CHAP : 1-3 ANATOMY & PHYSIOLOGY

ALL OF CHAPTER 2

INTRODUCTION 

Chemistry – science that studies the structure of matter matter – anything that takes up space and has mass 

mass - physical property that determines the weight of an object  in Earth’s magnetic field 

atoms – smallest units of matter 

The unique characteristics of each object (living or nonliving)  results from the types of atoms involved and the ways those  atoms combine and interact. 

ATOMS AND MOLECULES 

Atoms consist of subatomic particles (protons, neutrons, and  electrons) 

protons (p⁺) – similar in size and mass to neutrons; has a positive  electrical charge 

neutrons (n or n⁰)– similar in size and mass to protons; has a  neutral electrical charge 

electrons (e^-) – lighter (in mass) than protons; has a negative  electrical charge 

Mass of atom is determined mainly by the number of protons and  neutrons in the nucleus.

Atomic Structure 

Atoms normally contain equal numbers of protons and electrons. atomic number – number of protons in an atom 

electron cloud – three-dimensional area where electrons whirl  around the nucleus at high speed 

electron shell – two-dimensional representation of where the  electrons whirl around the nucleus 

Elements and Isotopes 

element – consists of atoms in which the number of protons (the  atomic number) generally equals the number of electrons;  each element has a chemical symbol 

mass number – the total number of protons and neutrons in an  atom’s nucleus. 

isotopes – atoms of the same element whose nuclei contain  different numbers of neutrons (ex.- hydrogen-1, hydrogen-2  - deuterium, hyrdrogen-3 - tritium) 

radioisotopes – isotopes with nuclei that spontaneously emit  subatomic particles or radiation in measurable amounts. 

Atomic Weights 

atomic weight – actual mass of an atom; average mass number  that reflects the proportions of different isotopes 

dalton (atomic mass unit or amu) – unit used to express the  atomic weight ; one dalton is very close to the weight of a  single proton

Chapter 2-2 

mole – quantity of any element that has a weight in grams equal  to the atomic weight; one mole of one element contains the  same number of atoms as any other element (Avogadro’s  number - 6.023x10²³ (600 billion trillion)) 

Electrons and Energy Levels 

Atoms are electrically neutral because every positively charged  proton is balanced with a negatively charged electron. 

Electrons occupy a series of energy levels that are often  illustrated as electron shells. Each energy level can  accommodate a specific number of electrons. 

The number and arrangement of electrons in an atom’s outermost  energy level determine the chemical properties of that element. • atoms with unfilled energy levels will react with other atoms,  ex.- hydrogen (Hindenburg zeppelin)  

• atoms with filled energy levels will not react (stable), ex.- helium (Goodyear balloon) 

Chemical Bonds 

Chemical Bonds 

inert – elements that do not readily take part in chemical  processes; outer energy levels are full 

reactive – atoms with unfilled outer energy levels; interact or  combine with other atoms 

Atoms can combine through chemical reactions that create  chemical bonds – hold participating atoms together; 3 basic  types of chemical bonds: ionic, covalent, and hydrogen 

molecule - chemical structure consisting of atoms held together  by covalent bonds

Chapter 2-3 

compound - chemical structure containing atoms of two or more  elements; a compound has properties that can be very  different from properties of its component elements 

ion – atom or molecule that has a positive or negative charge 

cations – ions with a positive charge 

anions – ions with a negative charge 

ionic bond – chemical bonds created by the electrical attraction  between anions and cations, when placed in water ionic  compounds dissolve; ex.- sodium chloride (table salt)  

In the formation of an ionic bond: Fig. 2-3, p. 33 

electron donor – atom that loses one or more electrons,  becomes a cation (positive charge) 

electron acceptor – atom that gains those same electrons,  becomes an anion (negative charge) 

attraction between the opposite charges draws the two ions  together ‚ ionic compound 

covalent bonds – chemical bonds created when atoms share  electrons to complete their outer electron shells 

• very strong 

• usually form molecules that complete their outer energy  levels of atoms involved 

single covalent bond - sharing one pair of electrons equally,  ex.- H₂ (hydrogen) 

double covalent bond – sharing of two pairs of electrons  equally, ex.- O₂ (oxygen)

