Jung S Kim

Chapter 2 Summary

All organisms are composed of matter and the chemistry is the science that deals with properties of matter. It’s particularly important in the study of microorganisms because understanding the metabolism of an organism, the structure of an organism, and how they affect humans in disease requires an understanding of the discipline. Matter can be thought of as building blocks with the smallest unit of chemical matter being the atom. Substances composed of only one type of atom is known as an element. Each element has individual properties that distinguishes it from another. Such substances include the gasses oxygen and nitrogen. Moreover, atoms of one element can combine with atoms of another element to create more unique substances. For example, two hydrogens will bind with oxygen to create water. When one atom chemically links itself with another it forms a molecule, when two or more atoms that are chemically linked are made up of different elements, this is known as a compound.

Atoms are composed of protons, neutrons, and electrons. Each proton and neutron has a mass equivalent to 1 amu (atomic mass unit). The protons and neutrons are packed together in a structure known as the nucleus while electrons move around them in patterns known as orbitals. The number of protons an atom has is known as the atomic number. It is a useful identifying trait of an atom as an elements proton count remains the same while its number of electrons and neutrons are subject to change. Protons are positively charged while electrons are negatively charged. The charge differential allows the atom to be structurally sound because the negative charges of the electrons are attracted to the positive charges of the protons. For conceptual purposes it’s helpful to think of the movement of electrons around a nucleus in terms of shells. Electron movement closer to the nucleus has less energy than a movement of electrons further away. The further an electron is away from a positively charged nucleus, the more energy it would require to maintain its “orbit”. The amount of electrons an atom has is usually equivalent to its number of protons. When thinking of electron movement around a nucleus as layered shells, electrons will fill the inner shells first before filling the next shell. The innermost shell of an atom can accommodate 2 electrons while the outer shell, known as a valence shell, can accommodate 8. The larger, or the more protons an atom has, the more electron shells it will have. In fact the valence shell can accommodate no more than 8 electrons, and this is the most stable state of the atom, in a principle known as the rule of octets.

An atom can be charged when it gains or loses an electron that creates a mismatch of charge between its orbiting electrons and the positive charge of the nucleus. When an atom gains more electrons than protons it will have a negative charge, and when an atom loses electrons bringing its electron count below its number of protons, it will have a positive charge. A positively

charged atom is known as a cation, while a negatively charged atom is known as an anion. An anion undergoes a name change when negatively charged, a chlorine atom when it gains an electron will be called chloride. An atom will have a tendency to form ions in an attempt to reach the more chemically stable state of 8 electrons in its valence shell. Thus, chlorine which has 7 electrons in its valence shell will have the tendency to gain an electron in order to reach a chemically more stable state. Ions do not all have to all be variants of elements however, compounds like OH-, known as hydroxide, are also ionic. Atoms as mentioned before, can also have a varying amount of neutrons.

When two atoms have the same number of protons and electrons, but vary in the number of neutrons, they are considered isotopes of one another. Carbon exists in nature with vary number of neutrons. The atomic mass number that gives the molecular weight of an element in the periodic table is an average of all the molecular weights that can exist in nature, due to the existence of isotopes. A mole is a term ascribed to a specific number 6.023X10^23, and atomic weights are represented in grams for a mole count an element’s atoms. Not all isotopes are stable, and unstable isotopes are considered radioactive in that they radiate subatomic particles, which may harm living organisms. Radioactive isotopes are known as radioisotopes. The chemical linking mentioned earlier is representative of an essential principle in chemistry known as bonding.

Molecules and compounds are formed via bonds and three main types of bonds exist in chemistry. The first of these bonds is the ionic bond where an atom of one element completely strips one or more electron from an atom of another. This occurs as a result of electronegativity or “desire for electrons” if one atom is much more electronegative than the other for example if one electron has a nearly filled valence shell and another has its own valence shell barely filled, it’s energetically favorable for an exchange of electrons to occur. Rather than exchanging, if two electrons share an electron this is known as a covalent bond. When sharing electrons two atoms can easily fill their valence shell without having to “possess” the electron. Two hydrogen atoms can share their electrons to fill their valence shell, which only happens to be two, whereas carbon will share 4 of its valence electrons to form 4 covalent bonds and thus have an effective 8 electrons in its valence shell. Electrons are shared in pairs each atom gives up a single valence electron to share with the other bonding atom. Equal sharing of electrons produces nonpolar compounds, which means that no charged regions exist within the compound.

