Zoology Notes: 005 Chapter 2

Chapter 2. The Chemistry of Living Matter Matter is made up of elements, substances which cannot be broken down by ordinary chemical means into simpler particles. Each element is a collection of a particular kind of discrete particle matter called the atom. An atom is the smallest unit of an element that retains the chemical properties of that element. Subatomic Particles. Atoms are made up of even smaller, subatomic particles: the proton, the neutron, and the electron. Protons have positive charges, electrons are negatively charged, and neutrons are neutral. Each element has a different number of protons. The atomic number is a count of the number of protons in the elemental atom. Oxygen, for example, has 8 protons therefore its atomic number is 8. Carbon has 6. Hydrogen has 1. Nitrogen has 7. Generally, atoms have approximately the same number of protons, neutrons, and electrons. Each proton or neutron has a mass of about 1.7x10-24 gram. For convenience, this mass is defined as 1 atomic mass or 1 Dalton. The mass of an electron is about 1/2000 that of a proton, so it is often disregarded when considering atomic mass. The protons and neutrons form the nucleus while electrons travel at the speed of light orbiting the nucleus. The atomic mass of an element is the number of protons plus neutrons in each nucleus. Isotopes. Atoms with the same number of protons but different number of neutrons are called isotopes. Two isotopes of ordinary hydrogen (1 proton, 0 neutrons) are deuterium (1 proton, 1 neutron) and tritium (1 proton, 2 neutrons). Isotopes share the same atomic number but differ in atomic mass, the sum of the atom’s protons and neutrons. Thus, all hydrogen isotopes have the atomic number 1, but atomic masses of 1, 2, and 3, respectively. Isotopes with extra neutrons are often unstable and undergo radioactive decay at typical and predictable rates, giving off subatomic nuclear particles until they reach stability. Tritium, with a half-life of 12.5 years, is very useful in biological research as a radioactive tag that allows hydrogen-containing compounds to be traced through metabolic pathways. Ions. Atoms with the same number of protons but different number of electrons form ions. NaCl (sodium chloride, table salt) when in water, dissolves and separates into its constituent ions, Na+ and Cl-. The Na ion is positively charged because one of its electrons has been “kidnapped” by the Cl ion. Na+ then, has 11 protons, 11 neutrons, and only 10 electrons. Cl- on the other hand, has 17 protons, 17 neutrons, but 18 electrons, making it negatively charged. Positively charged ions are called cations and negatively charged ions are called anions. Chemical Bonds. Following the octet rule, the innermost shell, or the lowest quantum level, for any atom never contains more than two electrons. Each shell external to this innermost shell may contain up to eight electrons. The number of electrons in the outermost shell determines the combining power (valence) of an atom. If the outermost shell contains eight electrons, (or in the case of He, 2 electrons in the outermost shell) the atom will be unable to bond with any other atom and the element is said to be inert. Atoms with less than eight electrons in the outermost shell form bonds with other atoms to saturate this shell. There are three major kinds of chemical bonds: covalent bonds, ionic bonds, and hydrogen bonds. Covalent bonds involve the sharing of electrons. The two atoms both lack electrons in their outer shells. They fill up the vacancies by 11

sharing a pair of electrons. Ionic bonds involve the transfer of electrons from one atom to another so the atom either loses or gains electrons. Hydrogen bonds form relatively weaker bonds between polar molecules or polarized side groups of non-polar molecules. They are important in maintaining the shape of macromolecules aiding in the performance of their biological functions.

Cl Cl Cl2 Fig. 2.1. Covalent bonds. Two atoms of chlorine form covalent bonds to produce chlorine gas.

Na

Cl

NaCl

Fig. 2.2. Ionic bonds. Atoms of sodium and chlorine form ionic bonds to produce salt.