Chapter 2-4 

triple covalent bond– sharing three pairs of electrons, ex.- N₃ (nitrogen) 

nonpolar covalent bond - a bond with equal sharing of  electrons, ex.- between carbon atoms 

polar covalent bond - unequal sharing of electrons creates a  polar covalent bond, weaker than other covalent bonds;  ex.- water molecule 

free radical – ion or molecule that contains unpaired electrons in  its outermost energy level, highly reactive; can damage or  destroy compounds, cells; ex.- nitric oxide (NO) 

hydrogen bond: 

• weak forces that act between adjacent molecules and even  between atoms within a large molecules 

• attraction between partial positive charge of one hydrogen  atom in a polar covalent bond with a partial negative  charge oxygen or nitrogen in another polar covalent  bond;  

• important force that can change the shape of molecules.  

Matter can exist as a solid, a liquid, or a gas, depending on the nature of the interactions among the component atoms or  molecules. 

solids – maintain their volume and shape at ordinary  temperatures and pressures 

liquids – have a constant volume but no fixed shape (shape  is determined by the shape of the container)

Chapter 2-5 

gases – has neither a constant volume nor a fixed shape  (gasses can be compressed or expanded, they will fill a  container of any shape) 

molecular weight of a molecule – equal to the sum of the atomic  weights of its component atoms; you can calculate the  quantities of reactants needed to perform a specific reaction  and determine the amount of product generated 

CHEMICAL REACTIONS 

chemical reaction – new chemical bonds form between atoms or  existing bonds between atoms are broken 

reactants – reacting substances in a chemical reaction products – substance formed in a chemical reaction 

metabolism – all the chemical reactions in the body. Through  metabolism, cells capture, store, and use energy to maintain  homeostasis and to support essential functions. 

Focus: Chemical Notation 

chemical notation – like a chemical shorthand, rules listed in  Table 2-2, p. 38. Chemical notation allows us to describe  reactions between reactants that generate one or more  products. 

Basic Energy Concepts 

work –movement of an object or a change in its physical  structure. 

Chapter 2-6 

energy – capacity to perform work. There are two major types of  energy: kinetic and potential 

kinetic energy – energy of motion, ex.- moving car or bullet 

potential energy – stored energy, energy that has the  potential to do work; may result from the position or  structure of an object; ex.- book on a shelf, coke can on  a table 

Energy is neither created nor destroyed (first law of  thermodynamics (conservation of energy)); it can only be  converted from one form to another. Conversions from  potential to kinetic energy are not 100% efficient; every such  energy exchange released heat. 

heat – increase in random molecular motion

Types of Reactions 

three types of chemical reactions: decomposition, synthesis, and exchange reactions 

decomposition reaction – reaction that breaks a molecule into  smaller fragments, ex.- digestion 

catabolism – decomposition of molecules within cells, cells  gain energy to power their functions by catabolism  

synthesis reaction: 

• opposite of decomposition, assemble molecules from small  fragments or components 

• may involve individual atoms or the combination of  molecules to form larger products 

• always involves the formation of new chemical bonds

Chapter 2-7 

anabolism – synthesis of new compounds within the body;  most of the energy gained from catabolism supports  anabolism; ex.- protein synthesis 

exchange reaction – parts of the reacting molecules are shuffled 

Specific chemical reactions may absorb or release energy,  usually as heat. 

exergonic reactions – reactions that release energy

endergonic reactions – reactions that require energy

Reversible Reactions 

Chemical reactions are reversible. Many biological reactions are  freely reversible. 

A + B ⮀ AB 

At equilibrium, the rates of two opposing reactions are in balance. 

concentration of a substance – number of atoms or molecules (or  moles) in a specified volume; the concentrations of reactants  and products in a chemical reaction have a direct effect on  the reaction rate 

hydrolysis – decomposition reaction involving water; one of the  bonds in a complex molecule is broken, and the components  of a water molecule are added to the resulting fragments

Enzymes and Chemical Reactions 

Most chemical reactions do not occur spontaneously or they  occur too slowly.

Chapter 2-8 

activation energy - the amount of energy required to start a  reaction.  

