Chapter 2

Anatomy & Physiology

Fifth Edition

Seeley/Stephens/Tate

(c) The McGraw-Hill Companies, Inc.

Basic Chemistry for Physiology

It is assumed that the students are familiar with basic chemistry. They should already be familiar with:

Atoms and Molecules

1. Structure of an atom: the subatomic particles are the nucleus consisting of proton (+), neutrons (0), and clouds of electrons (-).

2. Atomic number: the number of protons in an atom.

3. Chemical elements: the atoms with the same atomic number.

4. Atomic Weight: roughly equals to the sum of the number of protons and neutrons.

5. Isotopes: atoms with the same atomic number, but their nuclei contain different number of neutrons. Also known as radioisotope. Thus a different atomic weight and instability.

6. Electrons and Electron Orbital/shells: neutral atoms have an equal number of electrons and protons. A pair of electrons occupy each electron orbital and the orbital of similar energy form the shells K, L, M, etc…. These shells can occupy 2, 8, 10, electrons, respectively. The rule of 8 applies.

The electrons in the outermost shell determine the activities of the atom. If they are completely filled. The atom will be in active I.e, He, Ne etc….

Electrons and Chemical Bonding

Chemical bonding occurs when the outermost electrons are transferred or shared between atoms.

Two types of chemical bonds, Ionic bonds and covalent bonds (require a large amount of energy to break them up – around 100 Kcal/mole).

Then, there are other forms of bonds, often termed non-covalent bonds. They are hydrogen bonds, ionic attraction, hydrophobic attractions, which have much less energies than covalent or ionic bonds. ( 2-3 Kcal/mole)

Ionic Bonds

• An atom is electrically neutral because it has an equal number of protons and electrons. If an atom loses or gains electrons, the number of protons and electrons are no longer equal and a charged particle called an Ion is formed.Thus, they form anions (-) and cations (+).How do neutral atoms become ionized atoms? After an atom loses an electron, it has one more proton than it has electrons and is positively charged. i.e.,A neutral Na atom has 11 electrons, only one electron on its outermost shell, which tends to be lost and makes Na positive or electro-positive and if….

Neutral Cl atom has 17 electrons and 7 electrons in its outermost shell. It can accept one electron and become negatively charge, an Cl- anion or electro-negative atom.

Thus, when sodium atoms and chlorine atoms are close to each other, Na gives an electron to Cl and both become ionized atoms, establishing an ionic bond and will be held together with ionic bonds. This is what is seen in a solid sodium chloride crystal.

Covalent Bonds• They are formed when atoms share one or more pairs of

electrons. One pair of electrons form a single bond, two pairs forms a double bond, three pair form a triple bond.

• In covalent bonds, usually electrons are shared evenly between the two bonding atoms, called polar bonds. But in some molecules the electrons are not equally shared. In other words, the electrons tend to stay longer with one atom than the other. Then the atoms become slightly ionized and the ionization becomes added energy for the holding the atoms together forming a polar-covalent bond.

• A molecule is formed when two or more atoms chemically combine to form a structure that behaves as an independent unit.

• A compound is a substance composed of two or more different types of atoms that are chemically combined.

Intermolecular Forces ( non-covalent bonds) • They result from the weak electrostatic attractions between the

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

• The amount of energy found in these bond are small compared to the covalent or ionic bonds. The mere large large number found in biological macromolecules, makes them important

• Hydrogen Bonds – these are one of the most popular non-covalent bonds and are found every where in life. Usually they require the presence of hydrogen atom between two relatively small electronegative atoms, O, N, F, etc….

NH+ ····O¯= C• Ionic Interactions – they are interactions between ions with much

less energy than that of ionic bonds.=C=O¯····Na+

• Hydrophobic Interactions – these are forces that are found within the oily molecules which are excluded from water. It is the force that keep s oil droplets held together.

• Review the following terms:– Solubility– Dissociate– Electrolytes– Non-electrolytes

Chemical Reactions• The making and breaking of chemical bonds are the chemical

reactions. In the body it is metabolism.

• Synthesis Reaction – occurs when two or more reactions chemically combine to form a new and larger product. i.e., the combination of two amino acids to form a dipeptide (anabolism).

– Dehydration reaction- removal of water from a reaction.

• Decomposition Reaction – a larger reactant is chemically broken down into two or more smaller products (catabolism)

– Hydrolysis reactions – reactions that add water to a reaction.

Work, Energy, and Heat• Work – is the change in physical status, such as,

pushing a car ( the car must move to be recognized as energy being exerted)

• Energy and Heat - is the capacity to do work.

• Energy can be subdivided into two forms, Kinetic and Potential energies.

• Kinetic Energy – is the energy of motion. Moving atoms and molecules, as well as a moving car.