Fig. 2.3. Hydrogen bonds. Four water molecules bonded by hydrogen bonds (dotted line)

A

molecule consists of two or more atoms joined by bonds. The atoms composing a molecule may be the same (O2, H2) or different (H2O, CH4). A molecule composed of different atoms is called a compound. Electrolytes. The combination of water with a chemical compound dissolved in it is called a solution. A compound that dissociates into anions and cations when dissolved in water forms a solution which will conduct an electric current. Hence, any chemical compound which will dissociate into ions in water is called an electrolyte. Electrolytes are described as strong or weak, depending on how completely ionize. Strong electrolytes ionize completely; weak electrolytes ionize slightly. Acids, Bases, and Salts. The hydrogen ion H+ is one of the most important ions in living organisms. The hydrogen atom contains a single electron. When this electron is completely transferred to another atom (not just shared with another as in covalent bonds), only the hydrogen nucleus (essentially a single proton) remains. Any compound that releases H+ ions (protons) when dissolved in solution is called an acid. An acid is classified as strong or weak depending on the extent to which the acid molecule is dissociated in solution. Examples of strong acids that dissociate completely in water are hydrochloric acid (HCl) and nitric acid (HNO3). Weak acids such as carbonic acid (H2CO3) dissociate only slightly.

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A base, or alkali, is a compound that releases OH- ions or accepts hydrogen ions in solution. Examples are caustic soda (NaOH) and ammonia water (NH4OH) which are common household chemicals. Acids and bases, when concentrated, are severe irritants and will burn the skin and the delicate covering of the eyes and mouth. A salt is a compound resulting from the chemical interaction of an acid and a base. For example, common salt, sodium chloride (NaCl), is formed by the interaction of hydrochloric acid (HCl) and sodium hydroxide (NaOH). In water, the HCl dissociates into H+ and Cl- ions, the hydroxide reacts with H+ to form water and Na+ and Cl- remain as a dissolved form of salt. This reaction is shown in the following equation: HCl acid

+

NaOH base



NaCl salt

+

H2O water

Hydrogen Concentration (pH). pH means “potential hydrogen” where pH indicates neutrality. Pure water if fully ionized to H+ and OH- would potentially yield a molar concentration of 107 H+ and 107 OH- (i.e. pH 7). A mildly acidic solution if fully ionized would yield 106 H+ and 108 OH- and would be designated “pH 6” and so forth. With few exceptions, living systems do not tolerate strongly acidic or alkaline conditions, and their vital processes must take place within a range from pH 6 to pH 8. Saliva has a pH of 6.8. Gastric juice is the most acid substance in the body (pH 1.6). The pH of human blood must remain between 7.35 to 7.45. If human blood plasma merely becomes neutral, pH 7, this seemingly harmless deviation actually would represent a life threatening acidosis. This slightly basic range is zealously guarded by buffers that can neutralize excess H+ and OH-. description very basic

weakly basic neutral weakly acidic

very acidic

pH 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

examples NaOH, lye oven cleaner hair remover ammonia soap, milk of magnesia chlorine bleach, phosphate detergent seawater, egg white pure water urine, milk, saliva black coffee, rain water tomatoes, grapes vinegar, wine, soft drinks, beer, orange juice, pickles lemon juice, lime juice stomach acid HCl, battery acid

Table 2.1. The pH of some solutions.

Buffers. The hydrogen ion concentration in the extra-cellular fluid (ECF) must be regulated so that the metabolic reactions within the cells will not be adversely affected by a constantly changing hydrogen ion concentration (pH) to which they are extremely sensitive. To maintain pH within physiologic limits, there are certain substances that tend to compensate for any change in the pH when acids or alkalis are produced in metabolic 13

reactions or are added to the body fluids. These are called buffers. A buffer is a mixture of slightly ionized weak acid and its completely ionized salt. In such a system, added H + combine with the anion of the salt to form undisassociated acid, and added OH- combines with H+ to form water. The most important buffers in the blood and other body fluids are bicarbonates and phosphates. For example, blood contains carbonate buffers made up of salts sodium and potassium bicarbonate (NaHCO3 and KHCO3) and of the weak carbonic acid (H2CO3). If a strong acid, such as HCl, enters the blood, the salts of the buffer convert it to a weak acid which cannot lower the pH as much as HCl can: NaHCO3 sodium bicarbonate

