula C6H12O6. “Sugars can exist in a straight-chain form, but in water solution, they almost always form rings (Raven and Johnson).” isomers Isomers – forms of a molecule which have the same numbers and kinds of atoms but which differ in the arrangement of those atoms. Glucose is not the only sugar with the formula C6H12O6. Among the other monosaccharides that have this same empirical formula are fructose and galactose. They are isomers of glucose. Both contain carbonyl groups, but in glucose the carbonyl group is an aldehyde group attached to the end of the molecule. In fructose it is a ketone group in the interior of the molecule. Galactose differs from glucose in the orientation of one hydroxyl (-OH) group. Breakdown of monosaccharides to release energy Monosaccharides are burned, or oxidized to yield carbon dioxide and water: (CH2O)n + nO2 → (CO2)n + (H2O)n This is the reaction for cellular respiration that releases energy to power cellular work. Cellular work includes building large molecules, transport of substances through cell membranes, muscle contraction, other forms of cellular movements, etc. “As measured in a calorimeter, the oxidation of a mole of glucose releases 673 kilocalories (Curtis and Barnes, 1989)”: C6H12O6 + 6O2 → 6CO2 + 6H2O ΔH˚ = -673 kcal DISACCHARIDES Disaccharide – carbohydrates that are composed of two monosaccharides chemically joined together. (A double sugar) Importance of Disaccharides: 1. Disaccharides are metabolized to release energy. 2. Disaccharides are used to transport sugars particularly in plants. Although vertebrates transport sugar in the form of glucose, other organisms often use disaccharides for the same purpose. Disaccharides are formed by linking two monosaccharides. In the synthesis of a disaccharide molecule from two monosaccharide molecules, a molecule of water is removed from the molecules and a chemical bond forms linking the two monomers. This reaction is an example of dehydration synthesis or condensation. When a molecule of glucose is joined to another molecule of glucose, the resulting molecule is maltose: glucose + glucose → maltose When glucose combines with fructose, the resulting disaccharide is sucrose: glucose + fructose → sucrose Sucrose is cane sugar or table sugar. Sucrose is the form in which most plants transport glucose. The disaccharide lactose is formed by combining the monosaccharides glucose and galactose. glucose + galactose → lactose Lactose is a sugar that occurs only in milk. It is known as milk sugar. Lactose is found in the breast milk used to supply energy to infants. Utilizing lactose for supplying food to the baby has the effect of reserving energy for the child, since many adults, including virtually all non-white humans, lack the enzyme required to cleave the disaccharide into its two monosaccharide components. Since they lack this enzyme, adults cannot metabolize lactose (Raven and Johnson). “When a disaccharide is split into its monosaccharide units, which happens when it is used as an energy source, a molecule of water is added. This splitting is known as hydrolysis, from hydro, meaning “water”, and lysis, meaning “breaking apart” (Curtis and Barnes)”. “Hydrolysis is an energy-releasing reaction. The hydrolysis of sucrose, for example, releases 5.5 kilocalories per mole. Conversely, the formation of sucrose from glucose and fructose requires an energy input of 5.5 kilocalories per mole of sucrose (Curtis and Barnes)”. POLYSACCHARIDES Polysaccharides – carbohydrates that are made up of monosaccharides linked together in long chains. Functions of polysaccharides: polysaccharides are used for the storage of carbohydrate energy. They are also used for building the structure of organisms and for protection. Storage polysaccharides starch Starch is the principal form in which glucose is stored in plants. glycogen In animals glucose is stored in the form of glycogen, or animal starch. Glycogen differs from starch in that the average chain length is longer and that there are more branches in the chain. In glycogen the branches occur every eight to ten glucose units. structural polysaccharides Certain polysaccharides are important in building the structural components of living organisms. Cellulose makes up the cell walls of plants. It is the most common organic compound in the biosphere (Curtis and Barnes, 1989). Cellulose is composed of long chains of monomers of glucose, just as starch and glycogen are. Most animals do not have the enzyme that is necessary for the digestion of cellulose. Humans cannot digest cellulose; however, it is a source of fiber and necessary for the proper functioning of the digestive system. Certain microorganisms can digest cellulose. Cattle and other ruminants that live on vegetation, also lack the enzyme required to break down cellulose. However, they have a stomach that is composed of several parts. In the stomach there is a population of microorganisms. They break down the cellulose, making it possible for the animal to live on their diet of vegetation. Termites feed on rotting wood. They also lack the enzyme required for the digestion of cellulose. However, they have entered into a symbiotic relationship with a flagellate known as Trichonympha. This tiny protozoan lives within the intestine of the termite. It does have the enzyme that breaks down the cellulose, and makes the food energy available for the termite. In return, the protozoan has a protected location in which to live, and is provided with a steady source of food. Chitin Chitin is a polysaccharide that makes up the shell of arthropods such as lobsters, crabs, or insects. As such it forms a protective coat of armor around the animal. It also makes up the cell walls of fungi. LIPIDS Lipids – organic molecules that contain carbon, hydrogen, and oxygen. In a lipid, the hydrogen and oxygen are not in a 2:1 ratio, the ratio is much higher. The major function of lipids in living organisms is to store energy. When organisms have excess glucose they usually convert some of it into lipids and store it for when it is needed. In our bodies we have adipose tissue or fat which contains stored food. Some plants also store food energy as oils, especially in seeds and fruits. Lipids are also used for other purposes, phospholipids, glycolipids, and waxes are used for structural purposes. Some lipids serve as chemical messengers such as lipid hormones. Other lipids provide waterproof coverings for plant organs. Lipids are a general group of organic substances that are insoluble in polar solvents, such as water, but that dissolve readily in nonpolar organic solvents, such as chloroform, ether, and benzene (Curtis and Barnes, 1989). A fat or oil consists of three molecules of fatty acids joined to one glycerol molecule. Glycerol is a three-carbon alcohol that contains three hydroxyl groups. “A fatty acid consists of a long hydrocarbon chain that terminates in a carboxyl group (-COOH); the nonpolar chain is hydrophobic, whereas the carboxyl group gives one portion of the molecule the properties of an acid (Curtis and Barnes, 1989).” Because there are three fatty acids joined to a molecule, the resulting molecule is called a triglyceride. “The three fatty acids of a triglyceride do not have to be identical, and often differ markedly from one another (Raven and Johnson).” “Fatty acids vary in length. The most common are even-numbered chains of 14 to 22 carbons (Raven and Johnson).” The fatty acids are joined to the glycerol by the removal of a molecule of water. This is a dehydration synthesis or condensation reaction. Saturated and Nonsaturated Fats Saturated fats – fats that contain all the hydrogen that they can possibly hold. Saturated fats do not contain any double chemical bonds. Unsaturated fats – unsaturated fats contains one or more double chemical bonds. As a result, hydrogen atoms can be added by opening up the double bond. Saturated fats tend to be solid at room temperature. Many of these are animal fats such as butter and lard. They usually have high melting temperatures. Unsaturated fats tend to be liquid. Their chains bend at the double bonds. They also have low melting points. Unsaturated fats commonly are oils, such as olive oil, peanut oil, and corn oil. “It is possible to convert an oil into a hard fat by adding hydrogen. The peanut butter that you buy in the store has usually been hydrogenated to convert the peanut fatty acids to hard fat and thus to prevent them from separating out as oils while the jar sits on the store shelf.” “Fats and oils contain a higher proportion of energy-rich carbon-hydrogen bonds than carbohydrates do and, as a consequence, contain more chemical energy. On the average, fats yield about 9.3 kilocalories per gram as compared to 3.79 Kcal per gram of carbohydrate, or 3.12 Kcal per gram of protein (Curtis and Barnes, 1989).” “As you might expect, the more highly saturated fats are richer in energy than less saturated ones. Animal fats contain more calories than do vegetable fats. Human diets that contain relatively large amounts of saturated fats appear to upset the normal balance of fatty acids in the body, a situation that may lead to heart disease (Raven and Johnson).” Insulators and Cushions Large masses of fatty tissue surround mammalian kidneys and serve to protect these organs from physical shock (Curtis and Barnes, 1989).” Another mammalian characteristic is a layer of fat under the skin, which serves as thermal insulation. This layer is particularly well developed in seagoing mammals (Curtis and Barnes, 1989).” Among humans, females characteristically have a thicker layer of subdermal (“under the skin”) fat than males. This serves as a reserve food supply that nourishes the woman, but, more importantly the unborn child and the nursing infant (Curtis and Barnes, 1989).” PHOSPHOLIPIDS Phospholipids are composed of a molecule of glycerol joined to two molecules of fatty acids. The third carbon of the glycerol molecule is occupied by a phosphate group to which another polar group is usually attached. The phosphate end of the molecule is hydrophilic (Greek hydros “water” and philos “loving”). This means that it is attracted to water. The fatty acid portion is hydrophobic (Greek hydros + phobos “water-fearing or hating”), which means that it is repelled by water. Phospholipid molecules make up the middle layer of the cell membrane. In the cell membrane, the phospholipid molecules form a double molecular layer. One layer is arranged so that the hydrophilic “heads” (polar ends) of the molecules face the outside of the cell. They do so, because they are attracted to water, and water is found on the outside of the cell. Similarly, in the inner layer of phospholipid molecules, the hydrophilic “heads” all face toward the inside. This is because once again they are attracted to water and there is water inside the cell in the cytoplasm. The fatty acid tails of the phospholipid molecules in both layers face inward. Because the fatty acid portion of the molecule is hydrophobic, or repelled by water, the tails swing inward to get as far away from the water as possible. STEROIDS Steroids are a group of lipids, which are composed of ring of carbon atoms. “Although steroids do not resemble the other lipids structurally, they are grouped with them because they are insoluble in water (Curtis and Barnes, 1989).” The steroids form one of two major groups of hormones, the other being a group of hormones made of protein. Significance of lipids: As can be seen by considering their role in forming hormones, the lipids are important in regulating and controlling body function. The male sex hormone testosterone and the female sex hormone estrogen are steroids. Testosterone regulates the growth and development of the male sexual organs and regulates the process of spermatogenesis. Estrogen regulates the growth and development of the female reproductive organs and controls the menstrual cycle. Other steroid hormones include the hormones produced by the adrenal cortex. They are important in controlling the reaction to stress. Prostaglandins Prostaglandins are modified fatty acids. In a prostaglandin, two nonpolar tails are attached to a five-carbon ring (Raven and Johnson).” “Prostaglandins appear to act as local chemical messengers (Raven and Johnson).” “Some stimulate smooth muscle to contract or