Chapter 2 1

THE CHEMICAL LEVEL OF ORGANIZATION

CHAPTER 2

Anatomy and Physiology Lecture

Chapter 2 2 THE CHEMICAL LEVEL OF ORGANIZATION

1. Human body is composed of chemicals and all body activities are chemical in nature.

2. Most food we eat and drink are chemical substances that function in

our bodies to keep us alive. 3. To understand our body chemical make up, we need to know which

chemical elements are present in the body (human organism) and how they interact.

BASIC CHEMISTRY

1. The structure and function of your body result from thousands of interactions that take place at the chemical level of organization.

2. All life processes involve chemical reactions- e.g. - calcium

participates in muscle contraction for movements; - sodium and potassium are necessary for nerve impulses related to responsiveness.

3. To understand the nature of the matter that composes your body and

the changes it undergoes in health and in disease, you will need to know how it is organized and how different elements of matter interact with one another.

MATTER AND ENERGY

All living and nonliving things consist of matter. 1. Matter is anything that occupies space and has mass.

Chapter 2 3

Three States of Matter 1. Solid 2. Liquid 3. Gas (Although the terms mass and weight often are used interchangeably, there is a distinction.) Mass is the amount of matter that a substance contains. Weight is the gravitational force acting on an object of a given mass. (Although your mass is the same, your weight depends on where you are. In outer space, weight is close to zero but mass remains the same as it was on earth at sea level.) 2. Energy is the capacity to do work, that is, to put mass into motion.

*Mass and energy can be neither created nor destroyed, but one can be converted into the other.

Two Principal Kinds of Energy

a. Potential Energy - inactive or stored energy. b. Kinetic Energy - energy of motion. *Energy (Potential or Kinetic) exists in several different forms: i Chemical Energy is the energy released or absorbed in the breaking

apart or forming of chemicals. ii Radiant Energy such as heat and light, is energy that travels in

waves. iii Electrical Energy results from the flow of electrons or other charged

Chapter 2 4 particles such as ions.

-(Action potentials (impulses) in nerve and muscle cells are examples of electrical energy.) Chemical Elements All forms of Matter are made up of a limited number of building blocks called chemical elements. Chemical elements are substances that cannot be split into simpler substances by ordinary chemical reactions. -109 different elements are recognized by scientists; -92 of them occur in nature. *Elements are given letter abbreviations, usually derived from the first or first and second letters of the English or Latin name for the element called Chemical Symbols, e.g. H - Hydrogen C - Carbon O - Oxygen N - Nitrogen Ca - Calcium Na - Natrium = Sodium K - Kalium = Potassium Fe - Ferrum = Iron P - Phosphorus -26 of the 92 naturally occurring elements are present in your body. The following make up about 96% of the body's mass: oxygen carbon

Chapter 2 5 hydrogen nitrogen The following make up about 3.9% of the body's mass calcium phosphorus potassium sulfur sodium chlorine magnesium iodine iron Trace element - make up about 0.1% of the body's mass (because they are present in minute concentrations) Structure of Atoms Each element is made up of units of matter called atoms. An element is a quantity of matter composed of atoms, all of the same type. [A handful of the element carbon, such as pure coal, contains only carbon atoms.] [A tank of oxygen contains only oxygen atoms.] Atoms - the smallest units of matter that enter into chemical reactions. An Atom consists of three major types of subatomic particles: a. Electrons (e-) - negatively charged b. Protons (p+) - positively charged } Within the Nucleus c. Neutrons (n≅) - uncharged (neutral)