• Potential Energy – is the stored energy within a object placed high (I.e. force of gravity), a compressed spring, and in chemical potential when a solution is more concentrated than the other.

• These two energies could be interchangeable, as the kinetic energy brings up an object to a higher place.

• The conversion between the two could be wasted energy in the form of heat. Heat arises from the random motion of matter and when in increases, the temperature goes up also.

Classes of Reactions

• There are two types of chemical reactions: Exothermic (exergonic) and Endothermic (endergonic). The former releases heat during the reaction, I.e. get hot. The latter consumes heat during the reaction, i.e. gets cold.

• The reaction may also be classified as :

A. Decomposition (catabolism)

B. Synthesis (anabolism)

C. Exchange reaction (swapping)

D. Reversible reactions and equilibrium

E. Oxidation-reduction

Acids and Bases

• An acid releases hydrogen ions (protons) into a solution.

HCl H+ + Cl¯

• A base removes hydrogen ions or releases hydroxide ions into a solution

NaOH Na+ + OH¯

• Weak acids only partially dissociate in water.

Hac H+ + Ac¯

pH

• The concentration of hydrogen ions is very important in blood and other fluids since hydrogen is very reactive. Thus, people define a special concentration scale for this ion.

• The concentration of hydrogen ion is expressed in its negative logarithm.

pH = ¯log [H+]

• Thus, the smaller the number of pH, the higher the concentration of hydrogen ion.

• Furthermore, the change of one unit of pH equals to a factor of 10.

• Buffers are compounds that resist the change of pH. Antacids, sodium bicarbonate, and body fluids are buffers.

Inorganic Compound• Inorganic compounds are void of carbon, except carbon

dioxide (CO2).

Water• The most important inorganic compound in life is water,

which amount ups to 70% of human body.

• Bonding of two hydrogen atoms with oxygen (electronegative atom) has made the molecule slightly polar.

Some features of water are:

1. Water is a good solvent.

2. Water is involved in many biochemical reactions for hydration or condensation of molecules.

3. Water has a very high heat of capacity and heat of vaporization contributing to homeostasis of the body.

4. Water increases it volume upon freezing.

Inorganic Acids and Bases

Salts• is a compound consisting of a cation other than a

hydrogen and an anion other than a hydroxide ion. Salts are formed by the interaction of an acid and a base in which the hydrogen ions of the acid are replaced by the positive ions of the base.

• Solid in dry form and are held together with ionic bonds. They completely dissolve in water as ions. (NaCl, KCl, MgCl2)

• Salts are electrolytes, since their ionic form contributes to the flow of electrical currents. Abnormal concentrations of electrolytes in the body effect vital functions of the body. i.e cofactors such as Fe++, Zn++, Cu++, enzymes and vitamins.

Organic Compounds• Organic compounds contain carbon, except CO2, in

addition to H, and O are commonly found.• Less frequently found but equally important atoms

found in organic compounds are P, N, S, Fe, and metal ions.

Carbohydrates• Consist of C, H, and O in a ratio of 1:2:1., such as

cellulose (plants) and glycogen (humans).

• Monosaccharides – are important source of energy in metabolism and starches are excellent energy storage. A monosaccharide is a simple sugar and has up to 6 carbons. ( glucose, fructose, galactose)

• Disaccharides – have two sugars and breakdown to monosaccharides by hydration process., i.e. (glucose + fructose sucrose)

• Polysaccharides – are chain of monosaccharides. Long chains of starches that are glucose based, while animal polysaccharide –glycogen are a branched form of polymeric glucose. They are water insoluble. After being enzymatically digested to monosaccharides , then they will enter the metabolic cycles.

• Some plant starches may not be digested within human digested system, makes them a good diet food.

• Some carbohydrates makes a complex with protein and become a glycoprotein. These are often found in the cell membrane.

• Carbohydrates are also found as (in):– Ribose of DNA, RNA– Energy source– Structural support in plants, cell wall– Glycoproteins of membranes

Lipids• Like carbohydrates, lipids consist of C, H, and O, but

their ratio is that of having less Oxygen.

• They also contain small amounts of P, N and S.

• Example of lipids are: Fats, Oils, & Waxes.

• Lipids are water insoluble, but may be solubilized by binding without other molecules.

• When metabolized, lipids generate nearly twice as much energy as carbohydrates do. (low fat diet)

• Lipids constitute about 12% of body weight.

• Lipids function in various ways such as, protection, insulation, regulation as hormones, vitamins, membrane structure, energy source, etc……..

Fatty Acids: • Are long chains of carbons surrounded with hydrogen atoms

except for a carboxylic acid (COO¯ )at the end.

• Saturated F.A’s have all their there C-C bonds are single bonds. This type is found in butter, fatty meats, and ice cream.