to relax; others constrict or expand the diameter of small blood vessels (Raven and Johnson).” “Prostaglandins have been shown to be involved n many aspects of reproduction, and in the inflammatory response to infection (Raven and Johnson).” Aspirin works by inhibiting prostaglandin synthesis. As a result, it reduces pain, inflammation, and fever. Cholesterol Cholesterol, like the other lipids, is composed of carbon-containing rings. Cholesterol is a component of cell membranes. Cholesterol is also a major component of the myelin sheath, the membrane that surrounds nerve axons. It helps to speed up nerve impulses. Cholesterol is synthesized by the body. The site of synthesis is the liver. Dietary sources rich in cholesterol include meat, cheese, and egg yolks. Cholesterol has been implicated in atherosclerosis (also known as “hardening of the arteries”) and in heart disease. Cholesterol is transported in the blood in particles composed of a core of cholesterol surrounded by a coating of lipoproteins. There are two principal forms of the lipoproteins: low-density lipoproteins (LDLs) and high-density lipoproteins (HDLs). LDLs carry cholesterol to various destinations in the body, including the liver as well as hormone-synthesizing organs. HDLs function to dispose of excess cholesterol by carrying it to the liver where it is degraded and prepared for excretion. waxes Waxes form waterproof coverings on the surfaces of plant organs such as leaves. In this way they prevent the excessive loss of water from the plant. They also form protective coverings on the skin, fur, or feathers of animals. The exoskeleton of insects is often covered by a layer of wax (Curtis and Barnes, 1989). PROTEINS Proteins are organic molecules which contain carbon, hydrogen, oxygen, nitrogen, and sulfur. Proteins are composed of long chains of amino acids. Generalized formula for an amino acid: The amino acids are linked by peptide bonds to form polypeptides. Example: This reaction is an example of a dehydration synthesis reaction. The sequence of the amino acids in a polypeptide chain is determined by DNA in the nucleus of the cell. Functions of proteins 1. Proteins form the structure of living things. Proteins make up much of the form of the human body. For example most of the substance of our muscles is composed of proteins. 2. Proteins are found in the cell membrane Proteins, along with lipids, form the structure of the cell membrane. Proteins are found in the outer and inner layers of the cell membrane. Proteins control transport through the cell membrane Some proteins extend through the cell membrane from the outside to the inside. These proteins, which are known as transport proteins, contain pores or channels. They control the transport of substances into and out of the cell. They are involved in transport functions such as active transport and facilitated diffusion. Proteins serve as receptors that combine with hormones and neurotransmitters and help to convey their message to the cell On the surface of the cell, proteins form molecular binding sites or receptors. These are locations at which chemical messengers, such as hormones or neurotransmitters combine. Proteins form markers on cell surfaces that give the cell a particular identity We have unique proteins and glycoproteins on the surfaces of our cells which give these cells particular molecular identities. In defending our body, it is important for our immune system to be able to distinguish between the cells and tissues which belong in our body (“self”), from those that do not (“non-self”). Being able to make this distinction allows the immune system to target the non-self agents or antigens so that they can be attacked and eliminated. 3. Proteins form enzymes that control metabolic reactions in living organisms. Metabolic reactions in living organisms typically occur in a series of many steps. A particular enzyme catalyzes each step. The presence of absence of a particular enzyme may determine whether a particular reaction or even the entire metabolic sequence can take place. Enzymes are crucial for many vital metabolic functions. For example, the reactions of digestion depend upon enzymes. In the stomach, the enzyme pepsin begins the breakdown of proteins. In the intestine there are enzymes which carry out the breakdown of carbohydrates, proteins, fats, and nucleic acids. The breakdown of glucose to release energy consists of many individual reactions. Again, a particular enzyme controls each reaction. 4. Proteins form hormones that control and regulate body function. Protein hormones make up a major group of hormones. (The other major group of hormones is made of lipid). A hormone is a chemical substance that is produced in one part of the body, but which functions somewhere else in the body. Examples of Protein hormones: Growth hormone controls the rate of growth in living organisms. Thyroxine controls metabolic rate. ACTH controls reactions to stress. Insulin controls the transport of glucose into cells. 5. Proteins regulate the action of genes. Proteins regulate the action of genes. They form repressors which regulate transcription. 6. Proteins produce movement in living organisms. Muscle Contraction The contraction of muscle is produced by the interaction of proteins. The mechanism of muscle contraction is explained by the sliding filament hypothesis. According to this hypothesis, muscle tissue is composed of contractile units known as sarcomeres. In the center of this unit is a dark band called the A band. This is made of two proteins called actin and myosin. The myosin molecules make up thick myofilaments. The actin molecules make up thin myofilaments. In a sarcomere that is not in a contracted state, the actin filaments fit in between the myosin filaments. They come in from each side of the A band but do not meet in the middle. When the muscle contracts, the actin filaments slide inward between the myosin myofilaments. Beating of Cilia and Flagella The beating of cilia and flagella is caused by the interaction of proteins. Cell Motility Axoplasmic transport Cytoplasmic streaming Amoeboid movement 7. Proteins perform important functions in the blood and body fluids. Transport of oxygen and carbon dioxide Hemoglobin in the blood transports oxygen and carbon dioxide. In the lungs, hemoglobin combines reversibly with oxygen. This oxygenated blood is returned to the heart to be pumped to the cells and tissues. As the blood travels through the tissues, it gives up its oxygen to the cells and picks up the waste product carbon dioxide. The carbon dioxide is transported back to the heart and then to the lungs where the carbon dioxide can be eliminated in the exhaled breath. Transport of Hormones Hormones, such as thyroid hormone are transported in combination with proteins. As Antibodies, Proteins Protect the Body against Disease Antibodies are proteins. These are Y-shaped molecules which combine with disease-causing agents and lead to their destruction. Protein molecules are involved in the clotting of blood Proteins take part in the reactions leading to the blood clot. The protein fibrin is a major component of the blood clot. Proteins help to maintain the proper osmotic composition of the blood As plasma proteins, proteins help to maintain a balance of forces that act at the capillary membrane. Plasma proteins in the blood create a force that draws fluid into the capillary. This force tends to counteract the force of blood pressure that acts to force fluid out of the capillary. If the concentration of protein is reduced to levels that are below normal, the balance of forces is upset, and fluid begins to move from the blood into the tissues. This abnormal buildup of fluid produces swelling or edema. Proteins regulate acid-base balance in the blood and body fluids Because proteins contain both acid and basic groups, they can neutralize either acid or base. In this way, they function as buffers to maintain the pH of the blood or body fluids within a certain range. 8. Proteins function in storage Proteins in egg white or in seed function in the storage of nutrition. Ferritin stores ions. Casein stores ions in milk. Calmodulin binds calcium ions. Structure of Proteins Proteins are composed of long chains of amino acids. There are 20 kinds of amino acids. Generalized formula for an amino acid An amino acid has a central carbon atom. Like all carbon atoms, this carbon atom has four bonds extending from it. A hydrogen atom is connected to one of these bonds. An amino group (NH2) is attached to a second bond. The third bond is attached to a carboxyl group (COOH). The fourth bond is attached to various groups. This is the group that determines which specific amino acid is produced. In the generalized formula, this group is represented by the symbol R. Substituting a specific group in this position produces a specific amino acid, one of the 20 different kinds. The NH2 group (amino group) can function as a base. It can accept a hydrogen ion from the solution, becoming NH3+. The COOH can function as an acid. It can release a hydrogen ion (H+) into the solution. Because proteins have both acidic and basic groups, they can function as acid-base buffers. They can neutralize either acid or base. In a protein, the amino acids are joined by peptide bonds. This bond is formed between the amino group of one amino acid and the carboxyl group of an adjacent amino acid. The peptide bond is formed between the two amino acids as a molecule of water is removed from between them. This is a dehydration synthesis reaction. Linking together two amino acids produces a dipeptide. Linking together several amino acids produces a polypeptide. The DNA in the nucleus of the cell determines the sequence of the amino acids in the polypeptide chain. This sequence is very specific for particular proteins. Example of the specificity of a protein – sickle cell anemia The disease sickle cell anemia is caused by the presence of a defective hemoglobin molecule. “When oxygen is removed from them, these molecules change shape and combine with one another to form stiffened rod-like structures. Red blood cells containing large proportions of such hemoglobin molecules become stiff and deformed, taking on the characteristic sickle shape. The deformed cells may clog the smallest blood vessels (capillaries). This causes blood clots and deprives vital organs of their full supply of blood, resulting in pain, intermittent illness, and, in many cases, a shortened life span (Curtis and Barnes, 1989).” In the hemoglobin molecule, there are four polypeptide chains, two alpha chains and two beta chains. The defect that causes sickle cell anemia is a substitution of an incorrect amino acid in the sequence of amino acids in the beta chain of hemoglobin. The beta chain contains 146 amino acids. Sickle cell anemia results from a mistake in only one out of these 146 amino acids. In position 6 in the beta chain of hemoglobin, the amino acid valine replaces the normal glutamic acid. essential amino acids Humans can synthesize all but nine of the amino acids. The amino acids that must be supplied in the diet are called essential amino acids. These include the following amino acids: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine. THE LEVELS OF PROTEIN STRUCTURE The structure of proteins can be considered on four levels, going from the simplest to the most complex. These four levels are primary structure, secondary structure, tertiary structure, and quaternary structure. PRIMARY STRUCTURE The primary structure of a protein is the sequence of amino acids along the length of the polypeptide chain. In the polypeptide chain, the amino acids are linked together, like boxcars in a train. DNA determines the amino acid sequence in the polypeptide chain. “Each different protein has a different primary structure (Curtis and Barnes, 1989).” SECONDARY STRUCTURE There are two forms of secondary structure: the alpha helix and the beta pleated sheet. In the alpha helix, the polypeptide chain is coiled into a spiral or helical structure. The coiling is caused by the formation of hydrogen bonds between the CO and NH groups of the main chain. The beta-pleated sheet is formed by hydrogen bonding between several polypeptide chains. The hydrogen bonds connect the polypeptide chains between their NH and CO groups