Chapter 2 6 *(The number of electrons in an atom of an element always equals the number of protons => # p+ = # e-) *Atom is electrically neutral (its total charge is zero); since each electron carries one negative charge, the negatively charged electrons and the positively charged protons balance each other. Dalton or Atomic Mass Unit (amu) is the standard unit for measuring the mass of atoms and their subatomic particles. Neutron has a mass of 1.008 daltons Proton has a mass of 1.007 daltons Electron has a mass of 0.0005 daltons Atomic Mass (Atomic Weight) - adding up the masses of all the protons, neutrons, and electrons in an atom. *Number of Protons in the nucleus makes the atoms of one element different from those of another. (Each different kind of atom has a different number of protons in its nucleus.) Atomic Number - the number of protons in an atom. (Therefore each kind of atom, or element, has a different atomic number.) eg. oxygen has 8 atomic numbers, because its nucleus has 8 protons, while sodium has 11. Mass number - is the total number of Protons and Neutrons. -For sodium (Na), with 12 neutrons, the mass number is 23. (11 protons + 12 neutrons = 23) *Since electron has so little mass, the Atomic Mass of an atom may be nearly equal to its mass number.

Chapter 2 7 *Atoms of one electron, however, although chemically alike, may have different mass number because they have different number of neutrons. Isotopes - Different atoms of an element that have the same number of protons (atomic number) but different number of neutron, thereby having different Mass number. -All isotopes of an element have the same chemical properties because they have the same number of electrons.

Eg: Isotopes of oxygen are 16O, 17O, and 18O (or 0-16), 0-17, and 0-18). The numbers indicate the mass number (total number of Protons and Neutrons) in each Isotope.

Radioactive Isotopes (Radioisotopes) - Are unstable isotopes; their nuclear structure decays or changes to a more stable configuration. -In decaying they emit radiation. (alpha or beta particular or gamma rays.) Half-life is the time required for the radioactive isotope to emit half of the original amount of radiation. Electrons and Chemical Reactions Chemical reaction occurs when atoms combine with or break apart from other atoms. -In the process, new products with different chemical properties are formed. Electron interactions are the basis of all chemical reaction. -Electron, in their motion around the nucleus, tend to spend most of the time in specific atomic regions, which are represented as circles lying at varying distances from the nucleus. Electron shell is represented by each circle, which can hold a certain maximum of electrons.

Chapter 2 8 a. First Shell - the electron shell nearest the nucleus, and never holds

more than two electrons, no matter the element. b. Second Shell - holds maximum of eight electrons. c. Third Shell -holds up to 18 electrons. (Atoms whose atomic number is less than 20 can hold a maximum of 8 electrons, which more complex atoms can hold a maximum of 18 electrons on 3rd shell. d. Higher Shells (there are as many as seven) can contain many more

electrons. (e.g. Iodine, the largest element present in the human body, holds 18 electrons in the fourth shell and 7 in the fifth. *An atom tends to either empty their outermost shell of fill it to the maximum. *To do so, atom may give up, accept, or share electrons with other atoms, whichever is easiest. Valence (combining capacity) is the number of extra or deficient electrons in the valence shell (the outmost shell). Chlorine (Cl) Atomic Number = 17 Mass Number = 35 or 37 Atomic Mass = 35.453 (Has 7 electrons on the outermost, will be easier to pick up 1 electron). Sodium (Na) Atomic Number = 11 Mass Number = 22 or 23 Atomic Mass = 22.990 (Has 1 electron on the outermost, will be easier to give up than pick up more 7 electrons).

Chapter 2 9 Helium (He) Atomic Number = 2 Mass Number = 3 or 4 Atomic Mass = 4.003 (Outermost electron shell is completely filled, do not need to gain or lose electron. Are called Inert elements). Inert Elements are not chemically active and do not usually participate in chemical reactions. (E.g. Helium, Argon and Neon) (Atoms with incompletely filled outer shells, such as Na and Cl, tend to combine with each other in chemical reactions.) Molecule - results when two or more atoms combine in a chemical reaction. For example: Can be same atoms ( H + H --> H2) Can be different atoms ( H + Cl --> HCl) Compound - is a substance that can be broken down into two or more different elements by chemical means. (The molecules of a compound always contain atoms of two or more different elements). Electrons and Chemical Bonding Outermost electrons of an atom determine its chemical behavior. Chemical Bonding occurs when the outermost electrons are transferred or shared between atoms. Different Kinds of Chemical Bonds:

