Inorganic & Organic Chemistry

Chemistry Notes BI 171

I. ELEMENTS are pure substances; COMPOUNDS are combinations of elements. A. ATOMS are the smallest particles into which an element can be divided and still show the properties of that element. Atoms cannot be further divided by ordinary chemical and physical means. 1. Atoms are composed of PROTONS, NEUTRONS, and ELECTRONS. 2. An atom's NUCLEUS includes a set number of protons and a variable number of neutrons. a. The ATOMIC NUMBER is the number of protons. b. The ATOMIC MASS is the number of protons and neutrons. c. ISOTOPES are atoms of the same element with different numbers of neutrons. 3. A set number of electrons, equal to the number of protons, orbits around the nucleus. a. IONS are atoms with a positive or negative charge due to a deficit or excess of electrons. b. Electrons are attracted by the nucleus but repelled by each other; they move in ORBITALS. c. Electrons occur in discrete ENERGY LEVELS. The energy levels nearest the nucleus (the levels with the lowest energy) are filled first. 4. An atom's chemical properties are largely a result of THE NUMBER OF ELECTRONS IN THE OUTERMOST ENERGY LEVEL. a. An atom with a full outer level is INERT. b. Atoms with unfilled outer levels will react with other atoms to fill or empty those levels. II. Molecules are groups of atoms held together by MOLECULAR BONDS, which are links of pure energy based on shared or donated electrons. A. COVALENT BONDS form when atoms share electrons, which creates a molecular orbital around the nuclei. 1. A SINGLE BOND results from the sharing of one pair of electrons. 2. DOUBLE BONDS and TRIPLE BONDS result from the sharing of two or three pairs of electrons. 3. NONPOLAR COVALENT BONDS occur between two atoms that share electrons equally. 4. POLAR COVALENT BONDS occur where the shared electrons spend more time around one of the nuclei. which results in a slight negative charge around that atom and a slight positive charge around the other atom. B. HYDROGEN BONDS are weak bonds that involve the attrac- tion between a polar molecule with a negative pole and a polar molecule with a hydrogen atom bearing a slight positive charge. C. IONIC BONDS occur between positively- and negatively- charged ions. III. Water is essential to life. Cells are largely composed of water and exist in a watery medium. A. The polarity of water molecules and the hydrogen bonds between them affects the physical properties of water related to temperature. 1. Water has a HIGH SPECIFIC HEAT. Heat energy must first break the hydrogen bonds between molecules before their speed of movement can be increased. This feature moderates the temperature or organisms and their environment. 2. Water has a HIGH HEAT OF FUSION and resists the change to ice. 3. Water has a HIGH HEAT OF VAPORIZATION. Hydrogen bonds hold liquid water molecules together, and a molecule must have a high velocity to escape as a gas. By evaporating, water removes heat from its surroundings. B. Water's hydrogen bonds affect its mechanical properties. 1. COHESION is the tendency of like molecules to cling to each other. SURFACE TENSION is the tendency of water molecules at the surface of liquid water to stick to each other but not to the molecules of air above them. 2. ADHESION is the tendency of unlike molecules to cling together. CAPILLARITY is the tendency of a liquid such as water to move upward through a narrow space. 3. Ice is less dense than water and floats on it. C. Water has been called the universal SOLVENT, a sub- stance that can dissolve SOLUTES including polar molecules and ions. 1. HYDROPHILIC substances dissolve readily in water. 2. HYDROPHOBIC substances do not dissolve readily in water. D. Water molecules tend to IONIZE, or dissociate, into a hydrogen ion, H+, and a hydroxide (hydroxyl) ion, OH_. 1. An ACID is any substance that gives off hydrogen ions when dissolved in water. 2. A BASE is any substance that accepts hydrogen ions when dissolved in water. Such substances are called ALKALINE. 3. The pH scale measures the concentration of H+. 4. BUFFERS moderate changes in pH.