so that they come to lie side by side in a zigzag pattern. TERTIARY STRUCTURE Tertiary structure refers to the folding of helical (or randomly coiled) chains (Chemical Basis of Life, Sci. Amer.) to form proteins with a globular shape. This structure is determined by interactions between R groups. For example, a bond known as a disulfide bond may form between two cysteine molecules located along the polypeptide. QUATERNARY STRUCTURE The quaternary structure is determined by the combination of several different polypeptides along with non-protein groups to form a functional protein. The Hemoglobin Molecule as an Example of a Functional Protein with Quaternary Structure Hemoglobin is a protein found in our red blood cells. It is the red pigment that is responsible for transporting oxygen in our blood. It combines reversibly with oxygen in the lungs. From the lungs, the blood is returned to the heart and then pumped to all parts of the body. As the blood travels through the tissues, hemoglobin releases the oxygen to the cells. It then combines reversibly with carbon dioxide. The blood carries this carbon dioxide to the heart and then to the lungs. In the lungs, the carbon dioxide is expelled from the body in the exhaled breath. The hemoglobin molecule has a quaternary structure. It is made up of four polypeptide chains: two alpha chains and two beta chains. In addition there are four iron-containing, or heme groups. ENZYMES An enzyme is an organic catalyst. The term organic refers to a substance that contains carbon. A catalyst is a substance that speeds up the rate of a chemical reaction. Almost all known enzymes are proteins. Recently, an exception to this was discovered. It was found that RNA could function as an enzyme. This RNA is known as ribozyme. Enzymes catalyze chemical reactions by bringing substrates together in an optimal orientation conducive to the formation or breaking of chemical bonds. Many enzymes are named by adding the suffix –ase to the name of the substrate. For example, the enzyme sucrase works on sucrose, the enzyme lipase works on lipid, and so on. Not all enzymes are named this way. Pepsin and Trypsin, which act on proteins, are examples. Some enzymes require one or more nonprotein components, called cofactors in order to be active. The cofactor may be a metal ion or an organic molecule called a coenzyme; some enzymes require both (Lehninger, 1975). Coenzymes generally contain as part of their structure a vitamin, a trace organic substance required in the diet of certain species (Lehninger, 1975). EXAMPLE OF ENZYME ACTION As an example of the action of an enzyme, consider the joining of carbon dioxide and water to form carbonic acid. CO2 + H2O H2CO3 Carbon dioxide water Carbonic acid The reaction may proceed in either direction. Without the enzyme the rate of the reaction is very slow. Perhaps 200 molecules of carbonic acid form in an hour. In the presence of the enzyme carbonic anhydrase, the rate of the reaction is greatly increased. An estimated 600,000 molecules of carbonic acid form, not every hour, but every second. The enzyme has speeded the reaction rate about 10 million times. “Enzymes accelerate reactions by factors of at least a million. Indeed, most reactions in biological systems do not occur at perceptible rates in the absence of enzymes (Stryer, 1995).” How Enzymes Work Enzymes combine with specific substrates. The reason enzymes combine with specific substrates is explained by the lock and key theory. Enzymes combine with specific substrates. The substrate is the substance that the enzyme works on. The enzyme sucrase breaks down sucrose. It does not work on maltose or lactose. The enzyme pepsin breaks down protein into polypeptides. It breaks the protein at specific locations. Pepsin cleaves peptide bonds at the C-terminus of phenylalanine, leucine, tryptophan, and tyrosine. “Trypsin is quite specific in that it catalyzes the splitting of peptide bonds on the carboxyl side of lysine and arginine residues only (Stryer, 1995).” The enzyme combines with the substrate, forming an enzyme-substrate complex. E + S ↔ ES → E + P “The substrates are bound to a specific region of the enzyme called the active site. The reason that the enzyme works on specific substrates is explained by the lock and key theory. The lock and key theory was developed by Emil Fischer in 1890 (see Stryer, 1995). This theory states that the enzyme has a specific shape. This shape fits into a corresponding shape on the substrate. The shape of the enzyme may be compared to the shape of a key designed to fit a particular lock. The shape of the substrate may be compared to that of the lock. The enzyme and substrate fit together like a key fits a particular lock. A modification of the lock and key theory was postulated by Daniel E. Koshland, Jr. in 1958 (see Stryer, 1995). He pointed out that the binding of substrate markedly modifies the shapes of the active sites of many enzymes. “The active sites of these enzymes assume shapes that are complementary to that of the substrate only after the substrate is bound. This process of dynamic recognition is called induced fit (Stryer, 1995).” Enzymes speed up chemical reactions by lowering the energy of activation for particular reactions. The energy of activation is the energy required to get a reaction going. For example, imagine that you wanted to start a fire in a fireplace. You obviously could not start the fire by holding a match to a large log. The amount of heat would not be great enough to start the log on fire. Another way of saying this is that the energy supplied by the match was not sufficient to supply the energy of activation required to start the reaction. To get the large log to burn, we would need to put paper in the fireplace, then some small twigs, then some small logs, and then finally place our large log on top of this. The energy supplied by the burning of the smaller items would then be great enough to start the log on fire. We would have supplied sufficient energy of activation to get the reaction going. Enzymes speed up chemical reactions by lowering the energy of activation required to get the reaction going. This can be seen by examining two lines on the graph, one showing the energy of activation required for a reaction that is not catalyzed by an enzyme, and a second line showing a reaction catalyzed by an enzyme: Enzymes lower the energy of activation by bringing substrates together. They can then react more efficiently. An enzyme can also work by bringing certain groups of the enzyme into close proximity to certain bonds of the substrate. This alignment makes it easier for the bonds to be broken, thereby lowering the energy of activation for the reaction. Following the reaction, the enzyme has not been permanently altered, and can be recovered and used again. As a result, only tiny amounts of enzymes are required to catalyze reactions. FACTORS WHICH AFFECT THE FUNCTIONING OF ENZYMES Among the factors that affect enzymes are temperature, pH, and the concentrations of the enzyme and the substrate. 1. Temperature Temperature affects ordinary chemical reactions. Increasing the temperature increases the rate of a chemical reaction. For example, the rate of most chemical reactions is approximately doubled by a 10º C rise in temperature. The rate of a chemical reaction that is catalyzed by an enzyme is also increased by temperature. However, because the enzyme is a protein, as the temperature is increased and reaches a certain point, the reaction behaves differently. If we look at the effect of temperature on the rate of a reaction catalyzed by an enzyme, (graph) we will see that as the temperature increases, the rate of the reaction also increases. This happens until a certain high temperature is reached. At this temperature the enzyme is inactivated. The enzyme is denatured. An example of this is seen when an egg is boiled. Prior to boiling, the egg white, which is the protein albumin, is a clear liquid. After the egg is boiled, the clear albumin turns into the solid egg white. The change that took place was permanent and irreversible. It is an example of a protein being denatured. The same thing happens to an enzyme subjected to a very high temperature. The enzyme is denatured. This inactivates or destroys the activity of the enzyme. As a result, the rate of the reaction catalyzed by the enzyme levels off and then drops. “Although most enzymes are inactivated at temperatures above about 55 to 60º C, some are quite stable and retain activity at much higher temperatures, e.g., enzymes of various species of thermophilic bacteria inhabiting hot springs, which are still active at temperature exceeding 85º C (Lehninger, 1975).” https://pmgbiology.files.wordpress.com/2014/12/graph.jpg pH In order to function, enzymes must work within specific ranges of pH. “Most enzymes have a characteristic pH at which their activity is maximal; above or below this pH the activity declines (Lehninger, 1975).” For example, the enzyme pepsin, which functions to break down proteins in the stomach forming polypeptides, works best at a pH of 2 to 3 and is completely inactive at a pH above approximately 5 (Guyton, 1986). The enzyme salivary amylase, which functions in the mouth cavity to break down starch into maltose and dextrins, works best at a pH of 6.8. Other enzymes, which work in the small intestine, such as pancreatic lipase, work best at an alkaline pH of 8.0. http://www.slideshare.net/mpattani/biology-in-focus-chapter-6 CONCENTRATION OF ENZYME AND SUBSTRATE When the concentration of the enzyme is significantly lower than the concentration of the substrate, the rate of an enzyme-catalyzed reaction is directly dependent on the enzyme concentration. http://chemwiki.ucdavis.edu/Textbook_Maps/General_Chemistry_Textbook_Maps/Map\%3A_The_Basics_of_GOB_Chemistry_(Ball_et_al.)/18\%3A_Amino_Acids,_Proteins,_and_Enzymes/18.07_Enzyme_Activity EFFECT OF INCREASING THE SUBSTRATE CONCENTRATION We will examine the effect of the substrate concentration on the rate of an enzyme-catalyzed reaction. If the concentration of the substrate is increased, the rate at which the product is formed also increases, up to a maximum value. At that point the enzyme molecule is saturated with substrate (Alberts, et al. 1994). NUCLEIC ACIDS Nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids constitute the genetic material. They make up the genes which are found on the chromosomes and which determine our genetic traits. DEOXYRIBONUCLEIC ACID Deoxyribonucleic acid is made up of the following components: 1. Nitrogenous bases There are four nitrogenous bases in DNA: adenine, thymine, cytosine, and guanine. Adenine and guanine have a two-ring structure and are known as purines. Cytosine and thymine have a single-ring structure and are known as pyrimidines. 2. Deoxyribose sugar Deoxyribose is a 5-carbon sugar. 3. Phosphate groups The building unit of DNA is called a nucleotide. A nucleotide is composed of a nitrogenous base joined to a 5-carbon sugar, joined to a phosphate group. DNA is built of many repeating nucleotide units. DNA contains the genetic code that directs the synthesis of protein. This code is present in the form of the sequences of nitrogenous bases that are found along the length of the DNA molecule. RIBONUCLEIC ACID Ribonucleic acid (RNA) is a nucleic acid that helps DNA to construct a protein. RNA is a single-stranded molecule. It contains the following components: 1. Nitrogenous bases RNA contains the nitrogenous bases adenine, uracil, cytosine, and guanine. Note that in RNA, the nitrogenous base uracil replaces the thymine found in DNA. 2. 5-carbon sugar The 5-carbon sugar found in RNA is ribose (not Deoxyribose as in DNA). 3. Phosphate groups Types of RNA There are three main types of RNA: 1. Messenger RNA – carries the code for the construction of a protein from the DNA in the nucleus to the ribosomes in the cytoplasm. 2. Transfer RNA – picks up amino acids in the cytoplasm and brings them to the messenger RNA at the ribosomes. 3. Ribosomal RNA – makes up the structure of the ribosome. Recently, additional forms of RNA have been discovered that have important roles in transcription and gene control. These include: 4. Small nuclear RNA (snRNA) – involved in the splicing (removal of noncoding regions) of messenger RNA molecules prior to transcription. 