a. Ionic Bonds b. Covalent Bonds

Chapter 2 10 A. Ions and Ionic Bonds *(Atoms are electrically neutral because the number of positively charged protons equals the number of negatively charged electrons.) When an atom gains or loses electrons, however, this balance is upset. Cations - If the atom loses electrons, it acquires a positive charge. Anions - If the atom gains electrons, it acquires a negative charge. Ion is a negatively or positively charged particle. B. Covalent Bonding Covalent Bonding – When atoms share one or more pairs of electrons, resulting to a molecule. Single covalent bond – When an electron pair is shared between two atoms. Double covalent bond – When two atoms share four electrons, two from each atom. Nonpolar covalent bods – When electrons are shared equally between atoms, as in a hydrogen molecule.

*Bonds between two identical atoms always are nonpolar covalent bonds.

*Single covalent bond between carbon and hydrogen is another example of a nonpolar covalent bond.

Polar covalent bonds – When electrons are not equally shared between atoms, as in oxygen and hydrogen.

*Bond between oxygen and hydrogen in a molecule of water is the most important example in living systems.

Chapter 2 11

(Partial negative charge (∗-) indicates that atom that attracts electrons more strongly.)

(Partial positive charge (∗+) indicates the atom that does not attract electrons strongly.)

*Polar covalent bonds allow water to dissolve many molecules that are important to life.

Intermolecular Forces Intermolecular forces result from the weak electrostatic attraction

between the oppositely charged parts of molecules, or between ions and molecules.

Hydrogen Bonds

Provides temporary bonding between certain atoms within large complex molecules such as proteins and nucleic acids.

Hydrogen bond consists of a hydrogen atom covalently bonded to one oxygen atom or nitrogen atom but attracted to another oxygen or nitrogen atom.

*(Because hydrogen bonds are weak, only about 5% as strong as covalent bonds, they do not bind atoms into molecules.)

*(However, they do serve as bridges between different molecules or between various parts of the same molecule.)

Example: Between water molecules Between various parts of the same molecules

Chapter 2 12 Chemical Reactions and Energy Chemical Reactions involve the making or breaking of bonds between atoms. -After a chemical reaction, the total number of atoms remain the same, but because they are rearranged, they are new molecules with new properties. Metabolism refers to all chemical reaction occurring in an organism. Several factors that determine whether a collision will occur and cause a chemical reaction: 1. Concentration 2. Speed 3. Energy 4. Proper orientation A. Synthesis Reactions: Anabolism

Synthesis reaction - when two or more atoms, ions, or molecules combine to form new and larger molecules.

(Synthesis means "to put together", and synthesis reactions involve the forming of new bonds.)

Synthesis reaction can be expressed in the following way:

A + B ------- Combine to form AB

Atom, ion Atom, ion New molecule AB ∪ ∪ Reactants Product

Example: N2 + 3H2 ------- 2NH3

*All the synthesis reactions that occur in your body are collectively

Chapter 2 13 called anabolic reactions or simply anabolism.

E.g. Combining Amino Acids to form proteins; Combining glucose molecules to form glycogen.

B. Decomposition Reaction: Catabolism

To decompose means to break down into smaller parts.

In a decomposition reaction, bonds are broken. Large molecules are broken down into smaller molecules, ions, or atoms.

A decomposition reaction occurs in this way:

AB -----Breaks down into--- A + B

Molecule AB Atom, ion, or Molecule A Atom, ion, or molecule B

Example: CH4 ----- C + 2H2 One methane molecule one carbon atom two hydrogen molecules

*All the decomposition reactions that occur in y our body are collectively called catabolic reactions, or simply catabolism.

E.g.- Digestion of food molecules.