+

HCl hydrochloric acid



NaCl sodium chloride

+

H2CO3 carbonic acid

On the other hand, if a strong base, such as sodium hydroxide (NaOH) enters the blood, the carbonic acid will neutralize it: H2CO3 carbonic acid

+

NaOH sodium hydroxide



NaHCO3 sodium bicarbonate

+

H2O water

Water. Water is the predominant chemical component of living organisms. It makes up from 60 – 90% of the protoplasm. Its unique physical properties, which include the ability to solvate a wide range of organic and inorganic molecules, derive from water’s dipolar structure and exceptional capacity for forming hydrogen bonds. An excellent nucleophile, water is a reactant or product in many metabolic reactions. Water has a slight propensity to dissociate into hydroxide ions and protons. A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center. The two hydrogen atoms and the unshared electrons of the remaining orbitals occupy the corners of the tetrahedron. Water is a dipole, a molecule with electrical charge distributed asymmetrically about its structure. The strongly electronegative oxygen atom pulls electrons away from the hydrogen nuclei, leaving them with partial positive charge while its two unshared electron pairs constitute a region of local negative charge. This enables water to dissolve large quantities of charged compounds such as salts.

Fig. 2.4. (a) Water as a polar molecule. (b) Water forming hydration shells around chloride and sodium ions.

Organic Compounds Of the 92 naturally occurring elements, 16 can be found in living things, and only 4 make up 99% of living matter. These elements are carbon, hydrogen, oxygen, and nitrogen. In the study of animals, we will mostly be concerned with organic compounds, that is, compounds that always contain carbon and hydrogen. Four of the most important organic matters are carbohydrates, proteins, lipids, and nucleic acids. Carbohydrates. Glucose and other simple sugars (monosaccharides), as well as their polymers (polysaccharides), are called carbohydrates. Carbohydrates generally contain one oxygen and 2 hydrogen atoms for every carbon. For example, glucose and fructose consist of six carbon atoms, 12 hydrogen atoms, and 6 oxygen atoms, and have 14

the formula C6H12O6. Galactose, mannose, and many other monomers have this same formula, differing only in the arrangement of the elements. Common carbohydrates having different chemical formulas include ribose, xylose, arabinose, and ribose (C5H10O5); deoxyribose (C5H10O4); glucuronic acid and galacturonic acid (C6H12O7); and rhamnose (C6H12O5). Carbohydrates are synthesized from H2O and CO2 by plants through photosynthesis (a process on which all life depends because it is the starting point in the formation of food). They provide much of the immediate or ultimate food for animals and are much used by humans (food, fabrics, wood, paper, etc.). Fig. 2.5. The molecular structure of The main role of carbohydrates in the protoplasm is fructose (left) and glucose (right). to serve as a source of chemical energy. Monosaccharides are the end product in the digestion of carbohydrates. Over 200 are known but most important are glucose, fructose, and galactose. Except immediately after a meal, glucose is the only monosaccharide present in significant quantities in the blood and interstitial fluids of man and animals. There are two reasons for this: 1. Usually 80% to 100% of the monosaccharides absorbed from the gastrointestinal tract is glucose, and only rarely is more than 20% of these fructose and galactose together. 2. Within less than an hour after absorption from the gut, essentially all the fructose and galactose will have entered the cells and been converted into glucose. These 3 monosaccharides form disaccharides in the following manner: - glucose and fructose form sucrose (cane sugar) - glucose and galactose form lactose (milk sugar) - glucose and glucose form maltose The polysaccharide typical in animals is glycogen. It is commonly stored in vertebrate liver and can be reconverted into glucose for transport by the blood. Proteins. A protein consists of one or more polypeptides and may also include sugars or other kinds of small molecules. A polypeptide is a chain of amino acids linked together by carbon-nitrogen bonds called peptide bonds. They contain C, H, O, N, and usually S.