Sometimes it’s energetically favorable between two atoms to share more than two electrons. When another pair is shared between the two this is known as a double bond, and a third set of electrons shared between two atoms is known as a triple bond. Oxygen has a tendency to double bond with carbon because in doing so it reaches 8 effective electrons in its valence

shell whereas carbon will form two more bonds with other atoms to fulfill its own octet. When two atoms share electrons unevenly in that electrons spend most of their time closer to the one atom in a compound over another, also a product of electronegativity, it will create partially charged regions within the compound.

When the highly electronegative elements nitrogen, oxygen, or fluoride (the most electronegative element) is bound to a hydrogen, it produces a compound that is capable of hydrogen bonding. The partially positive charged region of this compound is hydrogen and the partially negative charged region is the electronegative element where the electron spends most of its time. Two compounds of this type will thus be attracted to each other because of their oppositely charged ends. The partially charged hydrogen of one compound will be attracted to the partially negative N, O, or F of the other. Examples of substances composed entirely of this type of interaction is water, where each compound is capable of forming 4 hydrogen bonds. The 2 hydrogens of the water can hydrogen bond with two oxygens of two other water compounds, whereas the oxygen can attract two hydrogens from two other compounds, for a total of 4.

Hydrogen bonding is very important to large organic molecules such as proteins and nucleic acids. Bonds within a compound are capable of storing energy. Thus an organism can break down the bonds of a compound, in a process known as catabolism, in order to make use of the released energy to do work. Bond formation or bond breaking is a chemical reaction and a chemical reaction that releases energy can be categorized as being exergonic. In the same way that an organism break down bonds to release energy, organisms can store energy by forming bonds, a process known as anabolism. Anabolic reactions, or bond formation, is usually an endergonic process in that they require energy.

Water is one of the most important chemical compounds in living organisms. Without it many organisms will perish relatively quickly. The most important quality of water is its polar nature. Water’s partially positive and negative ends make it an excellent solvent, in that it has the ability to dissolve materials effectively. Water’s partially charged ends for example will completely surround both positive and negative ions, breaking the attractions between them. The hydrogen bonding capability of water allows for a property known as surface tension where water molecules will adhere to itself and form thin films, an essential trait of cell membranes. Water’s hydrogen bonding nature allows for a high specific heat. Which means that a relatively large amount of energy is required to raise the temperature of water by a single degree. This allows for a stable internal environment within organisms that resists temperature fluctuations in the external environment. Water’s chemical properties allow for important chemical reactions to take place within an organism’s internal environment. In anabolic reactions H and OH groups are removed from reactants to produce larger molecules through

the formation of a water molecule in a process known as dehydration synthesis. In catabolic reactions, these same components of water are utilized to break the bonds within a compound to form smaller compounds in a process known as hydrolysis.

In chemistry, there is a distinction to be made between a mixture and a solution. A mixture is a mixing of two chemically distinct components in any proportion, that don’t interact with each other on a chemical basis. Whereas a solution is mixture of two or more substances in which the molecules of one substance is uniformly dispersed throughout the other in a chemical process. The medium being dissolved within a solution is known as the solute, whereas the medium doing the dissolving is referred to the solvent. As mentioned before, because of its polar properties, water is the primary solvent for most living organisms. Solutes can be any atom or compound which interacts with solvent to be uniformly dispersed. Solutes can be as small as an atom or as large as proteins. The amount of solute within a solvent is known as a concentration and organisms tend to prefer environments with low concentrations of solutes, relative the concentration of their internal environment.

Colloidal dispersions are composed of particles too large to be uniformly dispersed throughout solvent, but not so large that they precipitate out of a solvent. Thus they cannot be considered to be true solutions because they are not uniformly dispersed. Colloidal dispersions have the tendency to be murky and opaque, such as the substance milk.