Some Useful Generalizations Simple molecules linked together in various ways produce large molecules called MACROMOLECULES. In some cases, the formation of macromolecules consists of the production of long chains or POLYMERS; the simple molecules are the links of the chain or MONOMERS. SIMPLE ORGANIC COMPOUNDS MACROMOLECULES Monosaccharides Polysaccharides Fatty Acids and Glycerol Simple and Complex Lipids Amino Acids Proteins Nucleotides Nucleic Acids The PROCESS of joining simple molecules into larger ones is called DEHYDRATION SYNTHESIS or CONDENSATION, whereby the equivalent of a water molecule is removed at each bonding site. In living organisms enzymes catalyze these reactions. The PROCESS of breaking MACRO-MOLECULES into their constituent parts is known as HYDROLYSIS and takes place within the watery medium of the cytosol with the water supplying the H and OH molecules to the simple compounds. Once again, different enzymes catalyze these reactions in living systems. Most organic molecules in living organisms have 4 broad functions 1. some are essential to cellular and body structure 2. some serve primarily as energy-rich fuels in cellular respiration 3. some convey information controlling growth, differentiation, and biological specificity from one generation to another 4. some operate primarily as catalytic agents in the cell's and body's chemical processes Since there are hundreds of thousands of molecules in existence and there are only a hundred odd kinds of atoms from which they can be constructed, it follows that the uniqueness of the molecule must depend upon the: number, type, and spatial arrangement of the atoms Thus, IT IS OFTEN THE SHAPE OF THE MOLECULE THAT DETERMINES ITS PHYSICAL AND CHEMICAL PROPERTIES. Heterotrophic Metabolism involves both a catabolic (hydrolytic) phase and an anabolic (synthesis) phase. Reduced organic molecules are broken into smaller fragments and at the same time they are oxidized to obtain and ultimately store energy. In biosynthesis, small molecules are built up and atoms rearranged to make the monomeric units required by the cell (amino acids, fatty acids, nucleotides). Materials moving through a metabolic or pathway are called METABOLITES.
I. CARBOHYDRATES serve as structural components and energy reserves for the cell. They contain carbon, hydrogen, and oxygen. The hydrogen and oxygen are always in the same ratio as in water (2:1). The type of bond typical of carbohydrates is called a GLYCOSIDE BOND and is formed by removal of water at the bonding site. A bond formed by removal of water is called an ANHYDRO BOND. Thus GLYCOSIDE BONDS are ANHYDRO BONDS of carbohydrates. A. The basic building blocks of carbohydrates are the simple sugars or MONOSACCHARIDES. These monosaccharide monomers can be linked into two unit DISACCHARIDES or double sugars or into larger units known as POLYSAC- CHARIDES. B. The most important carbohydrate monomers are GLUCOSE, FRUCTOSE, and GALACTOSE. These have a common formula, C6H12O6, but different structural arrangements. The different structural arrangements cause the molecules to have different characteristics. When molecules have the same formula but are arranged differently they are called ISOMERS. C. Common disaccharides are SUCROSE which is table sugar, LACTOSE which is the sugar in milk, and MALTOSE which is used in brewing. Sucrose is made of glucose and fructose; Lactose is made of glucose and galactose, and Maltose is made of glucose plus glucose. D. Starch, glycogen, cellulose, chitin and agar are all examples of common polysaccharides. They differ pri- marily in the three-dimensional pattern is which the monomers are bonded to each other. they may be coiled or branched. E. Phosphorylation - Many sugars can react in biochemical processes, such as cellular respiration, only when phosphorylated -- that is, a phosphate group is added. (H2PO3) has replaced one or two of the -H in the sugar molecule). II. LIPIDS include a variety of molecules that can serve as energy storage molecules or as building blocks of cells. They consist of hydrogen, carbon, and oxygen, are not soluble in water but are soluble in alcohol, benzene, or chloroform. They are usually liquid in warm blooded animals and oils in cold blooded animals. The ANHYDRO BOND of lipids is known as an ESTER BOND. A. TRIGLYCERIDES include FATS and OILS 1. Each molecule contains a GLYCEROL molecule bonded to THREE (3) FATTY ACIDS 2. Because C-C and C-H bonds contain more energy than the C-O bonds common in carbohydrates, triglycerides have more energy than carbohydrates B. WAXES have long-chain fatty acids combined with long chain alcohols rather than glycerol C. PHOSPHOLIPIDS are like lipids but have a phosphate group in place of one of the chains, making the molecule hydrophilic. They are components of cell membranes D. STEROIDS are made of four interconnected rings of carbon atoms. They can pass through the hydrophobic molecules that make up cell membranes. Many are involved in the regulation of metabolism. They include such compounds as the MALE AND FEMALE SEX HORMONES, hormone groups from the outer portion (CORTEX) of the ADRENAL GLAND, CHOLESTEROL, and VITAMIN D. (See also: Lipid Derivatives of Biological Importance) III. PROTEINS come in a wide variety of forms. Structural proteins contribute to the growth, repair, and replacement of cells and enzymes catalyze cellular chemical reactions. They consist of hydrogen, carbon, oxygen, nitrogen and sometimes sulfur. A. Proteins are long chains of AMINO ACID subunits (monomers) folded into characteristic three-dimensional shapes. 