5. Signal recognition particle RNA (SRP RNA) – recognizes a signal sequence on a messenger RNA molecule and then attaches to a receptor protein in the endoplasmic reticulum to anchor the ribosome involved in translating the protein to the endoplasmic reticulum. 6. Micro-RNA (MiRNA) – involved in the control of gene expression. ADENOSINE TRIPHOSPHATE – ATP When energy is needed in the cell, for example to make muscles contract or to transport molecules across cell membranes, or to synthesize large molecules etc., the energy is supplied by the breakdown of adenosine triphosphate (ATP). The ATP molecule contains an enormous amount of energy within its chemical bonds. This energy is released when a phosphate group is removed from the molecule, forming adenosine diphosphate. The released energy is then used to power cellular work. Additional energy may be released by continuing the breakdown of the molecule. In this reaction a second phosphate group is removed from adenosine diphosphate forming adenosine monophosphate. The Structure of ATP The ATP molecule is made up of the following components: the purine base adenine, the five-carbon sugar ribose, and three phosphate groups. Adenine plus ribose comprise the molecule adenosine. Adenosine monophosphate is adenosine attached to one phosphate group. Adenosine diphosphate is attached to two phosphate groups. Adenosine triphosphate to three phosphate groups. The first phosphate group is attached to the adenosine by a normal chemical bond. This is indicated in the diagram by a straight line between the two components. The bonds between the next two phosphate groups are high-energy bonds. Wavy lines indicate the high-energy phosphate bonds. These bonds contain most of the energy in ATP, energy that is released when the bonds are broken. The Breakdown of ATP The breakdown of ATP begins with the splitting off from the molecule of a phosphate group. ATP → ADP + P + energy Adenosine triphosphate → Adenosine diphosphate + phosphate + energy The Building of ATP When there is an excess of energy available, the cells produce ATP. For example, lets assume that you have recently eaten a meal such as lunch and that it was rich in sugars. When you are resting the food is digested, the nutrients are absorbed, and enter the bloodstream. The level of sugar in the blood is high. The sugars enter the cell and are broken down via glycolysis and the Citric Acid Cycle to produce energy. This energy is then used to produce ATP. ATP is usually produced by starting with adenosine diphosphate (ADP). The energy from the breakdown of glucose is used to join a phosphate group to ADP, forming ATP. ADP + P + energy → ATP Adenosine diphosphate + phosphate + energy → Adenosine triphosphate Study Guide Organic Molecules and their Importance in Living Things draft 9 Revised 10/12/2019 PAGE 1 The Cellular Basis of Life Introduction Definition A cell is the basic unit of a living organism that contains genetic material and protoplasm, which is surrounded by a cell membrane. The cell is the structural unit of the organism, carries out its life processes, and forms new cells in the process of cell division. Discovery of Cells and Historical Development of the Cell Theory Discovery of Cells 1. Robert Hooke, an Englishman, discovered cells in 1665. Using a microscope that he made, Hooke observed thin slices of dried cork. Under the microscope, the cork appeared to be made up of tiny boxes. Hooke called these boxes cells, because they resembled the cells or rooms in monasteries of his day. Hooke was the first to use the word “cells” to describe the tiny compartments that together make up an organism. The cork cells that Hooke observed were not living cells. However, he observed living cells in elderberry plants. 2. Anton van Leeuwenhoek, a Dutch inventor and scientist examined many kinds of living cells. Leeuwenhoek used his microscope to examine all sorts of living material including the muscle fibers of a whale, the scales of his own skin, and the lens of ox eyes, various insects, and the wood of trees. One day he examined a drop of water from a pot that he used to measure rainfall outside in his garden. Imagine his amazement as he saw countless tiny animals swimming around inside the drop. Prior to this time, no one could have imagined that a tiny drop of water could teem with so many living creatures. Using his microscope, Leewenhoek had discovered a new world in a drop of water filled with previously unknown living creatures. Leewenhoek called the tiny organisms that he observed “animalcules”, meaning tiny animals. Cell Theory The Cell Theory was developed in the years 1838 and 1839 by two German Scientists, Schleiden and Schwann. Matthias Schleiden was a botanist. After studying many different kinds of plant tissues, he concluded that all plants were composed of cells. Theodor Schwann, a zoologist, reported that all animal tissues were also composed of cells. The Cell Theory, as developed by Schleiden and Schwann stated that all living organisms were composed of one or more units known as cells. In 1855, Rudolf Virchow, a German physician, contributed the concept that cells can arise only from previously existing cells. The Cell Theory in its modern form states that: 1) All living organisms are composed of one or more units called cells. 2) The metabolic reactions of a living organism, including its energy-releasing processes and its biosynthetic reactions, take place within cells. 3) Cells arise from other cells. 4) Cells contain the genetic information of living organisms, and this information is passed from parent cell to daughter cell. Types of Cells – Prokaryotic and Eukaryotic There are two main types of cells: prokaryotic cells and eukaryotic cells. Prokaryotic cells 1. Lack a membrane-bound nucleus 2. Lack membrane-bound organelles. 3. Have genetic material in the form of a single, circular molecule of DNA 4. Are found in Archaea, bacteria, and Cyanobacteria Eukaryotic Cells A eukaryotic cell is a cell having a membrane-bound nucleus, membrane-bound organelles, and chromosomes in which DNA is combined with histone proteins. Eukaryotic Cells: 1. Have a membrane-bound nucleus containing genetic material. 2. Contain membranous organelles. 3. Have rod-shaped chromosomes containing linear DNA bound to special proteins known as histones. 4. Are found in Protists, Fungi, Plants, and Animals. Structure of the Prokaryotic Cell Structures External to the Cell Wall Among the structures external to the cell wall are the: Capsule (slime layer) Flagella Axial filaments, and Pili (fimbriae) Capsule, or Slime Layer A capsule is a jelly-like coating that surrounds the cells of certain bacteria. Chemically, the capsule is composed of a gelatinous polymer of polysaccharide, polypeptide, or both. Functions: 1. It appears to prevent desiccation (drying) of the organism under adverse conditions. 2. Capsules often protect pathogenic bacteria from phagocytosis by cells of the host. Flagella Flagella are long threadlike appendages used for locomotion in certain bacteria. Bacteria can swim by rotating their flagella. Structure The flagellum has three basic parts: 1. The filament, the outer threadlike part composed of the protein flagellin. 2. Hook – a curved portion attached to the proximal end of the filament. 3. Basal body – anchors the flagellum to the cell wall and cytoplasmic membrane. The structure of the flagellum of bacteria is completely different from the cilia and flagella of eukaryotic cells. Mechanism of Movement In the basal body there is a helical rotor powered by a proton gradient that pushes the cell by spinning either clockwise or counter clockwise around its axis. Axial Filaments Axial Filaments consist of numerous fibrils that arise from both poles of the cell and are encased within a sheath. Axial filaments are found only in the spirochetes. These are corkscrew-shaped bacteria. One of the best-known spirochetes is Treponema pallidum, the causative agent of syphilis. The axial filaments are similar in structure to flagella but instead of being found outside the cell as flagella are, they are found inside the cell. They are attached to both poles of the cell and spiral around the organism between the plasma membrane and the cell wall. The function of axial filaments is movement. As they rotate or contract, the axial filaments cause the spirochete cell to turn in a corkscrew-like manner. Pili and Fimbriae Pili and fimbriae are filamentous projections that extend from the surface of certain bacteria. Fimbriae are shorter in length than pili and present in high numbers. Fimbriae function in the attachment of a bacterium to a surface. Neisseria gonorrhoeae, the bacterium that causes the disease gonorrhoeae, uses fimbriae to adhere to the cell it infects. Pili function in the process of bacterial conjugation in which genetic material is exchanged between two bacterial cells. Non-sex pili also function in attachment of bacteria to surfaces. The Cell Wall The cell wall is a semi rigid structure that surrounds the bacterial cell. The cell wall protects the cell when it is in a dilute environment. The high concentration of solute within the bacterial cell creates a high osmotic pressure that leads to the entry of water into the cell. The cell wall resists the pressure created by the inward flow of water preventing the cell from bursting. Structure of the Cell Wall The bacterial cell wall is composed of a material called peptidoglycan (poly-N-acetylglucosamine and N-acetylmuramic acid). The Gram Stain Bacteria can be divided into two large groups on the basis of a differential staining technique called the gram stain. One large group is called gram-positive and the other, gram-negative. Following the gram-staining procedure, gram-positive organisms will appear purple, gram-negative organisms will appear pink or red. This staining procedure is based upon differences in the structure of the cell wall between the two groups. Gram-positive bacteria have a thicker peptidoglycan wall. The cell wall contains polyalcohols called teichoic acids, some of which are lipid-linked to form lipoteichoicacids. Lipoteichoic acids link the peptidoglycan to the cytoplasmic membrane. Gram-negative bacteria contain less peptidoglycan. In the gram-negative bacteria, a thin layer of peptidoglycan is sandwiched between the plasma membranes and a second outer membrane. The outer membrane contains phospholipids and lipopolysaccharide, lipids with polysaccharide chains attached. Procedure for the Gram Stain 1. A bacterial smear is prepared and then stained with the purple stain crystal violet. 2. The slide is washed off with distilled water. 3. The slide is covered with Gram’s iodine, which is a mordant. The iodine combines with crystal violet to form a compound or precipitate that remains in gram-positive bacteria, but can be removed from gram-negative bacteria by washing with ethyl alcohol. 4. The slide is flooded with ethyl alcohol until the purple dye no longer appears in the alcohol flowing from the slide. If the bacteria are gram-positive, they will not be decolorized. The crystal violet dye will remain in the cells. Gram-negative bacteria are decolorized by the alcohol, losing the purple color of the crystal violet. 5. The slide is washed using distilled water, stopping the action of the alcohol. 6. The bacterial smear is counterstained using the red dye safranin. Gram-positive bacteria will retain the purple color of the crystal violet stain. Decolorized gram-negative bacteria will be stained pink by the safranin. 