Acids and bases are also chemical substances which are critical to understanding the chemistry within organisms. An acid refers to a substance which donates a positively charged hydrogen atom, (an hydrogen without an electron, essentially a proton) and are thus considered to be “H+ donors” whereas bases are proton acceptors or hydroxide ion donors. It either accepts the hydrogen ion or donates a hydroxide to bind with hydrogen. The concentration of hydrogen ions is measured by a logarithmic scale of molality known as pH. Most organisms can tolerate an external or internal environments of only a limited range of pH. As we go down the pH scale we get exponentially more acidic by a factor of ten for each whole index. Substances with pH’s below seven are known as acid and substances above the pH of 7 are known as bases. Acidic pHs are important in the digestive process because acid helps break down some substances, and has the capability of destroy potentially pathogenic organisms.

Organic chemistry is the study of compounds containing carbon. Which is an identifying component of compounds utilized by living or organic organisms. Compounds have the tendency to link with other carbons and form long chains. One common carbon chain compound is the hydrocarbon which is simply a chain of carbons with covalently bonding hydrogens. The way that organic compounds are structured, the number and types of bonds formed between its component atoms, and its molecular shape, can have a

significant impact upon the chemical properties of a molecule. Many of these properties are crucial for organisms to fulfill certain chemical tasks or “function” within their internal environment and thus an organic compound of a certain structure can be referred to as a functional group. Four significant functional groups within organism are aldehydes, ketones, alcohols and organic acids. An alcohol has one or more hydroxyl groups whereas an aldehyde has a carbonyl group at the end of a carbon chain. A ketone is a carbonyl group (which is a double bonded carbon and oxygen) within a carbon chain. Another key functional group is the amino group which accounts for nitrogen within proteins.

A given functional group may either be reduced or oxidized. Oxidation or reduction within organic compound often refers to the relative number of oxygens contained within the compound. Groups with more oxygen such as carboxyl are considered to be oxidized whereas groups with little oxygen such as alcohols are considered to be reduced. Oxidation or reduction can also refer to the removal of hydrogen or electrons from a substance. If a hydrogen or electron is removed from a substance, that substance is known to be reduced, whereas if a hydrogen or electron is gained, it’s known to be oxidized. The more reduced a molecule the more energy it gains. Hydrocarbons which often lack oxygen are great sources of energy, an example would be gasoline.

There are four main classes of large molecules within biological organisms. These large molecules are known as macromolecules and the four types are the following: carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates are primarily utilized as a source for energy for organisms, but they have serve several other functions. Carbohydrates can be structural such as the cellulose found on the walls of plant cells. Carbohydrates are utilized as markers on the surfaces of cell membranes. All carbohydrates are composed of the elements of carbon, hydrogen and oxygen. Carbohydrates can be classified into monosaccharides, di-saccharides, or poly-saccharides. Both di and poly variants are simply composed of 2 or many, many more monosaccharides. Monosaccharides are often a pentose or a hexose carbon ring with an additional functional group. Several monosaccharides exist and are often isomers of one another, which means that they have the same type and number of atoms, but are arranged differently within the molecule via bonding. The most prevalent monosaccharide is glucose and is a main component of several important disaccharides and polysaccharides. Glucose can be represented in chain form, in ring form, or as a 3 dimensional structure, the 3d structure being the most apt representation of this molecule. Monosaccharides can be reduced to form deoxy sugars and alcohol. Deoxyribose is a monosaccharide that is the key component of DNA, a nucleic acid chiefly responsible for the storage of our all our genetic information. Two monosaccharides form a disaccharide through glyosidic linkage. This is an example of dehydration synthesis mentioned earlier, and polysaccharides are simply more than two

monosaccharides bonded through such a linkage. Polysaccharides as with all the aforementioned macromolecules are polymers. It’s chief and distinct component from which it is built via glyosidic linkage, the monosaccharide, is known as a monomer.

Lipids represent a diverse group of substances that include fats, oils, phospholipids, and steroids. Due to their hydrocarbon structure, which are nonpolar, they are often insoluble in water. Fats contain the alcohol glycerol and one or more fatty acids. A fatty acid’s chemical composition can be described as a long hydrocarbon tail with a carboxyl head. The carboxyl group is the component which bonds with the glycerol.