1. There are about 20 amino acids commonly found in different types of cells although thousands of amino acids exist in nature. 2. Amino acids are covalently joined by ANHYDRO BONDS KNOWN as PEPTIDE BONDS. An amino acid is an organic acid in which the amino group (-NH2) has been substituted for a -H attached to a carbon atom other than the one to which the carboxyl group (-COOH) is attached. Two amino acids join to form a DIPEPTIDE; long chains are called POLYPEPTIDES or PROTEINS. B. Proteins have complex shapes based on four levels of structure. 1. A protein's unique linear sequence of amino acids is its PRIMARY STRUCTURE. This sequence of amino acids is genetically determined. The substitution of one amino acid in a sequence results in an entirely different kind of protein. The classical example is SICKLE CELL ANEMIA where the substitution of GLUTAMIC ACID to VALINE is the difference between normal hemo- globin and sickle cell hemoglobin. 2. A protein chain will assume a folding pattern, the SECONDARY STRUCTURE, that allows the maximum number of hydrogen bonds between amino acids. a. An ALPHA-HELIX occurs in proteins such as myoglobin. b. In BETA-PLEATED SHEETS, polypeptide chains lying side by side form accordion-like sheets. 3. The TERTIARY STRUCTURE is determined by the inter- action of the amino acid's side groups with their environment, generating the 3-dimensional shape of the protein molecule. The polypeptide continues to coil and fold over onto itself which provides a unique structure important in globular proteins such as enzymes and egg white (albumin). These folded areas may be held together by disulfide linkages. a. Antibodies and enzymes are important globular proteins. Egg white (albumin) is also globular. b. Collagen, actin, myosin, and keratin are examples of fibrous proteins. 4. QUATERNARY STRUCTURE is based on two or more folded polypeptide chains that fit together. The most common example is hemoglobin. The irreversible destruction of the primary level of protein organization, i.e. the breaking of the bonds joining the amino acids is known as DENATURATION. Removal of amino groups from an amino acid is called DEAMINATION. THE CHARACTERISTICS OF A PROTEIN ARE DETERMINED BY THE NUMBER, KIND AND SEQUENCES OF THE AMINO ACIDS COMPOSING THEM. Proteins fall into several major categories on the basis of functional activity. Two of the most common are: (See also: Classification Scheme of Proteins...) A. Structural Proteins - used for growth, repair and replacement they are the major structural components of most living tissues; often they are found in combination with other molecules - such combinational proteins are known as CONJUGATED PROTEINS. Some examples include: 1. nucleoproteins - proteins + nucleic acids 2. glycoproteins - proteins + oligosaccharides 3. lipoproteins - proteins + lipids 4. chromoproteins - proteins + colored pigments B. Catalytic Proteins - primarily ENZYMES which serve as ORGANIC CATALYSTS affecting the rate of biochemical reactions without being used up in the process; they normally speed up reactions which are already thermo- dynamically possible and allow them to proceed at a rate which makes life, as we understand it, possible. ENZYMES normally operate by reducing the ACTIVATION ENERGY required to start reactions and thus reducing the thermal energy (high temperature) which would otherwise be needed but detrimental to living systems. In general enzymes function by providing a convenient surface for bringing together the reactants and then becoming separated from them. Enzymes influence various types of reactions: 1. larger molecules may be synthesized from smaller ones 2. larger molecules may be hydrolyzed into smaller ones 3. atoms may be exchanged between molecules 4. atoms may be rearranged within molecules C. Some enzymes require the presence of specific ions (salivary amylase requires Cl-) to carry out their job. Some enzymes operate in two parts: an APOENZYME which is the protein portion and a COENZYME which is an organic molecule often constituted of a vitamin and a phosphate combination. Inorganic molecules which aid enzymes are often called COFACTORS. Enzymes influence reactions by: 1. reducing the amount of activation energy required 2. providing a surface upon which the possibility of contacts between reactants is increased D. The substance or molecule which is acted upon by an enzyme is known as the SUBSTRATE. The speed at which chemical reactions occur is known as the RATE OF REACTION. Reaction rate is more precisely defined as: the amount of substrate acted upon/unit of time (usually min.) Thus, when a great deal of substrate is altered by an enzyme every minute, the reaction is said to be proceeding at a rapid rate. In enzyme reaction rates, the rate depends on the CONCENTRATION of the enzyme and the CONCENTRATION of the substrate (CONCENTRATION rather than AMOUNT). Concentration refers to amount in a given volume of solution. In most enzyme reactions, enzyme concentration is small compared to the substrate concentration. Therefore, the rate of the reaction becomes proportional to the concentration of the enzyme. If the enzyme concentration is doubled, the reaction rate is doubled. At low substrate concentrations, the rate of the reaction is proportional to the substrate concentration, but at higher substrate concentrations the reaction rate is independent of substrate