• For unsaturated F.A.’s some C-C bonds are double bonds, such as those found in vegetable oils.

• The ratio of saturated to unsaturated F.A.’s are known to be important in relation to the risk of heart disease and other circulatory symptoms.

Glycerides• Are a conjugated form of fatty acids and is only

possible through the presence of another compound, such as glycerol. Glycerol is a three carbon compound is bound to three F.A’s by dehydration, thus synthesizing a substance called a triglycerides.

• Triglycerides, neutral fats, are common fats in the body serving as an energy reserve, fat droplets for heat insulation and protection.

• Saturated triglycerides are solid at room temp, while unsaturated triglycerides are usually liquid at room temp.

• Phospholipids, are important lipids in the formation of the double layer of the cell membrane.

• Phospholipids, important in cell membrane, consist of a di-glyceride attached to a molecule containing a phosphate (PO4³¯)

• Thus, a phospholipids consists of a water soluble head group and a water insoluble tails.

Steroids• Steroids are made of several carbon containing ring

structures and linear carbon chains.

• Cholesterol is one of the best known steroids.

• Cholesterol is a precursor for chemical messengers, hormones, such as testosterone and estrogen.

• Cholesterol comes from: – Diet, such as meat, cream, and egg yolks– Manufactured in the body in the liver. Thus making

it difficult to control the level of cholesterol in the blood with diet alone.

Proteins• There are about 100,000 different kinds of proteins, amounting to

20% of the total body weight.• Basically, proteins are single chain amino acids consisting of

primarily of C, N, O, H and small quantities of S and metal ions. So, proteins are different from carbohydrates in the amount of N.

Functions of Proteins:– Support– Movement– Transport– Buffering– Metabolic regulation with enzymes– Coordination of hormones– Defense (antibodies)

• Protein structure – they are made of amino acids brought together with peptide bonds into a non-branched molecule also called a polypeptide.

• There are about 20 AA’s in nature and human proteins use most of them, but not all.

• The sequence of AA’s determines the nature of the protein.

• The basic structure of an amino acid includes:amino group, hydrogen atom, carboxyl group, and a variable R side chain group.

• AA’s are bonded through peptide bonds to become polypeptides and proteins.

• The AA sequence determines their primary structure.

• Their secondary structure, alpha, beta, pleated sheet, and beta bends are the manner in which the polypeptides are held together firmly.

• The tertiary structure is how the secondary and random structures are folded together.

• The quaternary structure is the arrangement of subunits.

• The number of AA’s used in protein vary, i.e. insulin –51, ribonuclease – 124, cytochrome C –104, myoglobin- 153 et…….

• The overall structure of proteins are:– Globular – Elongated– Fibrous

• Proteins are sensitive to changes of temperature, at 43°C, many proteins will denature (no longer active) and will cause the death of the organism.

Enzymes and Chemical Reactions

• In order for a chemical reaction to take place, two atoms or molecules must first collide. Usually, the kinetic energy of collision, especially after raising the temperature, may be sufficient to initiate the reaction. This energy is the activation energy.

• In the biologically systems, increasing the temperature is not always possible and in viscous solutions the energy of collision will not be really that great.

• Thus, enzymes reduce the activation energy

• A substrate fits into the active site of the enzyme. The enzyme and substrate interaction can be visualized conceptually by “lock and key” model and the “induced fit” concept.

• Each enzyme has it’s optimal pH and temperature range.

Nucleic Acids

• In addition to high content of C, H, O and N, the concentration of P is high in nucleic acids.

• The sequence of nucleotides in a nucleic acid is the source of metabolic and genetic information.

• There are two types of nucleic acids: Deoxyribonucleic acids (DNA) and Ribonucleic acids (RNA).

• DNA is the primary source of genetic information which will determine what kinds of proteins will be made, hence genetically determined appearances.

• Since most enzymes are proteins, the regulation of synthesis of proteins will also affect the rates of many biochemical reactions.

• There are several forms of RNS, which will be discussed later.

Structure of Nucleic Acids

• Nucleic acids are made of a pair of poly-nucleotides.

• Each nucleotide consist of: 5- carbon sugar, phosphate group, and a nitrogenous base.

• The sugar for DNA is Deoxyribose and for RNA is ribose.

• The bases for DNA are adenine (A), guanine(G), cytosine ©, and Thymine (T). How they are sequenced in the chain of nucleic acid determines the information

• The base for RNA is uracil (U) and it replaces Thymine (T).

• For humans, DNA comes in a pair of coiling nucleotide strands (double helix), bases pairing A-T and C-G, form the complementary base pairs.

• Structure of RNA – RNA remains as a single chain. It however may partially base pair on itself.

• ATP forms a high energy source.

The End.