Many reactions can be activated by changes in temperature or  acidity; in cells major changes in those two conditions would  be fatal; cells use enzymes 

Enzymes: 

• special protein that by lowering the activation energy  requirements 

• control many chemical reactions within our bodies • organic catalysts – substances that accelerate chemical  reactions without themselves being permanently  

changed or used up 

• very specific 

The complex reactions that support life proceed in a series of  interlocking steps called pathways. A different enzyme controls  each step in a pathway. 

INORGANIC COMPOUNDS 

nutrients – essential elements and molecules normally obtained  from the diet 

metabolites – all the molecules synthesized or broken down by  chemical reactions inside our bodies 

Nutrients and metabolites can be broadly classified as inorganic  or organic. 

Chapter 2-9 

inorganic compounds – generally do not contain carbon and  hydrogen atoms as the primary structural basis 

organic compounds – carbon and hydrogen atoms form the  primary structural basis 

Most important inorganic compounds in the body: carbon dioxide,  oxygen, water, inorganic acids, bases, and salts

Water and Its Properties 

Water is the most important component of the body (2/3 of total  body weight). A change in body water content will affect all  physiological systems and can have fatal consequences. 

Properties of water: 

1. a lot of inorganic and organic molecule will dissolve in water ‚ solution – a uniform mixture of two or more substances,  consists of a medium (or solvent), in which atoms, ions, or  molecules of another substance (or solute), are dispersed.  In aqueous solutions, water is the solvent. 

2. chemical reactions occur in water, and water molecules  participate in some reactions. 

3. (a) high heat capacity – ability to absorb and retain heat  (b) freezing and boiling points are far apart 

This is important because: 

• Temperature must be high before individual molecules  can break free to become water vapor. (water  

stays in the liquid state over a wide range of  

temperatures)

Chapter 2-10 

• when water changes from a liquid to a vapor, it carries  away a lot of heat (ex.- why your body sweats to  

cool you down) 

• takes a large amount of heat energy to change the  temperature of water 

thermal inertia – once a quantity of water has  

reached a particular temperature, it will  

change temperature slowly 

the blood plasma transports and redistributes large  amounts of heat as it circulates within the body 

4. effective lubricant, reduces friction between two surfaces, (ex.- between body cavities, joints in bones) 

Aqueous solutions 

water is a polar molecule (or dipole) - that makes water an  unusually effective solvent 

ionization (or dissociation) – ionic bonds are broken apart as ions  interact with positive and negative ends of polar water  molecules 

hydration sphere – cations and anions surrounded by water  molecules, (Fig. 2-8, p. 41) 

electrolytes – soluble inorganic molecules whose ions will conduct  an electrical current in solution, (Table 2-3, p. 43) 

• changes in body fluid concentrations of electrolytes will  disrupt vital body functions 

• electrolyte body fluid concentrations are regulated by the  kidneys, digestive and skeletal system

Chapter 2-11 

organic molecules usually contain polar covalent bonds that  attract water molecules 

hydrophilic molecules – molecules that willingly interact with  water, ex.- glucose 

hydrophobic molecules – molecules that do not willingly  interact with water, ex.- gasoline, fat deposits 

solute concentrations can be reported in several different ways: • number of solute atoms, molecules, or ions in a specific  volume – moles per liter, or millimoles per liter (mmol/l);  physiological concentrations are reported in this  

manner 

• terms of weight of material dissolved in a unit volume of solution – milligrams per deciliter (mg/dl) or grams per  deciliter (g/dl); used to give plasma protein  

concentrations in blood samples 

colloid – a solution containing dispersed proteins or other large  molecules. Particles or molecules will remain in solution  indefinitely; ex.- liquid Jell-O^TM 

body fluids may contain large, complex organic molecules  (proteins and protein complexes) 

suspension – a solution containing large particles that will settle  out of solution, ex.- sand and water, whole blood

Hydrogen Ions in Body Fluids 

Hydrogen ion concentration in body fluids is accurately regulated 

Dissociation of water is a reversible reaction: H₂O ⮀ H⁺ OH The dissociation of a water molecule yields one hydrogen ion H⁺,  and one hydroxide ion OH^-

