Principles of Human Anatomy and Physiology, 11e 1

Chapter 2

The Chemical Level of Organization

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HOW MATTER IS ORGANIZED

• Chemical Elements– substances that cannot be split into simpler

substances – 112 elements

• O, C, H, N, Ca, and P make up 98.5% of total body weight

– Trace elements are present in tiny amounts • copper, tin, selenium & zinc

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Structure of Atoms• All elements = atoms of same type

• Subatomic particles– Nucleus

• protons (p+) • neutrons (n0)

– Electrons (e-) move about nucleus in energy levels

– In neutral atom, # e- = # p+

• Atomic Number (Z)– # protons in nucleus– Identifies atom

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ISOTOPES

• Atoms of an element w/ same # of protons but different # of neutrons

• Isotopes– Stable isotopes do not change nuclear structure

over time– Radioactive isotopes

• Unstable nuclei decay to form simpler & more stable configuration

• Assessment of internal abnormalities

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Ions & Molecules• Ions form when an atom gives up or gains electrons

– (+) or (-) charge due to unequal # of p+ and e-

– Goal: atomic stability

• Molecule results from two or more atoms sharing electrons

– Ex: H2, N2, O2, CO2, H2O

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Free Radicals• Electrically charged atom/molecule w/ unpaired electron • Unstable & highly reactive chain reactions• Can become stable

– giving up an electron– taking an electron from another molecule

• Antioxidants inactivate oxygen-derived free radicals

• Ex: superoxide radical = oxygen w/ extra electron– can induce tissue damage if chain rxn allowed to propagate

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Free Radicals & Your Health

• Possible sources: absorption of UV energy in sunlight, x-rays, breakdown of harmful substances, & normal metabolic reactions

• Cancer, diabetes, Alzheimer, atherosclerosis and arthritis

• Dietary antioxidants: vitamins C and E, selenium & beta-carotene (precursor to vitamin A)

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CHEMICAL BONDS

• Forces of attraction holding atoms of compound together

• Valence e- determine:– type of bonding– chemical stability

• 8 e- in outer shell = stable• <8 e- in outer shell gain/lose/share e- • octet rule

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Ionic Bonds• Loss or gain of valence electron results in ion

formation

• Oppositely charged ions attracted to one another– Cations – Anions

• Electrolytes

• Ex: NaCl in Fig 2.4

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Covalent Bonds• Formed from sharing one, two, or three pairs of valence e-

– Strongest chemical bonds in the body– Single, double, or triple covalent bonds

• Bond polarity– Nonpolar covalent bond

• Equal sharing of electrons

– Polar covalent bond• Unequal sharing of electrons• Electronegativity difference• N—H & C—O

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Polar Covalent Bonds• Unequal sharing of electrons between atoms• Different centers of positive & negative charge • In a water molecule, O attracts H electrons more strongly

– Oxygen has greater EN (indicated by negative delta sign)– Overall polarity of molecule is in direction of oxygen

• See Fig 2.6

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Hydrogen Bonds

• Special polar covalent bonds btwn H atom & electronegative atom– N…H or O…H

• Very weak intermolecular bonds

• Cohesive properties of water

• Occur between δ+ H of one H2O

& δ- O of another H2O (See Fig 2.7)

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Chemical Reactions• New bonds form and/or old bonds are broken

• Metabolism = sum of all chemical reactions in the body

• Law of conservation of mass – Total mass of reactants equals total mass of products

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Forms of Energy• Energy = capacity to do work

– Kinetic energy = energy of motion• Temperature

– Potential energy = energy stored by matter due to its position

• Chemical energy

• Energy:– Conserved in rxn

– May be converted

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Energy Transfer• Exergonic reaction

– bond broken has more energy than one formed – extra energy is released

• usually as heat • catabolism of food molecules

• Endergonic reaction – requires energy be added to form a bond

• usually from a molecule of ATP• EX: building proteins from amino acids

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Energy Transfer in Chemical Reactions