7. The slide is washed, blotted dry, and allowed to dry at room temperature. Microscopic Examination This slide is examined microscopically. Gram-positive bacteria will appear purple. Gram-negative bacteria will appear pink. Structures Internal to the Cell Wall Plasma (Cell) Membrane The plasma membrane is a thin membrane internal to the cell wall that encloses the protoplasm of the cell. It is composed of protein and phospholipid molecules. Functions of the Cell Membrane 1. It controls the transport of most compounds entering and leaving the cell. 2. Produces a separation of protons (H+) from hydroxyl ions (OH-) generating a proton motive force. This force is responsible for driving functions such as transport, motility, and synthesis of ATP. Cytoplasm Cytoplasm is the substance contained within the cell membrane. Cytoplasm consists mostly of water. Dissolved and suspended in the water there are many substances including inorganic ions, nucleic acids, proteins, carbohydrates, lipids, inorganic ions, and a variety of compounds of low molecular weight. There are no membranous organelles in the cytoplasm of a bacterial cell, but there are ribosomes, internal membranes, a cytoskeleton, and storage granules. Internal Membranes In photosynthetic bacteria, internal membranes within bacterial cells may serve as a location for photosynthetic reactions. Cytoskeleton The prokaryotic cytoskeleton consists of structural filaments within the protoplasm. The Cytoskeleton functions in cell division, or to produce changes in cell shape. Storage Granules Storage granules contain phosphate or sulfur. Magnetosomes are particles of the iron mineral magnetite – Fe3O4. They allow bacteria to respond to a magnetic field. Ribosomes Ribosomes are small granules that are composed of RNA and protein. Ribosomes are the site of protein synthesis. Ribosomes are numerous in the cytoplasm of bacterial cells. Observation with the electron microscope shows that the cytoplasm is quite densely packed with ribosomes. Several antibiotics, such as streptomycin, neomycin, and tetracycline exert their antimicrobial effects by inhibiting protein synthesis. Nuclear Area The nuclear area, or nucleoid, of bacterial cells contains a single, long, circular molecule of DNA, referred to as the bacterial chromosome. This is the cell’s genetic information. Unlike the chromosomes of eukaryotic cells, bacterial chromosomes are not surrounded by a nuclear envelope. Eukaryotic cells have rod-shaped chromosomes containing linear DNA bound to special proteins known as histones. Bacteria often contain, in addition to the bacterial chromosome, small cyclic DNA molecules called plasmids. Plasmids Plasmids are extrachromosomal genetic elements; that is, they are not connected to the main bacterial chromosome. Plasmids are used to transfer genetic material from one cell to another. Plasmids can pass from one cell to another cell by passing through the cell wall. When it enters the cell that receives it, it introduces new genetic information into that cell. Plasmids are now used in Genetic Engineering Research to introduce genetic material into recipient cells. Endospores Endospores are highly durable, dehydrated bodies with a thick wall. Endospores are formed by bacterial cells in response to harsh conditions such as lack of food, lack of water, high temperatures, freezing temperatures, etc. They are formed inside the bacterial cell wall. Since one vegetative cell forms a single endospore, which after germination remains one cell, sporogenesis in bacteria is not a means of reproduction. There is no increase in the number of cells. Endospore formation is important from a clinical viewpoint, because endospores are quite resistant to processes that normally kill vegetative cells. Such processes include heating, freezing, desiccation, use of chemicals, and radiation. Whereas temperatures above 70º C kill most vegetative cells, endospores may survive in boiling water for an hour or more. Endospore-forming bacteria are a problem in the food industry, since some species produce toxins that result in food spoilage and disease. Reproduction Asexual Reproduction Binary fission – bacteria reproduce asexually by binary fission. First, the single chromosome duplicates and then the two chromosomes move apart into separate areas; then the cell membrane grows inward and partitions the cell into two daughter cells, each of which now has its own chromosome. Under favorable growth conditions, fission may occur in approximately 20 to 30 minutes. Sexual Reproduction Three types of genetic recombinations are known in bacteria – conjugation, transformation, and transduction. Conjugation – the transfer of genetic material between two bacterial cells that are temporarily joined. In the process of conjugation, two cells, an F+ cell and an F- cell come together side by side. The F+ acts as a donor cell or “male” cell to transfer genetic material to the F- cell which acts as a recipient cell or “female” cell. F+ cells contain an F plasmid. The F plasmid contains genes that code for the production of an F pilus by the donor cell. The F pilus attaches to a specific receptor on the F+ cell and then retracts, drawing the cells together. The F pilus serves as a protoplasmic bridge that connects the two cells. Within the donor cell, one strand of the plasmid DNA is nicked and this single strand moves through the F pilus into the F+ cell. Replication of DNA by the rolling circle mechanism then replaces the transferred strand in the donor cell. The single strand that enters the F+ cell is also replicated. This results in two F+ cells. Transformation – a genetic change in a recipient bacterium resulting from the absorption of DNA released from another cell. Transduction – a virus-mediated transfer of bacterial DNA from one bacterium to another. Structure and Function of a Eukaryotic Animal Cell The Structure and Function of Cellular Organelles The Cell Membrane Functions of the Cell Membrane 1) It serves as a boundary or barrier that maintains the cell’s integrity 2) It controls the transport of substances into or out of the cell. The cell membrane or plasma membrane surrounds the cell and encloses the protoplasm. The cell membrane allows substances that the cell needs, such as oxygen, glucose, amino acids, fatty acids and glycerol to enter the cell, and wastes such as carbon dioxide and urea to leave the cell. The cell membrane is described as selectively permeable. This means that the cell membrane allows certain substances such as water to pass through it, but does not allow certain others, such as polysaccharides to pass through. The Structure of the Cell Membrane The structure of the cell membrane is described by the Fluid-Mosaic or Singer model. The cell membrane is composed of lipid and protein. The lipid layer is composed of a double layer of phospholipid molecules. The Phospholipid molecules that comprise the cell membrane have a hydrophilic end containing a phosphate group that is attracted to water, and a hydrophobic tail composed of fatty acid molecules that are repelled by water. In the cell membrane, one layer is arranged so that the hydrophilic “heads” (polar ends) of the molecules face the outside of the cell. There, they are close to the water that is found on the outside of the cell. Similarly, in the inner layer of phospholipid molecules, the hydrophilic “heads” all face toward the inside, toward the water inside the cytoplasm of the cell. The fatty acid tails of the phospholipid molecules in both layers face inward. They are hydrophobic, or repelled by water, and the tails swing inward to get as far away from the water as possible In addition to the phospholipid molecules, the cell membrane also contains proteins. In the fluid mosaic model, the phospholipids bilayers are viewed as fluid. The globular proteins are inserted into the lipid bilayer. The hydrophobic ends of the proteins are embedded deeply in the interior of the lipid bilayer, in contact with the hydrophobic lipid “tails”, while the hydrophilic end of the protein remains at the surface, in contact with the hydrophilic lipid “heads” and the aqueous medium surrounding the membrane. The proteins have been compared to icebergs floating in a sea of lipid. Some of the proteins, which were large enough to span the entire thickness of the membrane, had two protruding hydrophilic ends and a hydrophobic embedded interior. Some of the proteins that extend through the membrane contain channels. Their function is to control the transport of substances through the cell membrane. The Cytoskeleton The cytoskeleton is a network of protein filaments that extends throughout the cytoplasm of a eukaryotic cell. Functions: The cytoskeleton is responsible for producing various types of movements in cells. These include such movements as changes in cell shape, the crawling of cells on a substratum, the transport of organelles in the cytoplasm, and the separation of chromosomes during mitosis. Structure The cytoskeleton is composed of three types of protein filaments: 1. Microfilaments Microfilaments are composed of the protein actin. They are essential for many movements of the cell, especially those on its surface. Microfilaments are smaller than microtubules. Microfilaments are involved in changes in cell shape during development and motility, and in protoplasmic streaming in plant cells. 2. Microtubules Microtubules are tiny tubes composed of the protein tubulin. They are thought to be the primary organizers of the cytoskeleton. Microtubules form the spindle fibers of dividing cells, on which chromosome movement takes place. Microtubules are also found in the cilia and flagella of motile cells. They are found in the pseudopods of certain protozoans or in the extremely elongated axons of nerve cells. 3. Intermediate filaments Intermediate filaments, composed of fibrous proteins such as vimentin or lamin, seem to have the function of providing cells with mechanical strength. Motor Proteins Cytoskeletal filaments also serve as supports for intracellular transport. Motor proteins generate the movements. They can move along either actin filaments or microtubules using the energy from the breakdown of ATP. An example of a motor protein is myosin. This is the protein that causes muscle contraction by moving along actin filaments. Kinesins are motor proteins that move along microtubules. They are involved in the movement of chromosomes along spindle fibers during cell division. They also function in the movement of mitochondria, Golgi bodies, and vesicles. Cytoplasmic dyneins are involved in the transport of vesicles and organelles. Cilia and Flagella Cilia Cilia are minute, hair-like, motile processes that extend from the surfaces of the cells of many animals. Functions: 1. Locomotion of single-celled organisms such as Paramecia through their aquatic environment. 2. Propulsion of fluids and materials across the surfaces of epithelial cells. Ciliated epithelial cells in the trachea propel dust-ladened mucus lining the surface of the cells toward the mouth, clearing the respiratory system of particles of dirt. This mechanism is a dust-removal or filtration system. 3. Cilia sweep eggs along the oviduct. Flagella A Flagellum is a long whip-like structure that extends from the surface of certain animal cells. They are found in flagellated protists, animal spermatozoa, and sponges. Structure of Cilia and Flagella The cilium and flagellum are both made up of nine pairs (doublets) of microtubules surrounding a central pair of microtubules that runs down the center of the shaft. This arrangement is called the “nine-plus-two” pattern. Cilia are shorter than flagella and more numerous per cell. Flagella are longer than cilia, and there are fewer per cell in comparison to cilia. The distinction between cilia and flagella is that a cilium propels water parallel to the surface to which the cilium is attached whereas a flagellum propels water parallel to the main axis of the flagellum. The molecular basis for the movement of cilia or flagella (in eukaryotic cells) is the same. It should be noted that the flagella of bacteria are completely different from the cilia and flagella of eukaryotic cells. The protein dynein generates the movement of cilia and flagella. The interaction of ciliary dynein with adjacent microtubules generates a sliding force between the microtubules. Because the adjacent microtubules are linked together, the sliding movement is converted to a bending motion. Centrosomes The centrosome is the major microtubule-organizing center in almost all animal cells. In interphase it is typically located to one side of the nucleus, close to the outer surface of the nuclear envelope. Embedded in the centrosome is a pair of cylindrical structures arranged at right angles to each other in an L-shaped configuration. These are centrioles. The centrosome duplicates and splits into two equal parts during interphase, each half containing a duplicated centriole pair. These two daughter centrosomes move to opposite sides of the nucleus when mitosis begins, and they form the two