C. Exchange Reactions

Are partly synthesis and partly decomposition.

AB + CD --------6 AD + BC

(Bonds between A and B and between C and D break in a decomposition process. New bonds then form between A and D and

Chapter 2 14 between B and C in asynthesis process.)

D. Reversible Reactions

The product can revert to the original reactants. A reversible reaction is indicated by two arrows.

Combines to form

A + B ≡ AB Breaks down into

Some reactions are reversible only under special conditions: Heat is applied

A + B ≡ AB Water is added Inorganic Chemistry

-Usually lack carbon. -Usually small in living systems -Are ionically bonded molecules

Examples: Water, oxygen, carbon dioxide, many salts, acids, and bases

a. Water

-Most abundant inorganic substance in living systems. 60% of Red blood cells

75% of Muscle tissue 92% of Blood plasma (liquid portion of blood)

Chapter 2 15 -Functions:

1. An excellent solvent and suspending medium

Solvent + Solute = Solution

*Termed a "universal solvent" since it serves as a solvent for many solutes.

2. Participate in chemical reactions. 3. Absorbs and releases heat very slowly. 4. Requires a large amount of heat to change from a liquid to a gas. 5. Serves as a lubricant - in several regions of the body.

b. Inorganic Acids, Bases, and Salts

When molecules of inorganic acids, bases, or salts dissolve in water, they undergo ionization or dissociation; that is, they separate into ions.

-Particles formed during ionization are called Electrolytes because the solution will conduct an electric current.

i An Acid - a substance that when dissolved in water; dissociated

into one or more hydrogen ions (H+) and one or more anions (negative ions).

H+

HCL-------in water -------- Cl-

-Acids are Proton donors. ii A Base - a substance that when dissolved in water, dissociates

into one or more hydroxide ions (OH-) and one or more cations (positive ions).

K+

KOH ------in water---------- OH-

Chapter 2 16 -Bases are Proton acceptors. iii A Salt - a substance that when dissolve din water, dissociates into

cations and anions, neither of which is H+ or OH- K+ KCl ----in water------------ Cl- *Acids and Bases react with one another to form Salts. HCl + KOH -------- KCl + H2O Acid Base Salt Water Acid-Base Balance: The Concept of pH Body fluids must maintain a fairly constant balance of acids and bases. *pH is used to describe the degree of Acidity or Alkalinity (basicity) of a solution. Exhibit 2.2 pg. 40 Increasing Acidity 7--------------------------------------9 Neutrality pH Scale 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 8Increasing Alkalinity (basicity) Organic Chemistry Χ Usually have carbon Χ Usually have hydrogen > Most frequently found elements Χ Usually have oxygen Χ Usually have nitrogen

Chapter 2 17 Χ Usually have sulfur > Less frequently found Χ Usually have Phosphorus Χ Are Covalently bounded molecules Examples: Carbohydrates, lipids, proteins, nucleic acids, and adenosine

triphosphate (ATP). A. Carbohydrates

Composed of carbon, hydrogen, and oxygen. Have 2:1 ration of hydrogen to oxygen.

Also known as sugars and starches. -Provide most of the energy needed for life.

Can be divided into three major groups on the bases of size.

i Monosaccharides (simple sugars) are compound containing from

three to seven carbon atoms; e.g. Ribose (C5H10O5); glucose (C6H12O6); Fructose (C6H12)6),etc.

ii Disaccharides are also sugars, and consist of two monosaccharides

joined chemically.

C6H12)6 + C6H12O6 ---> C12H22O11 + H2O Glucose Fructose Sucrose Water (Monosaccharide) (Monosaccharide) (Disaccharide)

Dehydration Synthesis is a process of disaccharide formation (combination of two monosaccharides) in which water is lost.

Digestion (hydrolysis) is a process by breaking down disaccharides into smaller molecules by adding water.

iii Polysaccharide consist of several monosaccharides joined together

through dehydration synthesis.