Fig. 2.6. Structural formula of some amino acids. From left: methionine, alanine, tryptophan, and lysine.

Most abundant of organic materials in animal protoplasm are the proteins. They function as enzymes, components of cell membranes, contractile elements of muscle, hormones, receptors on the cell surface and within the cell, antibodies, buffers, oxygen carriers (hemoglobin) and oxygen storers (myoglobin), blood constituents (albumin – most abundant), blood clotting factors, sources of energy, and as important components of intracellular fabric of connective tissue. 15

There are basically 20 amino acids that form all kinds of proteins found in living things. Ten are classified as essential amino acids, meaning those that cannot be synthesized in the body and must be supplied in the diet in adequate quantities. Deficiency will result in a negative nitrogen balance with loss of weight and arrest of growth. The other ten are classified as non-essential amino acids, meaning they can be synthesized by the body. Essential Amino Acids Phenylalanine arginine isoleucine valine threonine leucine tryptophan histidine lysine Non-essential Amino Acids alanine glutamine praline asparagine glutamic acid serine aspartic acid glycine tyrosine Table 2.2. Essential and non-essential amino acids.

methionine

cysteine

Pepsin II and gastricin (pepsin I) are the most important peptic enzymes of the stomach; they are most active at a pH of 2 to 3 and completely inactive at a pH of 5. Pepsin is capable of digesting collagen. They break down proteins into proteoses, peptones and polypeptides. These are then hydrolyzed by pancreatic enzymes trypsin and chymotrypsin into dipeptides and smaller polypeptides. Dipeptidases and aminopolypeptidases in the epithelial cells of the small intestine are responsible for the hydrolysis of peptides into amino acids. Lipids. Unlike other biological polymers, lipids are not defined by specific, repeating, monomeric subunits. Rather, they are defined by their waterrepellant property. The only Fig. 2.7. Glycerol with fatty acid showing reactive site. common structural theme shared by all lipids is a large proportion of non-polar hydrocarbon groups. These hydrocarbon groups are often made from polymers of two-carbon compound called acetate. Lipids are fats and other related substances. They are insoluble in H2O but soluble in organic liquids like ether, chloroform, and acetone. Three types of lipids generally exist in animals: neutral fats, phospholipids, and sterols. Neutral Fats. Neutral fats (triglycerides) are composed of a glycerol and three molecules of fatty acids. Neutral fats make up the major fuel of animals. Phospholipids. Phospholipids (where one of the three fatty acids is replaced by phosphoric acid and an organic base) is an important component of the molecular organization of tissues especially membranes (e.g. Lecithin is an important phospolipid of nerve membrane). Sterols. Sterols are complex alcohols which have fat-like properties. Cholesterol, the most common sterol in animal tissue, is a component of cell membranes. Cholesterol can also undergo rearrangement to form such substances as sex hormones and bile acids. Fats are emulsified in the small intestines by bile acids and broken down into glycerol and fatty acids by enteric and pancreatic lipases. 16

Nucleic Acids. The most complex biological polymers are nucleic acids The two most common nucleic acids are deoxyribonucleic acids and ribonucleic acids. DNA and RNA are polymers made up of repeated units called nucleotides; nucleotides are composed of: a sugar, a nitrogenous base, and a phosphate group. Sugar Nitrogenous base Purine

DNA deoxyribose

RNA ribose

Adenine (A) Adenine (A) Guanine (G) Guanine (G) Pyrimidine Cytosine (C) Cytosine (C) Thymine (T) Uracil (U) Table 2.3. Differences between molecules of DNA and RNA.

Nucleic acids are unique because they can replicate themselves. Furthermore, DNA can make RNA, which guides the assembly of proteins. Nucleic acids form the molecular foundation for every living organism.

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