poles of the mitotic spindle. Not all microtubule-organizing centers contain centrioles. Plant cells lack centrioles. Centrioles Centrosomes consist of two centrioles, which are seen as a pair of cylinders situated at right angles to each other. Centrioles organize the microtubules that serve to separate chromosomes during cell division. The wall of each cylinder is composed of nine groups of microtubules. Each group consists of a triplet of microtubules (9 + 0). Basal Bodies Basal bodies are found at the base of cilia and flagella. The basal bodies have the same structure as centrioles (9 + 0). Microvilli Microvillus - a cylindrical projection with a rounded top found on the surface of many animal cells. Function Microvilli increase the surface area of the cell for absorption. For example, microvilli greatly increase the surface area of the epithelial cells lining the intestine. This leads to increased absorption of nutrients such as amino acids, simple sugars, glycerol and fatty acids from the intestine. Junctional Complexes between Cells Tight Junction A tight junction is a region of actual fusion of cell membranes between two adjacent cells. Desmosome A Desmosome is a discoid structure that serves as an intracellular connection. Gap Junctions Gap junctions – formed from tiny canals between cells so that the cytoplasm becomes continuous, and molecules can pass from one cell to another. Gap junctions provide a means of intercellular communication. Cytoplasmic Organelles Cytoplasm - the cytoplasm is the protoplasm that is located between the cell membrane and the nuclear membrane. The cytoplasm contains organelles. The organelles are small internal organs of the cell – organized units of living substance having specific functions in cell metabolism. The cell organelles include: Centrioles (centrosomes), Microtubules, Mitochondria, Endoplasmic reticulum, Golgi apparatus, Lysosomes, and Peroxisomes. Mitochondria Mitochondria are small rod-shaped bodies located in the cytoplasm and which function in the production of energy. Size – 0.2 to 5.0 μm Mitochondria are found in all types of eukaryotic cells. Location – mitochondria are especially concentrated in areas of cellular activity. For example, mitochondria are numerous in muscle tissue and at nerve endings. Structure A double-layered membrane surrounds the mitochondrion. The outer membrane surrounds the outside of the mitochondrion. The inner membrane is folded inward forming partitions or cristae. The intermembrane space lies between the outer membrane and the inner membrane. The matrix is the fluid-filled interior of the mitochondrion. It lies inside the inner membrane. Function The mitochondria complete the breakdown of glucose to carbon dioxide and water. The energy released in this process is used to make ATP. The breakdown of glucose to carbon dioxide, water, and energy is known as cellular respiration. The reaction for cellular respiration is: C6H12O6 + 6O2 → 6CO2 + 6H2O + energy The breakdown of glucose begins in the cytoplasm outside the mitochondrion. There glucose is broken down into pyruvic acid. The pyruvic acid enters the mitochondrion. The pyruvic acid is broken down into an acetyl group and combined with coenzyme A forming acetyl coenzyme A. The acetyl coenzyme A then enters the reactions of the Citric Acid Cycle. As the molecules in the Citric Acid Cycle are oxidized, energy is released. The energy is captured in the form of ATP. ATP production – occurs in the mitochondrial membrane in what is known as the electron transport chain. Mitochondria Contain DNA Mitochondria contain DNA. The fact that mitochondria contain DNA supports the hypothesis that mitochondria were once free-living bacterial cells that were captured by another cell that evolved into eukaryotic cells. This theory is called the endosymbiotic theory. It will be discussed more fully later. Endomembrane System A eukaryotic cell contains a system of membranes that extends throughout its cytoplasm. This system, known as the endomembrane system includes the endoplasmic reticulum, the Golgi apparatus, lysosomes, and vesicles. These organelles are interconnected and function together. They provide surfaces for the synthesis of lipids and proteins, divide the cell into compartments, and serve as a transportation system throughout the cell. Endoplasmic Reticulum The endoplasmic reticulum is a system of membranes that extends throughout the cytoplasm of a eukaryotic cell. The endoplasmic reticulum extends from the nuclear membrane on the inside to the plasma membrane on the outside of the cell. Function Function – the endoplasmic reticulum is concerned with the synthesis of lipids and proteins. Types of Endoplasmic Reticulum There are two types of endoplasmic reticulum: rough and smooth. Rough Endoplasmic Reticulum Rough endoplasmic reticulum is associated with tiny granules known as ribosomes. Ribosomes are tiny granules that are composed of protein and ribonucleic acid (RNA). They are the sites of protein synthesis. Rough endoplasmic reticulum functions in protein synthesis. Smooth Endoplasmic Reticulum Smooth endoplasmic reticulum, or smooth ER lacks bound ribosomes. Smooth Endoplasmic Reticulum synthesizes lipids and detoxifies lipid-soluble drugs including amphetamines, morphine, codeine and phenobarbital, as well as various harmful compounds produced by metabolism. The endoplasmic reticulum also regulates the accumulation and release of Ca2+ from the cytosol (the part of the cytoplasm that contains organic molecules and ions in solution). Other Functions of the Endoplasmic Reticulum In addition to its role in synthesis, the endoplasmic reticulum has the following functions: 1) It is a kind of cytoskeleton 2) Provides surfaces for chemical reactions (keeps chemical reactions in the cell separated and prevents them from interfering with one another) 3) It serves as a pathway for transport of materials 4) Collection depot for synthesized materials (prepares synthesized materials by forming vesicles that are transported to the Golgi apparatus) Ribosomes Ribosomes are granules that consist of RNA and protein. Function: protein synthesis. Ribosomes are often found in clusters known as polyribosomes. The Golgi Apparatus The Golgi apparatus is composed of stacks of parallel, double-layered membranes. It is named after its discover, Camillo Golgi, the nineteenth-century Italian physician. The Golgi apparatus (also called the Golgi complex) is a major site of carbohydrate synthesis. It combines carbohydrate with proteins (brought to them through the canals of the endoplasmic reticulum) to form compounds called glycoproteins. It also sorts, packages and distributes the products of the ER to the plasma membrane, lysosomes, and secretory vesicles. Each Golgi stack has a receiving end, known as the cis face (or entry face), which is usually located near the ER, and a discharging end called the trans face (or exit face). Lysosomes Lysosomes are vesicles that contain powerful digestive enzymes. The Golgi apparatus forms lysosomes. Functions of Lysosomes 1) Digestion of large particles that enter the cell (intracellular digestion) 2) Digestion of substances external to the cell (extracellular digestion) 3) The digestion of the cell itself Microbodies Microbodies … INTRODUCTION TO BIOLOGY Definition Biology is the scientific study of living things. Biology is one of many sciences. It is classified as a natural science. Other natural sciences include Chemistry, Physics, Geology, Astronomy, Earth Science, Meteorology, Oceanography, as well as a number of others. Subdivisions of biology pertinent to this course Biochemistry – the study of chemical substances found in living organisms and the chemical reactions that they undergo. The reactions include metabolic pathways that break down large molecules to produce energy or that synthesize carbohydrates, lipids, proteins, and nucleic acids. Molecular Biology – The study of the synthesis, structure, and function of biologically important macromolecules such as DNA, RNA, and proteins. It investigates genetics at the molecular level and includes the study of the replication, transcription, and translation of nucleic acids. It is also concerned with the sequencing of DNA, the manipulation of DNA, and the control of genes. Bioinformatics – The application of techniques from applied mathematics, informatics, statistics, computer science, and chemistry, especially biochemistry to solve biological problems usually on the molecular level. Cell Biology – the study of the structure and functions of the cell. Genetics – the study of heredity and variation. Developmental Anatomy – the study of growth and development during the entire life of the organism. Embryology – the study of the origin and development of the organism from the egg to birth. Anatomy – the study of the structure of living things. Comparative Anatomy – the comparative study of the structure of vertebrates. It is closely related to evolutionary biology and phylogeny. Phylogeny – the origin, evolutionary development, and genealogical history of a taxonomic group of organisms, both living and extinct. Physiology – the study of the functioning of living things. Comparative Physiology – the comparative study of the function of vertebrate cells, tissues, organs, and systems. Taxonomy – the study of the classification of living things. Microbiology – the study of microorganisms, including bacteria, viruses, protists, and fungi. Botany – the study of plants. Zoology – the study of animals. Parasitology – the study of parasites (organisms that live at the expense of other organisms), their hosts, and the relationship between them. Marine Biology – the study of ocean life. Evolution – the change in the genetic makeup of a population with time. Behavior – the study of the activities of animals and their response to stimuli in their environment, including how they interact with one another, find and defend resources, establish territories, choose mates and reproduce, and care for their young. Ecology –the study of the relationship between living things and their environment. Subdivisions Based Upon the Kind of Organism Being Studied Examples: Entomology – the study of insects, Ornithology – the study of birds, etc. Characteristics of living things What is life? No satisfactory definition exists. However, we can approach the problem by comparing living and nonliving things and by establishing the characteristics of living things. Living and nonliving things compared Some characteristics which may be used to distinguish living from nonliving things are as follows: I. Organization Chemical Organization Living things are composed primarily of carbon, hydrogen, oxygen, nitrogen, and phosphorous, organized into complex, high molecular weight molecules. Enzymes mediate chemical reactions in living things. The same and other chemical elements occur as compounds in nonliving materials but their molecular weights are small (below 2,000) and they are not highly organized. Deoxyribonucleic acid (DNA) is uniformly present in all living things. Protoplasmic Organization The material of which living matter is made is known as protoplasm. Cellular Organization Cellular organization is characteristic of all living things. (Viruses – an exception) Cells are organized into tissues and organs in higher forms. Morphological Organization Living things have a characteristic form and size and are arranged as definite individuals. II. Life Processes 1. Metabolism Metabolism includes the physical and chemical changes by which materials derived from the environment are transformed and utilized for energy production on one hand and synthesis on the other. The process by which energy is produced is a process of breakdown and is known as catabolism . The building up process or synthesis is called anabolism . Energy production involves a series of reactions termed Glycolysis and the Citric Acid Cycle . Although certain of the reaction steps may differ in certain organisms, these reactions are found generally in all living things. A good deal of the energy that is produced is trapped and stored in the form of a molecule known as ATP or Adenosine Triphosphate . Synthesis in living organisms is under genetic control and components are built according to a specific pattern found originally in the DNA characteristic of that organism. Processes Related to Metabolism Nutrition – the intake and transformation of food so that it can be utilized. Living things seek out raw materials and/or energy necessary for life. Absorption – the taking in of solids. Secretion – the process by which something is compounded in one part of the body that can be used in another. Respiration – the intake of O2 and discharge of CO2. Circulation or Transport – the movement of materials throughout the organism. Excretion – the giving off of waste material. Other Life Processes 2. Irritability and Conductivity (Response) Living things respond to changes in the environment. These changes are known as stimuli. The ability to respond to a stimulus is known as irritability . Irritability is also known as responsiveness. We can say that living things respond to stimuli. Conductivity is the ability to conduct an electrical impulse. Although all protoplasm can conduct an impulse, this ability is especially well-developed in nerve cells. 