Chapter 2 18

-Have the formula (C6H10O5)n -Can be broken down into their constituent sugars through hydrolysis reactions.

-Usually not soluble in water. -Usually lack characteristic sweetness of sugar like fructose (monosaccharides) or sucrose (disaccharides).

Example: Glycogen (animal starch).

B. Lipids

-Like carbohydrates, are composed of carbon, hydrogen, and oxygen-Unlike carbohydrates do not have a 2:1 ration of hydrogen to oxygen -Most lipids are hydrophobic (are insoluble in polar solvents such as water) -Nonpolar solvents such as chloroform and Ether, readily dissolve lipids.

Examples: Triglycerides (neutral fats), Phospholipids (lipids that contain phosphorous), Steroids (cholesterol, cortisol, vit. D, Sex hormones) Carotenes (the yellow-orange pigments in carrots), Vitamins A, E and K, and Eicosanoids. *For efficient transport in blood, lipids combine with proteins to form water-soluble lipoprotein.

1. Triglycerides (neutral fats)

-Are the most plentiful lip in your body and in your diet. -At room temperature, may be either solids (fats) or liquids (oils) -Are the body's most highly concentrated source of chemical energy -Provide more than twice as much energy per gram as either carbohydrates or proteins -Our capacity to store triglycerides in fat (adipose) cells is unlimited -Excess carbohydrates, proteins, or fats are converted to triglycerides and stored in adipose (fat) tissue

Chapter 2 19 *A triglyceride consist of two types of building blocks: Glycerol and Fatty acids

a. Saturated Fats are triglycerides that contain only single covalent bonds between fatty acid carbon atoms.

-Each carbon bonds to the maximum number of hydrogen atoms; thus each fatty acid is saturated with hydrogen atoms. -Tend to be solid at room temperature. -Occur mostly in animal tissues and few plant products (cocoa butter, palm oil, and coconut oil).

b. Monosaturated Fats contain fatty acids with one double covalent bond between two carbon atoms.

-Are not completely saturated with hydrogen atoms -Olive oil and peanut oil

c. Polyunsaturated fats contain more than one double covalent bond between fatty acid carbons.

-Corn oil, safflower oil, sunflower oil, cottonseed oil, and soybean oil.

C. Proteins

Types of protein: Structural Regulatory

Contractile Immunological Transport Catalytic Amino Acids and Polypeptides (Chemically, proteins always contain carbon, hydrogen, oxygen, and nitrogen. Many contain sulfur) Amino Acids are the building blocks of protein, just as monosaccharides

Chapter 2 20 are for polysaccharide. -There are 20 different amino acid; each has three important groups attached to a central carbon atom.

1. an amino group (-NH2) 2. a carboxyl (acid) group (-COOH) 3. a side chain (R group)

*(At the normal pH of body fluid, both the amino group and carboxyl group are ionized.) *(The distinctive side chain gives each amino acid its individual identity.) Synthesis of Protein involves in stepwise fashion: -One amino acid is joined to a second, a third is then added to the first two; etc. *Peptide bond is the covalent bond between each pair of amino acids.

-Forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another. -A molecule of water (a dehydration synthesis reaction) is removed during formation of a peptide bond: *[hydrolysis is addition of water which breaks peptide bonds.]

a. Dipeptide - when two amino acids combine b. Tripeptide - when three amino acids combine; c. Polypeptide - further additions of amino acids; may contain from 10 to more than 2000 amino acids

*Using only 20 amino acids to produce different proteins is similar to using 26 alphabets to write millions of books and publications. Think about it. Level of Structural Organization Proteins exhibit four levels of structural organization: 1. Primary structure is the unique sequence of amino acids making up a

Chapter 2 21 polypeptide strand. It is genetically determined.

