THE CHEMISTRY OF LIFE

Characteristics of Life

• The health status of a patient may be determined by evaluating their gross anatomy and micro-anatomy, their physiological processes, and their internal chemical composition. The characteristics of life include:

• a) movement • b) growth • c) definite form • d) reproduction • e) response to stimuli and • f) metabolism.

Nutrition and Chemistry

• Nutrition is literally a branch of biochemistry, and an understanding of the concepts of chemistry is a necessary prerequisite to all nutrition courses. In this particular portion of the course, we will focus on the chemical nature of life and nutrients.

Metabolism

• Metabolism may be defined as the sum of all of the chemical reactions within a living organism that are involved in maintaining or performing its life sustaining processes. A living organism may be viewed as a collection of chemical reactions which are working together in order to maintain life.

Matter

• Matter may be defined as anything that takes up space and has mass (weight). All matter is composed of elements.

Elements

• An element is a substance that cannot be broken down further into simpler components by ordinary chemical means. A molecule of water is composed of two atoms of hydrogen bonded to one atom of oxygen. It would be possible to break a water molecule down into simpler components (two individual hydrogen atoms and one oxygen atom) by a variety of simple chemical procedures. We would find it very difficult, however, to break the individual hydrogen and oxygen atoms down into simpler components through ordinary chemical means. Hydrogen and oxygen would therefore, be considered as elements and appear on the “Periodic Table of the Elements”.

Atoms

• Atoms, such as hydrogen and oxygen are the building blocks of matter.

Atomic Structure

• Atoms consist of three essential subatomic particles. These subatomic particles are:

• a) protons b) neutrons and c) electrons. Protons are endowed with a positive electrical charge, neutrons have no electrical charge, and electrons have a negative electrical charge.

Typical Atomic Structure

Protons

• Protons are endowed with a positive electrical charge

Neutrons

• Neutrons have no electrical charge. The neutrons are strategically placed within the nucleus in order to prevent the positively charged protons within the nucleus from repelling each other and fragmenting the nucleus.

Electrons

• Electrons have a negative electrical charge.

Planetary Arrangement

• The nucleus consists of protons and neutrons and consequently is positively charged. The negatively charged electrons orbit the nucleus. The electrons of an atom orbit its nucleus in much the same fashion as the planets of a solar system orbit their sun. The core of an atom is its nucleus. It is for this reason that we refer to the organization of the subatomic particles as a “planetary arrangement”. The neutrons are strategically placed within the nucleus in order to prevent the positively charged protons within the nucleus from repelling each other and destroying the nucleus.

Planetary Arrangement of Subatomic Particles Making Up An Atom

Health Note: Antiperspirants

• The concept of opposite charges attracting and like charges repelling has many applications. The openings of a seat gland are charged negatively and these “like” charges will cause the edges of the sweat gland to repel each other and keep the gland open so that sweat may freely flow from the gland. Antiperspirants contain aluminum chlorohydrate which is a positively charged compound. When aluminum chlorohydrate is sprayed the skin, the positive aluminum chlorohydrate causes the edges of the sweat glands to attract each other and close the gland. Exposure to aluminum has been implicated in the development of osteoporosis and possibly Alzheimer’s disease.

Electrons

• The electrons of an atom are the smallest of the three essential subatomic particles. The electrons orbit the nucleus of an atom is designated orbits referred to as energy levels. The electrons travel in these energy levels at the speed of light (186,000 miles per second).

Opposite Charges VS Like Charges

• Particles that have opposite charges will attract each other, while particles with the same charges will repel each other. The electrostatic attraction of the positive proton for the negative electron (and vice-versa) will hold the electrons in their designated orbits.

Capacity of an Individual Energy Level for Electrons

• Each energy level has a certain capacity for electrons. The capacity of an orbital for electrons can be determined by the formula:

• 2 (n)2 . The letter “n” represents the specific energy level. The first energy level can hold a maximum of two (2) electrons (2 (1)2). The second energy level can hold a maximum of eight (8) electrons (2 (2)2). An atom can possess as many energy levels as is necessary to contain its electrons.

Energy of Electrons

• Electrons that orbit close to the nucleus (first energy level) have the least amount of energy. Electrons that orbit farther away from the nucleus have more energy. Atoms can exist in one of two states depending upon the status of their electrons.

• • Ground State• Excited State

Ground State

• Ground State: occurs when all of the electrons are in their proper orbits.

Excited State

• Excited State: occurs when an atom has been given extra energy and the electrons move from a lower to a higher energy level.