• In living systems, ender- & exergonic reactions occur together

• Coupled reactions essential to metabolism– energy released from one reaction drives another

– Ex: glucose breakdown releases energy, which is used to build ATP molecules

– Ex: ATP fuels transport across membranes, muscle contraction & nerve impulses

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Activation Energy• Energy needed to break bonds & begin reaction (Fig 2.9)

• Increasing probability of collision

increases chance for reaction

• Increasing concentration & temperature are ways of overcoming Ea, thus ↑ chances for collision

– more particles are in a given space – particles move more rapidly

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Factors Influencing Chemical Rxns

• Concentration• Temperature• Catalysts

– speed up chemical reactions by lowering amount of energy needed to get reaction started (activation energy, Ea)

– do not alter difference in potential energy between the reactants & products

– orient colliding particles– unchanged at end of reaction often re-used many

times– relevance??? Biological enzymes are catalysts!

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Effectiveness of Catalysts

Difference in PE

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Types of Chemical Reactions

• Synthesis – > two atoms/ions/molecules combine to form new & larger

molecules– anabolic reactions (bonds are formed)

A + B AB – generally endergonic

– Decomposition – a molecule is broken down into smaller parts– catabolic reactions (bonds are broken)

AB A + B– usually exergonic

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Reversible Reactions

• Chemical reactions can be reversible

• Indicated by the 2 arrows pointing in opposite directions between the reactants and the products

AB A + B

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Water

• Most important & abundant inorganic compound in all living systems

• Polarity makes it a good solvent almost “universal” solvent– Hydrophilic compounds

• Usually are polar• Dissolve in water

– Hydrophobic compounds• Usually nonpolar

• Do not dissolve in water

• Excellent medium for metabolic reactions of the body

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Water as a Solvent• Polar covalent bonds (hydrophilic vs. hydrophobic)• Dissolves or suspends many substances

– Each water molecule interact w/ 4 ormore neighboring ions/molecules

– Hydration spheres

• Fig. 2.11 shows how water’s shape makes it such an effective solvent.

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Water in Chemical Reactions

• Hydrolysis: add’n of water breaks molecules apart• Dehydration synthesis

– two simple molecules join together– eliminate a molecule of water in process

• High heat capacity– Resists changes in temperature maintain body temp– Due to hydrogen bonding

• High heat of vaporization– amount of heat needed to change from liquid to gas– evaporation of water from skin removes lots of heat

why sweat cools you

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Water as a Lubricant

• Major component of mucus & other lubricating fluids– mucus in respiratory and digestive systems– synovial fluid in joints– serous fluids in chest and abdominal cavities

• organs slide past one another

• Found wherever friction needs to be reduced or eliminated

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Inorganic Acids, Bases & Salts• Dissociate into ions in water

– Acids: H+ + A- HCl H+ + Cl-

– Bases: OH- + cation NaOH Na+ + OH-

• Acid + base salt & H20– HCl + NaOH NaCl + H2O

• Salts dissociate into cations & anions in water

– metal and nonmetal ions: NaCl + H2O Na+ + Cl-

– not H+ or OH- !!

• Electrolytes – important salts in body (Na, Cl, K)– carry electric current (in nerve or muscle)

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Acid-Base Balance & pH

• pH: measure of [H+] in moles/liter (M)• pH scale: 0-14

– pH = 7 neutral [H+] = [OH-]– pH < 7 acidic [H+] > [OH-]– pH > 7 alkaline [H+] < [OH-]

• A solution’s acidity or alkalinity is based on the pH scale

• Biochemical reactions are very sensitive to even small changes in pH – pH of blood is 7.35 to 7.45

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The Concept of pH• pH is a logarithmic scale—it is NOT linear!