2. Secondary structure of a protein is the repeated twisting or folding of

neighboring amino acids in the polypeptide chain. 3. Tertiary structure refers to the three-dimensional of a polypeptide

chain. 4. Quaternary structure describes the arrangement of the individual

polypeptide chains and how they bond to each other. *Denaturation - if a protein encounters a hostile environment in which temperature, pH, or electrolyte concentration is altered, it may unravel and lose its characteristic shape (secondary, tertiary, and quaternary structure). -Denatured proteins are no longer functional. -A common example of denaturation is seen in frying an egg. (In a raw egg the egg white protein (albumin) is soluble and appears as a clear, viscous fluid. when heat is applied to the egg, however, the protein changes shape, becomes insoluble and looks white). Enzymes Normal body temperature and pressure are too low for chemical reactions to occur at a rate rapid enough to maintain life. Although raising the temperature, pressure, and the number of reacting particles can increase the frequency of collisions and also increase the rate of chemical reactions, such changes and denature proteins and damage or kill cells. Enzymes are the living cell's solution to this problem. -They speed up chemical reactions by increasing the frequency of collisions, lowering the activation energy and properly orienting the colliding molecules. In living cells, enzymes function as catalysts.

Chapter 2 22 Catalysts - substances that can speed up chemical reactions by increasing the frequency of collisions or by lowering the activation energy, without themselves being altered. Apoenzyme - protein portion of enzyme } Together apoenzyme and

cofactor form a Holoenzyme or whole enzyme

Cofactor Coenzyme - nonprotein portion Nucleic Acids: Deoxyribonucleic acid and ribonucleic acid Nucleic Acid are huge organic molecules that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. Two Varieties of nucleic acid 1) Deoxyribonucleic acid (DNA) forms the genetic code inside each cell.

Each gene is a segment of a DNA molecule. 2) Ribonucleic acid (RNA) relays instructions from the genes to guide

each cell's assembly of amino acids into proteins. *The basic units of nucleic acids are nucleotides. *A molecule of DNA is a chain composed of repeating nucleotide units. *Each nucleotide consists if three building blocks: 1) A base (Nitrogenous base) - four nitrogen-containing structure

containing atoms of C,H, O, and N called bases or nitrogen bases are present in DNA - Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

RNA - Adenine (A), Uracil (U), Cytosine (C), and Guanine(G). *(Nucleotides are named according to the base that is present; eg. nucleotide containing thymine is thymine nucleotide)

Chapter 2 23

2) A Pentose Sugar - a five - carbon sugar called deoxyribose attached to each base of DNA.

3) A Phosphate Group - alternating phosphate (PO43-) and

pentose groups (PO43-) and pentose from the backbone of a DNA strand, while bases protrude from the backbone chain.

Adenosine Triphosphate Adenosine Triphosphate (ATP) is a molecule that is indispensable to the life of the cell. -It is found universally in living systems and has the essential function of providing energy for various cellular activities. -It is the "energy currency" of living systems. -Consists of three phosphate groups attached to an adenosine unit composed of adenine and the five-carbon sugar ribose. Removal of the terminal phosphate group leaves a molecule called Adenosine diphosphate (ADP). ATP------------------------> ADP+ P + E Adenosine Triphosphate Adenosine diphosphate Phosphate group Energy *The energy supplied by the catabolism of ATP into ADP is constantly being used by the cell. *Since the supply of ATP at any given time is limited, a mechanism exists to replenish it: a phosphate group P is added to ADP to manufacture more ATP. ADP + P + E ----------------> ATP Adenosine Diphosphate Phosphate group Energy Adenosine Triphosphate *The energy needed to attach a phosphate group to ADP is supplied mainly by the breaking down of glucose in a process called Cellular respiration.

Chapter 2 24 Two Phases of Cellular Respiration 1. Anabolic - in the absence of oxygen, glucose is partially broken down

by a process called glycolysis into pyruvic acid. 2. Aerobic - in the presence of oxygen, glucose is completely broken

down into carbon dioxide and water, generating heat and a large number of ATP molecules.