3. Movement Movement is characteristic of living things. Movement is change of place or position. Living things move volitionally (of their own will). 4. Growth and Life Cycle A living organism grows by divisions of cells. Living organisms grow by development of new parts between or within older ones. Living things have the capacity to repair or to replace protoplasm. Each kind of organism has a definite life cycle: birth, growth, maturity, and death. If nonliving things increase, they do so by external addition, as with crystals, and there is no orderly cycle of change. Living things do not merely accrete through external addition (like e.g. crystals). 5. Reproduction Living things have the ability to reproduce themselves in kind. The continuation of the species depends on reproduction. Genetic and hereditary characteristics are transmitted through DNA. Nonliving things cannot reproduce. 6. Adaptability Adaptation – Any characteristic of living organisms, which in the environment they inhabit, improves their chances of survival and ultimately of leaving descendants, in comparison with the chances of similar organisms, without the characteristic; natural selection therefore tends to establish adaptations in a population (Abercrombie, et al., A Dictionary of Biology, 1951). Homeostasis Living matter shows homeostatic responses to the environment. Homeostasis – the maintenance of constant conditions within the internal environment of the body. Homeostasis is a central concept in the field of human physiology. The term was coined by the eminent United States Physiologist, Walter Cannon. The concept is generally accredited to the great French scientist, Claude Bernard. The word is derived from the Greek words homios, meaning “like” or “similar”, and stasis, “a standing still”. Examples of Homeostasis Man is capable of remaining active and typically retaining a remarkably constant body temperature under an imposing variety of temperature extremes, ranging from intense desert heat to extreme arctic cold. Even though external temperature may vary widely, man’s internal body temperature remains constant at 98.6( F. When the temperature varies, even a degree or two, we realize we are “sick”, that something is wrong. Concentration of respiratory gases in the Body Fluids O2 and CO2 levels within the body must be maintained within close limits. A constant supply of O2 is essential for living cells. CO2 a waste product must not be allowed to build up. If the CO2 level rises, this stimulates the brain and structures known as chemoreceptors. The nervous system then signals the respiratory system to bring about an increase in the rate of respiration. This eliminates the excess CO2, brings about an increase in O2 and restores homeostasis. pH of body fluids The pH of the arterial blood remains constant at pH 7.4. If the pH of the arterial drops to pH 7.0 and remains there for longer than a few minutes, the person will go into a coma and die. If the pH rises to pH 7.8 and stays there for more than a few minutes the person will go into convulsions. Even in disease conditions the pH of the arterial blood almost never becomes more acidic than 7.0 or more basic than 7.8. Special chemicals in the blood known as buffers maintain constant blood pH by neutralizing excess acid or base. The urinary and respiratory systems also have important roles in the regulation of acid base balance. Evolution Living things are undergoing evolution. Evolution – the change in the genetic makeup of a population with time. Introduction to Biology Study fall 2021 PAGE 7 Introduction to Chemistry Study Guide Chemical Level of Organization Introduction Chemistry Chemistry is the study of the composition, structure, and properties of substances, as well as their reactions with one another. Matter All living and nonliving things are made of matter . Matter – anything that takes up space and has mass. Elements The matter of the universe is composed of a limited number of basic substances called elements. Element – a substance that cannot be decomposed into simpler substances by ordinary chemical reactions. An element is a substance that consists only of atoms with the same number of protons (designated the atomic number), and therefore the same nuclear charge. Common examples of elements include carbon, hydrogen, iron, sodium, and chlorine. There are a total of 118 chemical elements. The first 94 of these elements are believed to occur naturally on the earth. The elements with atomic numbers 95 and above do not occur naturally, and are known only as a result of their synthesis in nuclear reactors or particle accelerators. Chemical Symbols Each element is designated by a chemical symbol of either one or two letters that stands for its English or Latin name. Thus H is the symbol for hydrogen, O for Oxygen, C for carbon, Cl for chlorine, Mg for magnesium, K for potassium (the Latin name is Kalium), Na for sodium (the Latin name is Natrium), etc. Exercise For each of the symbols, give the name of the element Symbol Element N ____________________ P ____________________ S ____________________ Ca ____________________ Mg ____________________ For each element, give the chemical symbol Element Symbol Iron ____________________ Iodine ____________________ Mercury ____________________ Lead ____________________ Flourine ____________________ Elements important in Living Organisms The most abundant elements in living organisms are carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. Other elements such as calcium, sodium, potassium, magnesium, and iron are not as abundant but are still essential for life. Trace elements are present in minute quantities yet are also essential for life. Examples include manganese, zinc, copper, and iodine. Atoms Matter is composed of tiny units known as atoms. Atom – the smallest unit of an element, not divisible by ordinary chemical means. A chemical symbol represents one atom of the element, e.g. N stands for a single atom of nitrogen. Atomic Structure Atoms are composed of three fundamental particles: protons, neutrons, and electrons. Fundamental Particles Particle Mass Charge (µ or Daltons) (electronic charge units) Electron 5.485 7990 x 10-4 ‒1 Proton 1.007 276 47 +1 Neutron 1.008 664 90 0 The protons and neutrons are found in the nucleus of the atom. The nucleus contains the positive charge and almost all the mass of an atom. Each proton carries an electronic charge of +1. The neutrons, as their name implies, have no charge. Protons and neutrons have roughly the same mass, which is close to one. Atomic Number Atomic number – the number of protons in the nucleus of an atom. The number of protons in the nucleus is unique for each element. The atomic number is usually written as a subscript immediately before the chemical symbol. For example, 1H indicates that the atomic number of hydrogen is one, i.e. its nucleus contains only one proton. Similarly, 8O indicates that oxygen nuclei contain eight protons. Mass Number The mass number is the total number of protons and neutrons in a nucleus. The mass number is commonly written as a superscript before the chemical symbol. For example, most atoms of oxygen contain eight protons and eight neutrons; the mass number is therefore 16 and the nucleus can be symbolized as O16 or, if we wish to show both the atomic number and the mass number as 8O16. Other Examples: 17Cl35 Chlorine 17 protons 18 neutrons 11Na23 Sodium 11 protons 12 neutrons 6C12 Carbon 6 protons 6 neutrons 7N14 Nitrogen 7 protons 7 neutrons 15P31 Phosphorous 15 protons 16 neutrons If we are given the atomic number and the mass number, we can determine the number of protons, the number of neutrons, and the number of electrons in a normal, neutral atom. For example in 17Cl35 the atomic number is 17 so there are 17 protons. The mass number, the total number of protons plus neutrons is 35. If we subtract the atomic number (17) from the mass number (35) we get the number of neutrons (18). We can also determine the number of electrons. In a normal neutral atom, the number of electrons equals the number of protons. So in chlorine, if there are 17 protons there are also 17 electrons. Isotopes Isotopes – forms of the same element which have the same number of protons, but which differ in the number of neutrons in the nucleus. All atoms of a particular element must have the same number of protons. If the number of protons changed, the atom would become a different element. However, the number of neutrons can be different for atoms of the same element. These different forms of the same element are known as isotopes. Because the number of neutrons is different for the isotopes of an element, so also is the mass number. Examples: There are three different forms of the element Hydrogen: Hydrogen 1 Hydrogen 2 Hydrogen 3 1H1 1H2 1H3 Hydrogen 1 has one proton in the nucleus and no neutrons, Hydrogen 2 has one proton and 1 neutron, and Hydrogen 3 has 1 proton and 2 neutrons. There are three isotopes of Oxygen: Oxygen 16 Oxygen 17 Oxygen 18 8O16 8O17 8O18 Oxygen 16 has 8 protons and 8 neutrons, Oxygen 17 has 8 protons and 9 neutrons, and Oxygen 18 has 8 protons and 10 neutrons. There are three naturally occurring isotopes of carbon: carbon 12, carbon 13, and carbon 14. Carbon 12 Carbon 13 Carbon 14 6C12 6C13 6C14 It is possible to create new isotopes that do not exist in nature using nuclear reactors. Some isotopes are radioactive. Their nuclei are unstable and tend to break down, emitting energy in the form of radiation. Importance of Radioisotopes Radioisotopes have been used as tracers to identify the steps in metabolic reactions. For example, the reactions of photosynthesis were worked out using radioactive carbon dioxide. Radiation is used to treat cancer. Radioisotopes are used to visualize structures in the body to locate disorders. For example, the coronary arteries of the heart can be made visible, allowing the detection of blockage. The Electrons The electrons are negatively charged particles that encircle the nucleus of the atom. Electrons have very little mass. Each electron has a charge of –1; its charge is exactly opposite to that of a proton. In a normal neutral atom, the number of electrons is equal to the number of protons. The positive charges of the protons cancel out the negative charges of the electrons, making the atom as a whole electrically neutral. Consequently, in a neutral atom, the atomic number represents both the number of protons inside the nucleus and the number of electrons circling around the nucleus. Examples: 17Cl35 17 protons 18 neutrons 17 electrons 19K39 19 protons 20 neutrons 19 electrons Orbitals The electrons travel around the nucleus of the atom in regions known as orbitals. The distance of an electron from the nucleus is a function of its energy; the higher the energy, the farther from the nucleus will be the probable location of the electron. The average energy levels of electrons in an atom correspond to a series of so-called electron shells, which can conveniently be represented by concentric circles located at specified distances from the nucleus. In an atom of oxygen, for example, there are two electrons in the first shell and six in the second shell. The Orbitals of electrons may have different shapes. In the first electron shell, this shape is always spherical (it