Health Note• The movement of electrons from a lower energy level to a higher energy

level is a phenomena that occurs naturally in the body and is useful in producing the energy currency of the body known as adenosine triphosphate (ATP). This phenomena also occurs outside the human body and may have detrimental affects upon our health. Let us use a fluorescent lamp as an example. Unlike an incandescent lamp, fluorescent lamps do not have a metallic filament. Fluorescent lamps contain one of the Nobel gases. When a light switch is turned on and electrical energy is introduced into the gases within the lamp at the positive pole, the electrical energy excites the gas atoms by causing the electrons to move from a lower to a higher energy level. These gas atoms will now travel across the lamp towards the negative pole. As the gas atoms move across the lamp, the extra electrical energy that they received will be released and the excited electrons will drop back down to their normal energy levels from the higher energy levels. The extra electrical energy will be released as light, heat and electromagnetic radiation. Electromagnetic radiation has been linked to cancer and birth defects

Atomic Number• Atoms are identified by their atomic number and their atomic weight.

The atomic number of an atom is defined as the number of protons that are contained within the nucleus. All atoms, in their natural states, are electrically neutral. If the atomic number of an atom of the element carbon is six (6), it indicates that the atom has six (6) protons in its nucleus. Since all atoms in their natural states are electrically neutral, one can assume that orbiting this nucleus, there exists six (6) negative electrons. Two (2) of these electrons would be contained within the first energy level, and the remaining four (4) electrons would be contained within the second energy level. The six negative charges of the electrons will neutralize the six positive charges of the protons within the nucleus, and the atom will be electrically neutral.

Atomic Weight

• The atomic weight of an atom is the number of protons plus the number of neutrons within the nucleus. Sodium, for instance, has eleven protons in its nucleus which gives it an atomic number of 11 and it contains twelve (12) neutrons within its nucleus. If the number of protons and neutrons are added together, it will give the sodium atom an atomic weight of twenty three (23).

Molecular Bonding

• Atoms do not generally exist alone in nature. Atoms can generally be found bound chemically to other atoms. Sometimes an atom may bind to another atom which is identical to itself, such as in the case of oxygen. When two (2) oxygen atoms combine with each other, the resulting molecule is called O2. Other atoms may combine with two or more different atoms. An example of this would be two (2) hydrogen atoms combining with one (1) oxygen atom to form a molecule of water (H2O). Atoms generally combine with other atoms in nature in order to become more stable.

The Octet Rule

• The “Octet Rule” states that atoms are most stable when they have a filled outer shell. It usually requires eight (8) electrons to fill the outer shell of an atom and make it more stable. The “Octet rule” was so named in order to reflect this phenomena.

Atoms With a Filled Outer ShellAre Stable Atoms

Types of Chemical Bonds

• Four basic types of molecular bonds exist in nature. These four types of bonds include:

• a) ionic

• b) covalent

• c) polar covalent

• d) hydrogen.

Ionic Bonds: Ions

• Atoms in their natural states should be electrically neutral. It is possible, however, that an atom may either gain or lose an electron. Ions are electrically charged atoms that have gained or lost electrons. If an atom loses an electron we say that it has been oxidized and it becomes a positive ion. If an atom gains an electron, we say that the atom has been reduced and it becomes a negative ion.

Electron Affinity

• The electron affinity of an atom will determine whether an atom will gain or lose an electron. Electron affinity is a term used to describe the degree of attraction an atom has for electrons. If an atom has a low electron affinity, it will lose electrons, but if it has a high electron affinity, it will gain electrons. The electron affinity of an atom can be determined by observing its position on the Periodic Table of the Elements. The electron affinity of elements increases as you move from the left side of the Periodic Table of Elements to the right side. Therefore, elements that are located on the left side of the Periodic Table of the Elements have a low electron affinity and will lose electrons, while elements on the right side of the Periodic Table of the Elements will have a high electron affinity and gain electrons.

Electron Affinity Increases As You Move from Left to Right On The Periodic Table of the

Elements

Sodium (Na)

• Sodium chloride (NaCl) is also known as common table salt. Sodium has an atomic number of eleven (11) and therefore contains 11 protons within its nucleus. Orbiting the nucleus of a sodium atom, are eleven (11) electrons. Two (2) of these electrons will exist within the first energy level, eight (8) electrons will exist within the second energy level, and one (1) electron will be found within the third energy level. Sodium does not satisfy the requirements of the “Octet Rule” since it does not have eight (8) electrons within its outer orbital and is not considered stable.

Sodium (Na)

Chlorine (Cl)

• Chlorine has the chemical symbol (Cl). It has seventeen (17) protons in its nucleus. Since atoms in their natural form are electrically neutral, it has seventeen (17) electrons orbiting its nucleus. Two (2) electrons exist within the first energy level, eight (8) electrons exist within the second energy level, and a single electron exists within the third electron. Since only seven (7) electron (not eight) exists within the outer energy level, chlorine does not satisfy the “Octet Rule” and is also not considered stable.