Chapter 2-12 

The concentration of hydrogen ions in a solution of pure water is  0.0000001 mol per liter. [H⁺] = 1 x 10^-7 mol/l 

The pH of a solution indicates the concentration of hydrogen ions  it contains. pH of a solution – negative logarithm of the  hydrogen ion concentration in moles per liter 

pH number is an exponent 

pH scale is logarithmic  

a pH of 6 is 10 times greater than a pH of 7  

neutral – solution with a pH of 7, contains equal numbers of  hydrogen and hydroxide ions 

acidic - solution with a pH below 7, contains more hydrogen ions  than hydroxide ions 

basic – solution with a pH above 7, contains more hydroxide ions  than hydrogen ions 

human blood pH ranges from 7.35 – 7.45. Abnormal fluctuations  in pH can damage cells and tissues 

acidosis – low blood pH (ph below 7.35) causes abnormal  physiological state 

alkalosis – high blood pH (ph above 7.45) causes  uncontrollable, sustained skeletal muscle contractions 

Inorganic Acids and Bases 

acid – any solute that dissociates in solution and releases  hydrogen ions, lowers pH, proton donor

Chapter 2-13 

base – a solute that removes hydrogen ions from a solution,  raises pH, proton acceptor 

Strong acids and strong bases ionize completely, whereas weak  acids and weak bases do not. 

Salts 

salt – an electrolyte whose cation is not hydrogen (H⁺) and whose  anion is not hydroxide (OH^-); dissociates completely in  water, ex.- NaCl (table salt) 

Buffers and pH Control 

buffers – compounds that stabilize the pH of a solution, remove or  replace hydrogen ions in solution. Buffers and buffer  systems maintain the pH of body fluids within normal limits 

ORGANIC COMPOUNDS 

Organic compounds always contain carbon and hydrogen and  generally oxygen as well.  

• many contain long chains of carbon atoms linked by covalent • many are soluble in water 

Major classes of organic compounds include carbohydrates,  lipids, proteins, and nucleic acids. High-energy compounds  are small in terms of their abundance but absolutely vital to  the survival of our cells. 

Carbohydrates 

Carbohydrates: 

• contain carbon, hydrogen, and oxygen in ratio near 1:2:1

Chapter 2-14 

• ex.- sugars, starches 

• most important as an energy source for metabolic processes 

The three major types are monosaccharides, disaccharides, and  polysaccharides 

monosaccharide – simple sugar, a carbohydrate containing  from three to seven carbon atoms, water-soluble; ex.- glucose, fructose, galactose 

isomers – molecules that have the same molecular  formula but different shapes 

disaccharide – two simple sugars, water-soluble; ex.- sucrose (table sugar) 

dehydration synthesis (condensation reaction) – 

process that links molecules together by removing  a water molecule 

polysaccharides – complex sugars, polysaccharide chains  can be straight or highly branched, ex.- starches,  

cellulose, glycogen 

Lipids

Lipids: 

• contain carbon, hydrogen, and oxygen, not in 1:2:1 ratio • water-insoluble molecules 

• ex.- fats, oils, and waxes 

• form essential structural components of all cells • important energy reserves 

Chapter 2-15 

There are six important classes of lipids: fatty acids, eicosanoids,  glycerides, steroids, phospholipids, and glycolipids. 

fatty acids – long carbon chains with hydrogen atoms  attached; one end of the carbon chain contains a  

carboxylic acid group the other is a hydrogen tail 

eicosanoids – lipids derived from arachidonic acid, two  classes: prostaglandins, leukotrienes 

prostaglandins – short-chain fatty acids that have five of  their carbon atoms joined in a ring; chemical  

messengers that coordinate local activities 

glycerides – lipids composed of glycerol bound to fatty acid monoglycerides - consist of one fatty acid plus glycerol diglycerides - consist of two fatty acids and glycerol 

triglycerides (neutral fats) - consist of three fatty acid  molecules attached by dehydration synthesis to a  

molecule of glycerol 

important functions of triglycerides: 