concentration. That is, further increase in the amount of substrate present per unit volume does not cause the reaction to proceed at a faster rate because all available enzymes are already saturated or tied up in reactions. This was first described mathematically in 1913 by Michaelis and Menten as: rate = V(S)/K+S where V and K are constants V = maximum velocity of saturated enzyme-substrate complex K = Michaelis constant S = substrate concentration when S is very small the denominator is not affected very much and rate = V/K(S) when S is very large the denominator becomes effectively equal to S and the rate becomes effectively equal to V or independent of substrate concentration this assumes no product inhibition ------------------------------------------------------- | ^ V | S + E <=======> ES <=======> ES* <=======> EP <=======> P + E ES = enzyme-substrate complex; an intermediate compound ES* = activated complex Most of these reactions are essentially reversible, and the direction of the reaction depends upon the concentration of the reactants in relation to the concentration of the products The enzyme imparts no net energy to the system. The portion of the enzyme at which the substrate combines is known as the ACTIVE SITE of the enzyme and represents a spatial arrangement of atoms complementary or nearly complementary to a specific portion of the substrate. The rate at which the reactants are converted to products, in enzyme catalyzed systems, is controlled by pH, enzyme concentration, temperature, substrate concentration, and product concentration. The interaction of these factors imposes a delicately balanced system of controls on the rate of metabolic activity within the living system. Enzymes are commonly named by attaching the suffix -ASE to a stem word which designates either (1) the substrate they affect; (2)reaction type which they catalyze; or (3) the type of bond holding the molecule together. For example: proteinase, lipase, maltase, sucrase, amylase, OR oxidase, hydrolase, tranferase, mutase, OR peptidase, esterase. General Characteristics of Enzymes 1. Chemically, all known enzymes are proteins 2. Usually they are soluble in water, or dilute saline (salt solution) 3. They are usually most active within the small range of temperature tolerated by living cells 4. Their influence is very specific with respect to: a. type of reaction b. type of substrate 5. In general their influence is reversible, with the speed and direction of the reaction depending upon: a. concentration of enzyme b. concentration of substrate c. concentration of products d. pH - each enzyme functions best within a specific range of pH e. temperature - each functions within its own range f. inhibiting substances (enzyme poisons such as Pb++ [lead], Hg++ [mercury]; inhibitors such as chloroform) IV. NUCLEIC ACIDS are information-carrying molecules or energy-carrying molecules. They are the largest of the biomolecules. A. Nucleic acids are made of monomers called NUCLEOTIDES. Nucleotides consist of: a 5 carbon sugar, phosphoric acid (phosphate group), and one of 5 different nitro- genous bases. Phosphate \ Sugar - Nitrogen Base THREE REPRESENTATIVE / Phosphate NUCLEOTIDES \ Sugar - Nitrogen Base JOINED / TOGETHER Phosphate \ Sugar - Nitrogen Base B. DNA is a double stranded helix, RNA a single-stranded molecule. (1) DNA contains deoxyribose sugar, phosphoric acid groups, and Adenine, Thymine, Guanine, & Cytosine. The strands of the double helix are COMPLEMENTARY to each other. Adenine is always bonded to Thymine and Guanine is always bonded to Cytosine. Thus the pairing of the nitrogen bases is key to the struc- ture and the characteristics of the molecule. (2) Specific segments of DNA represent coded informa- tion called GENES. Each gene codes for a type of protein (structural, catalytic, etc.). Each protein is responsible for certain characteristics of the organism. THUS THE SEQUENCE OF NITROGEN BASES IN THE DNA MOLECULE REPRESENTS THE CODE OF LIFE. (3) DNA is capable of self-replication and thus is the root of reproduction at all levels. It is also capable of being mutated and thus represents a means for change in the genetic code and thus in the characteristics of an organism or the type of organism itself. (4) RNA contains ribose sugar, phosphoric acid, and Adenine, Guanine, Cytosine or Uracil. Uracil replaces Thymine in RNA molecules. (5) There are 3 types of RNA molecules. All are single stranded, although some are twisted rather than straight. All 3 types are produced based on infor- mation provided in the structure of the DNA. (a) mRNA - messenger RNA (b) tRNA - transfer RNA (c) rRNA - ribosomal RNA (6) RNA's carry out the instructions set forth by the DNA molecules in the production of proteins. Thus, RNA is directly involved in protein synthesis. (7) The enzymes used in the construction of nucleic acids are called POLYMERASES - DNA polymerase or RNA polymerase C. DNA and RNA are both composed of four different kinds of bases, so the number of symbols in the genetic code is four. Since the efficiency of a communication system is inversely proportional to the number of symbols used in the code, DNA and RNA represent a highly efficient means of communication. D. Nucleotides may function as (a) energy carriers, (b) coenzymes, or (c) components of genetic systems. ADENOSINE PHOSPHATES are not polymers. This class includes ATP, the universal energy molecule and cAMP, which carries chemical signals. ADP is also in this group.