Chlorine (Cl)

Mechanism of Ionic Bonding of Sodium Chloride (NaCl)

• When an atom of chlorine and an atom of sodium enter into a chemical reaction together, chlorine (because of its high electron affinity) will take the single outer electron of sodium away and incorporate this new electron in its third energy level. Sodium will now have only two (2) energy levels. The second energy level of sodium will be filled with its maximum compliment of eight (8) electrons and now be considered stable. The chlorine atom will now have eight (8) electrons within its outer shell and it too will be considered stable. Sodium, however, is now a positive ion since it lost an electron. The electrostatic attraction between the positive sodium ion and the negative chlorine ion will form an ionic bond between the two atoms. Ionic bonds result from the transfer of electrons between atoms, are generally weak, and are used in the formation of acids, bases, and salts.

Sodium Chloride (Ionic Bond)

Ionic Bonding of Sodium Chloride (NaCl)

NaCl Crystal Formation

Covalent Bonds

• Sometimes, the electron affinity of the atoms which are reacting with each other are very similar. In this case, one atom will not be able to take an electron from another atom. The atoms which are reacting together to form a more complex molecule will have to share the electrons. When two atoms combine by sharing electrons, the resulting bond is referred to as a covalent bond. Covalent bonds are extremely strong and stable bonds, and they are very common in biological systems.

Characteristics of Covalent Bonds

• Covalent bonds are extremely strong and stable bonds, and they are very common in biological systems.

Carbon and Hydrogen

• Carbon has an atomic number of six (6). Two (2) of the six electrons that orbit a carbon atom exist on the first energy level, while the remaining four (4) electrons exist within the second energy level. According to the “Octet Rule”, carbon would not be a stable atom. Carbon must fill its second energy level with four more electrons, in order to give it a total of eight (8) electrons within its outer shell, by sharing electrons with another atom or atoms. Hydrogen is an atom that commonly shares its electrons with carbon. Hydrogen has an atomic number of one (1) and therefore contains a single proton in its nucleus and a single electron within its first energy level.

Mechanism of Covalent Bonding

• Since the first energy level can hold two (2) electrons and hydrogen has only one (1) electron, it is also considered unstable. Four (4) hydrogen atoms will be required to share their electrons with a single carbon atom in order to fill its outer shell with eight (8) electrons. The carbon atom will be sharing its electrons with each one of the hydrogens, in order to provide each hydrogen atom with the two (2) electrons required to fill their outer shells.

Carbon and Hydrogen (Covalent Bond)

Covalent Bonds

Polar Covalent Bonds• When two atoms share electrons in order to form a bond, it is possible to that one atom

will have an electron affinity which is greater than that of the other atom to which it is going to form a bond. This unequal sharing of electrons will form a polar covalent bond. Water (H2O) is formed when two hydrogen atoms bond to one oxygen atom. Oxygen is located on the right side of the Periodic Table of Elements and has a very strong electron affinity. Hydrogen, however, is located towards the left hand side of the Periodic Table of Elements and has a relatively low electron affinity. The atomic number of oxygen is sixteen (16). The electron configuration of oxygen will be characterized by the existence of two (2) electrons on the first energy level, eight (8) electrons on the second energy level, and six (6) electrons on the third energy level. Oxygen atoms are unstable, since they do not have eight (8) electrons within their outermost energy level. In order for oxygen to achieve stability, it must share two electrons with another single atom or an appropriate number of a group of other atoms. Each hydrogen atom found within the water molecule will share one electron with an oxygen atom in order to help oxygen achieve stability. Oxygen will share one electron with each of the two hydrogens in order to fill their outer shells, and help them achieve stability. Since the oxygen atom has a greater electron affinity than the hydrogen atoms, the electrons will orbit around the nucleus of the oxygen atom more often than they will orbit around the nucleus of the hydrogen atoms. When this occurs, the two extra electrons orbiting the oxygen atom will cause it to become negatively charged, while the hydrogen atoms will become positively charged. Since the two atoms are sharing electrons (albeit unequally), and since a positive pole and a negative pole exists within the molecule, we call this type of bond a “polar covalent bond.

Water (H20) (Polar Covalent Bond)

Hydrogen Bonds

• Hydrogen bonds are weak electrostatic bonds that occur between positive hydrogen atoms and a slightly negative atom of another molecule or between parts of the same molecule. If two water molecule are in close proximity with each other, the positive hydrogen atoms of one water molecule will attract the negative oxygen atoms of another water molecule. The bond that forms between the hydrogen and oxygen atoms is referred to as the “hydrogen” bond. Hydrogen bonding between water molecules give water its surface tension. Hydrogen bonds also are necessary for the formation of the three dimensional structures of protein molecules, and hold the antiparallel strands of deoxyribonucleic acid (DNA) together. Polar covalent bonds are a necessary pre-requisite for the formation of hydrogen bonds.