is symbolized by s). In the second electron shell, both the spherical shape (s) and a dumbbell shape (symbolized by p) occur. Additional shapes occur in succeeding electron shells. It has been shown that there is a maximum number of electrons that each shell can contain. The first electron shell can contain a maximum of 2 electrons, the second shell can contain 8, the third shell 18, and the fourth shell 32, etc. Although the third and successive shells can hold more than eight electrons, they are in a particularly stable configuration when they contain only eight. For our purposes, then, the first shell can be considered complete when it holds two electrons and every other shell can be considered complete when it holds eight electrons. Electron Distribution and the Chemical Properties of Elements If the outer shell of electrons is complete, as it is, for example in Helium, which contains 2 electrons in its outer shell, or in neon, which contains 8 electrons in its outer shell, the element has very little tendency to react chemically with other atoms. Valence electrons – the electrons in the outer shell of an atom are known as valence electrons. The valance electrons are important in determining the chemical properties of elements and whether they will combine with one another. Electron Shell Diagrams We can represent the structure of atoms using Electron Shell or Bohr diagrams. In such a diagram, the number of protons and neutrons are indicated in a circle that represents the nucleus of the atom. The electrons are placed in Orbitals around the nucleus. Exercise Given the information below, construct Bohr diagrams of each atom. 19K39 12Mg24 15P31 Atomic Mass The atomic mass of an element is the ratio of its mass to one twelfth the mass of an atom of carbon-12, a unit known as a Dalton or µ. The atomic mass is calculated by averaging the atomic masses of all the chemical element’s isotopes, weighed by isotopic abundance and dividing it by one Dalton (µ), which is equal to 1.660538782 x 10−27 kg. Chemical Bonds Elements combine to form molecules and compounds. Molecule – consists of two or more atoms that have been bound together by chemical bonds A molecule is the smallest chemical unit of a substance that is capable of a stable, independent, existence. Compound – a compound is composed of two or more different kinds of elements joined together by chemical bonds. The difference between a molecule and a compound is that in a molecule the elements comprising the molecule may be the same or different. For example, H2, N2, O2, CH4, and C6H12O6 are all molecules. In the above list, CH4, and C6H12O6 also are compounds because they contain different kinds of elements. Water (H2O) is also a compound. However, H2, N2, and O2 are molecules of the element hydrogen, nitrogen, and oxygen respectively. They contain only one kind of element. Elements combine to form compounds. Example: Sodium + Chlorine → Sodium Chloride There are two types of Chemical Bonds: Ionic bonds and Covalent bonds. Ionic bonding – bonding by transfer of electrons. Covalent bonding – bonding by sharing of electrons. When atoms of elements combine, the atoms usually become more stable by completing their outer shells of electrons (2 electrons for the first shell, eight electrons for the outer shells). Ionic Bonding Ionic bonding is bonding by transfer of electrons. Electrons are transferred from the outer shell of one atom to the outer shell of a second atom. By this process both atoms usually attain stability by completely filling their outer shells with electrons. An example of ionic bonding is the reaction in which sodium combines with chlorine to form sodium chloride. Sodium + Chlorine → Sodium Chloride The substances on the left side of the equation, sodium and chlorine, are reactants. The arrow means yields. The substance(s) on the right side of the equation are products. The equation reads: sodium and chlorine react to yield sodium chloride. Using chemical symbols, 11Na23 + 17Cl35 → NaCl Using Bohr diagrams, Examining the Bohr diagrams for sodium and chlorine, we can see that the sodium atom contains 11 electrons. Two electrons are in the first shell, eight in the second, and there is 1 electron in the outermost shell. Sodium would attain greater stability if it had a complete outer shell of 8 electrons. Chlorine has 17 electrons. Two electrons are in the first shell, 8 electrons are in the second shell, and the remaining 7 electrons are in the third and outermost shell. Chlorine would attain a more stable arrangement by having a complete outer shell of eight electrons. Both sodium and chlorine could attain complete outer shells containing eight electrons if the single electron in the outer shell of sodium were transferred to the outer shell of chlorine. When sodium combines with chlorine, an electron is transferred from the outer shell of sodium to the outer shell of chlorine. This creates an ionic bond joining the two elements together. When sodium loses an electron by transferring it to chlorine, the sodium atom becomes electrically charged. Prior to the transfer, the sodium ion was electrically neutral. There were 11 protons and therefore 11 positive charges in the nucleus. 11 electrons with 11 negative charges canceled these. When the electron was transferred from sodium to chlorine, the electrical charges no longer equaled each other. There are 11 positive charges contributed by the 11 protons, but now there are only 10 negative charges from the 10 electrons. The sodium now has become a charged particle – a sodium ion . Ion – a charged particle. A charged atom or group of atoms. By reacting with sodium, the chlorine gains an electron. It now has 18 electrons and 17 protons. This gives it a charge of –1. The chlorine atom is now a chloride ion. A useful principle to learn is that opposite electrical charges attract one another. Like charges repel one another. Opposite electrical charges attract one another. The positively charged sodium ion is attracted to the negatively charged chlorine ion. This creates an ionic bond joining the two ions together. The product of the reaction is sodium chloride, that is, ordinary table salt. Positive ions are called cations . Negative ions are called anions . These ions are named according to their migration in an electrical field. If the ions are placed in an electrolytic cell and are in solution, the positive ions will migrate toward the negative terminal or cathode. They are therefore called cations. The negative ions will migrate toward the positive terminal or anode. They are therefore called anions. Covalent Bonding Covalent bonding is bonding by sharing of electrons. In forming a single covalent bond, two atoms each share one of their electrons with the other. These two shared electrons effectively fill an orbital in each atom and thus form a covalent bond between these two atoms. The atoms of the elementary gases hydrogen, oxygen, nitrogen, fluorine, and chlorine, form stable diatomic (consisting of two atoms) molecules by covalent bonding. A molecule is the smallest chemical unit of a substance that is capable of a stable, independent existence. Formation of H2 Two hydrogen atoms join together to form a molecule of hydrogen gas. When the atoms combine, each hydrogen atom shares one of its electrons with the other atom. Each hydrogen atom has one electron circling its nucleus. Its outer shell of electrons would be complete if it had two. In order to achieve this stable state, each hydrogen atom shares its electron with the other. Most of the time, the single electron will orbit around its own nucleus. However, part of the time, it will circle the nucleus of the other atom. This creates a strong covalent bond that holds the two atoms together. The sharing of the electrons produces the effect of complete outer shells containing two electrons. For at least some of the time, the two electrons may orbit one of the nuclei, giving it in effect, two electrons. At other times they will circle the other nucleus. In this way they attain stable outer shells. Formation of water The oxygen atom has six electrons in its outer shell. It would attain greater stability by gaining two electrons, thereby completing its outer shell with eight electrons. In forming a molecule of water, the oxygen atom combines with two atoms of hydrogen. Each of the hydrogen atoms shares one of its electrons with oxygen; together with the six electrons that oxygen already has, this gives oxygen a complete outer shell at least part of the time. Each hydrogen atom borrows one electron from oxygen, giving each a complete outer shell as these electrons orbit the hydrogen nuclei. By sharing two pairs of electrons the two hydrogen atoms and the oxygen atom are joined by covalent bonds. The electrons are not shared equally between the hydrogen atoms and oxygen atom. Because oxygen is a larger atom, it has a greater electronegativity. This means that it has a greater attraction for the electrons than hydrogen. As a result, the electrons spend more time circling around the oxygen than the hydrogen. This leads to a greater negative charge around the oxygen, and because the negatively charged electrons are pulled away from the positively charged hydrogen nuclei, a positive charge develops around the hydrogens. Water, thus, is a polar molecule i.e. a molecule with an unequal distribution of electrical charge. Weak chemical bonds Hydrogen Bonds Hydrogen bond – a weak chemical bond between a negatively charged nitrogen or oxygen atom and a positively charged hydrogen atom. Because opposite electrical charges attract one another, a negatively charged oxygen atom will be attracted to a positively charged hydrogen atom. This creates a weak chemical bond between the two atoms. For example, if two water molecules are adjacent to one another, the negative oxygen end of one water molecule is attracted to the positive hydrogen end of the other water molecule. These bonds create links between water molecules and are responsible for the forces of cohesion observed between water molecules. Another example of hydrogen bonds is found in DNA. In DNA, nitrogenous bases are stacked in pairs in the center of the DNA molecule between the two strands which comprise the molecule. Hydrogen bonds form between the negatively charged nitrogen atoms of nitrogenous bases and positively hydrogen atoms of adjacent nitrogenous bases. This creates hydrogen bonds that hold the two strands of DNA together. Chemical reactions Synthesis Reactions When two or more atoms, ions, or molecules combine to form larger molecules, the process is called a synthesis reaction. Example: 2H2 + O2 → 2H2O Decomposition Reactions In a decomposition reaction, large molecules are broken down to form smaller ones. Example: C6H12O6 + O2 → CO2 + H2O Exchange Reactions In an exchange reaction, the atoms of one compound switch places with atoms in another compound. HCl + NaHCO3 ⇌ NaCl + H2CO3 Reversible reactions The above reaction is also a reversible reaction. It can go in either direction. In the above reaction HCl can combine with NaHCO3 to form NaCl and H2CO3, or NaCl can combine with H2CO3 to form HCl and NaHCO3. Chemical Compounds Compounds can be divided into inorganic compounds and organic compounds. Inorganic Compounds Inorganic compounds – compounds which do not contain carbon. Carbon dioxide is an exception to the above definition. Carbon dioxide contains carbon. Nevertheless, it is considered to be an inorganic compound. This is because the properties of carbon dioxide are more like those of the other inorganic compounds. Inorganic compounds are usually small, ionically bonded molecules. They include water, many salts, such as NaCl, and many acids, such as HCl. Organic Compounds Organic compounds – compounds which contain carbon. Carbon dioxide is an exception to the above definition also. Although it contains carbon, It is classified as an inorganic rather than organic compound. Organic compounds are held together primarily by covalent bonds. They tend to be very large molecules. Organic compounds include carbohydrates, lipids, proteins, and nuclei acids. References McQuarrie D, Rock PA, Gallogly EB. General Chemistry. 4th ed. Mill Valley (CA): University Science Books; 2011. Introduction to Chemistry Study Guide draft 9 (Corrected 12/26/2018) PAGE 1