1. energy reserve 

2. insulation 

3. cushion to protect 

Steroids - large lipid molecules with a distinct carbon  framework, ex.- cholesterol 

important functions 

1. are involved in the structure of cell membranes 

2. regulate sexual function 

3. regulating metabolic activities

4. are important in lipid digestion 

phospholipids –a phosphate group links a diglyceride with a  nonlipid group 

glycolipids – a carbohydrate is attached to a diglyceride

phospholipids and glycolipids:  

• have hydrophobic and hydrophilic ends 

• structural lipids – form and maintain the cell membranes

Proteins

• most abundant organic components of the human body • account for 20% of the total body weight 

• perform a great variety of functions in the body  

Seven major functional categories: 

1. Support – provide strength, organization, and support for  cells, tissues and organs 

2. Movement – muscular contraction; movement of individual  cells 

3. Transport – transport materials in the blood and inside cells 4. Buffering – prevent dangerous changes in pH 

5. Metabolic regulation – accelerate chemical reactions 6. Coordination and control – influence the metabolic activities  of cells, organs, organ systems 

7. Defense – protect body from environmental hazards,  disease 

Proteins - long chains of amino acids. Each amino acid consists  of an amino group, a carboxylic acid group, and an R group  (side chain). (Fig. 2-18, p. 51)

Chapter 2-17 

polypeptides - a linear sequence of amino acids held together by  peptide bonds – covalent bond between the carboxylic acid  group of one amino acid and the amino group of another 

There are four levels of protein structure:  

1. primary structure (amino acid sequence) 

2. secondary structure - (amino acid interactions, such as  hydrogen bonds) 

3. tertiary structure - (complex folding, disulfide bonds, and  interaction with water molecules), ex.- myoglobin 

4. quaternary structure - (formation of protein complexes from  individual subunits), ex.- hemoglobin 

The shape of protein determines its functional properties, shape is  determined by the sequence of amino acids 

Substrates - the reactants in an enzymatic reaction, interact to  yield a product by binding to the enzyme at the active site 

Three characteristics of enzymes: 

• Specificity – catalyze only one type of reaction, attach to only  one type of substrate molecule 

• Saturation limits – rate of enzymatic reaction is proportional  to the concentration of substrate molecules and  

enzymes 

• Regulation – a variety of factors can turn enzymes “on” or  “off” 

cofactors - ions or molecules that must bind to the enzyme before  substrate binding can occur 

coenzymes – nonprotein organic cofactors commonly derived  from vitamins.

Chapter 2-18 

Each protein works best at an optimal combination of temperature  and pH and will undergo reversible or irreversible  

denaturation at temperatures or pH values outside the  normal range. 

Denaturation – temporary or permanent change in an  enzyme’s tertiary or quaternary structure 

Glycoproteins and Proteoglycans – combinations of protein and  carbohydrate molecules 

Glycoprotein – large proteins with small carbohydrate groups  attached 

Proteoglycan – large polysaccharide molecules lined by  polypeptide chains 

Nucleic Acids 

Nucleic acids – large organic molecules, store and process  information at the molecular level inside living cells.  

There are two kinds of nucleic acids: deoxyribonucleic acid  (DNA) and ribonucleic acid (RNA) 

DNA: 

• determines our inherited characteristics 

• encode the information for protein synthesis 

• regulates all cellular metabolism 

• double helix 

• deoxyribose sugar 

RNA: 

• manufactures proteins 

• single strand

• ribose sugar 

Nucleic acids are chains of nucleotides. Each nucleotide contains  a sugar, a phosphate group, and a nitrogenous base 

The nitrogenous bases found in DNA, which is a two-stranded  double helix, are adenine, guanine, cytosine, and thymine.  RNA, which consists of a single strand, contains uracil  instead of thymine. 

High-Energy Compounds

Cells store energy in the high-energy bonds of high-energy  compounds for later use.  

The most important high-energy compound is ATP (adenosine  triphosphate). Cells make ATP by adding a phosphate  group to ADP (adenosine diphosphate) through the process  of phosphorylation.  

When ATP is broken down to ADP energy is released, and this  energy may be used by the cell to power essential activities

CHEMICAL AND LIVING CELLS  

Biochemical building blocks form functional units called cells. The  continuous removal and replacement of cellular organic  molecules (other than DNA), a process called metabolic  turnover, allows cells to change and adapt to changes in  their environment.