Hydrogen Bonds

Hydrogen Bonds

Important Chemical Reactions

• Hydrolysis

• Dehydration Synthesis/Condensation Rxn

• Oxidation Reduction/Redox Rxn

Hydrolysis

• Hydrolysis is the process through which a living cell breaks a chemical bond by adding water. Hydrolysis is very important in the process of digestion.

Dehydration Synthesis (Condensation Reaction)

•• Dehydration Synthesis (condensation

reaction) refers to any chemical reaction that will remove a molecule of water and form a chemical bond. The body uses these types of chemical reactions when it needs to for a complex molecule from simpler molecules.

Oxidation Reduction Reactions/ Redox Reactions

• In a previous part of this laboratory exercise, oxidation was defined as the process through which an atom loses electrons. Reduction, however was defined as the process through which an atom gains electrons. In order for many chemical reactions to occur, one atom has to lose electrons while another atom will gain these electrons. Within the cell, oxidation reduction reactions are used to generate energy. The “flow” of electrons from that are losing electrons to atoms that are gaining electrons will create a type of electric current within the cell that can be used to generate adenosine triphosphate (ATP).

Acids, Bases and Salts• ACID, BASES, and SALTS

• The human body can only remain healthy if its fluids exist within a narrow band of pH. The pH scale measures the relative concentrations of hydrogen ions (H+) and hydroxide ions

• (OH-). The pH scale goes from zero (0) to fourteen (14).

•• Mucous Blood• O | | 7 | 14

Acid Base

• 6.9 7.4• Neutral

Acids

• An acid may be defined as a substance that releases hydrogen (H+) ions when placed into solution. Acids will have a pH of less than seven (7). Bases (alkaline) are defined as substances that will release hydroxide ions when put into solution. Bases generally have a pH of greater than (7). The pH of an acid is represented by the following mathematical formula:

• _____1________• pH Acid = Logarithm [H+]

Bases

• The pH of a basic or alkaline substance is represented by the following mathematical formula:

• ____1___________ • pH Base = Logarithm [OH −]

• The strength of an acid or a base is determined by the ability of the substance to dissociate into its constituent ions. Acids, bases and salts are formed by ionic bonds. If we were to study the structure of hydrochloric acid, we would see that it consists of one (1) hydrogen atom bonded to one (1) chlorine atom.

Determining the Strength of Acids and Bases

• The strength of an acid or a base is determined by the ability of the substance to dissociate into its constituent ions. Acids, bases and salts are formed by ionic bonds. If we were to study the structure of hydrochloric acid, we would see that it consists of one (1) hydrogen atom bonded to one (1) chlorine atom.

Neutralization• It is common knowledge that an acid will neutralize a base and a base

will neutralize an acid. If we were to mix hydrochloric acid (HCl) together with the base known as sodium hydroxide (NaCl) the two substances will neutralize each other. When we place hydrochloric acid (HCl) into solution, it dissociates into positive hydrogen ions (H+) and negative chlorine ions (Cl−). When sodium hydroxide (NaCl) is placed into water, it dissociates into positive sodium ions (Na+) and negative hydroxide ions (OH−). If the two solutions are mixed together, the positive sodium ions (Na+) from the sodium hydroxide (NaOH) and the negative chlorine (Cl−) ions from the hydrochloric acid will combine to form common table salt (NaCl). The hydrogen ions (H+) from the hydrochloric acid (HCl) and the hydroxide ions (OH−) from the sodium hydroxide (NaOH) will combine to form water (H2O).

• Acid: HCL −−−−−−> H+ and CL− • Base: NAOH −−−−−> OH−− and Na±• H2O NaCl

Health Note• This ingestion of caustic substances such as acids or bases is

always a life threatening condition that must be handled immediately and managed properly. Vomiting should not be induced when treating cases of acid or base ingestion. Acids and bases will damage the tissues of the digestive tract when they are swallowed. If vomiting is induced, the acid or base will damage the tissues of the digestive tract a second time as they move up through the gastro-intestinal tract. When treating individuals who have ingested these materials, the practitioner should try to neutralize the acid or base in the stomach. The universal antidote for either acid or base ingestion is a cocktail of raw egg whites, water and milk. In addition to this, acids may also be neutralized with over the counter antacids which may be readily available. The individual should then be transported to a local hospital emergency room for further evaluation and/or treatment.

Water

• Water is necessary for life as we know it. Water is necessary for the occurrence of the chemical reactions that occur inside and outside of a living cell and stabilizes cell (plasma) membranes. Water can also dissolve a great number of substances, and for this reason, it is known as the universal solvent. The cohesive nature of water molecules (due to the hydrogen bonding between them) allows blood and body fluids to flow smoothly through vessels and tissue spaces, and allows for a uniform distribution of solutes. Water also helps us to maintain our normal body temperature