– Therefore—each unit in scale means 10-fold Δ in [H+]

• Ex: a change of two pH units represents 100-fold diff in [H+]

– pH 1 contains 10-1 M H+ & pH 3 contains 10-3 M H+

– the diff in H+ ion concentration is 100—not 2!• Ex: pH 8 vs. pH 11

– pH 8 = 10-8 M H+ & pH 11 = 10 -11 M H+

– pH 8 is 1000x more acidic than pH 11 (even tho both are basic!)

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Maintaining pH: Buffer Systems• pH in body maintained fairly constant by buffer systems

• Buffers resist Δ in pH even when acid/base added– consist of a weak acid & a weak base– convert strong acids/bases into weak acids/bases

– Ex: carbonic acid-bicarbonate buffer system in blood• HCO3

- acts as weak base• H2CO3 acts as weak acid• H2CO3 ↔ H+ + HCO3

-

• H2CO3 H+ + HCO3- (in presence of XS base)

• H2CO3 H+ + HCO3- (in presence of XS acid)

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ORGANIC COMPOUNDS:Carbon and Its Functional Groups

• Carbon forms bonds w/ itself– Large complex molecules of varying shapes

• Most compounds do not dissolve easily in water– useful for building body structures

• C compounds held together by covalent bonds – 4 valence e- forms 4 bonds

• Decompose easily– good source of energy

• Functional groups have distinct chemical properties when attached to organic molecule

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Functional Groups• Many different functional groups can attach to carbon skeleton

• Very large molecules = macromolecules

• Isomers have the same molecular formulas but different structures (glucose & fructose are both C6H12O6)

• STRUCTURAL FORMULA OFGLUCOSE (Fig 2.14)

C6H12O6 ISOMERS

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Carbohydrates (CHO)• Primary energy source in humans

– Include sugars, starches, glycogen, and cellulose– Used to generate ATP– Structural building blocks (DNA)

• Structurally, one H2O molecule/C atom

• Function as food reserves– glycogen stored in liver & muscle

• Divided into three major groups based on size:– Mono-/di-/polysaccharides

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SUGARS: Monosaccharides• Names of sugars generally end in “-ose”• Monosaccharides

– 3-7 carbon atoms – Monomers for building large CHO molecules in body– Ex: glucose (a hexose) is main energy-supplying

compound in body

• Humans absorb only 3 simple sugars without further digestion in small intestine– glucose found in syrup or honey– fructose found in fruit– galactose found in dairy products

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SUGARS: Disaccharides• Formed from two monosacch. by dehydration synthesis

– glucose + fructose sucrose (table sugar)

– glucose + glucose maltose

– glucose + galactose lactose (milk sugar)

• Can be split back into simple sugars by hydrolysis

• Figure 2.15

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Polysaccharides• Polymers of up to hundreds of monosaccharides

• Primary polysaccharide in humans = glycogen– Stored in liver or skeletal muscles– Hydrolyzed in response to ↓ blood sugar glucose

released into blood (from liver only)

• Cellulose – Plant polysaccharide– Not digestible by humans “fiber”

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Lipids• Contain carbon, hydrogen & oxygen

– Fewer oxygens than CHO (not 2:1 H:O ratio)• Nonpolar covalent bonds

– Hydrophobic– Insoluble in polar solvents such as water (plasma)

• Only very short-chain fatty acids dissolve in plasma• Increase solubility by forming lipoproteins

“cholesterol”

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LIPIDS: Triacylglycerols (TAG)

• TAG (also called triglycerides) are what we call “fat”• Most plentiful lipids in the body provide protection,

insulation, and energy • Found in fats and oils

– Fats = solid @ room temperature– Oils = liquid @ room temperature– Most concentrated form of energy

• 9 Calories/gram• Proteins & carbs have only 4 Cal/gram!

– Unlimited storage capacity in body adipose tissue• ANY excess food energy is stored as fat

– All TAG contain glycerol backbone & three fatty acids

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Saturation of Fatty Acids• Determined by number of single or double covalent bonds• Saturated FA contain single covalent bonds & maximum

possible # of H atoms– Saturated fats = TAG w/ only saturated fatty acids– Ex: lard, tallow

• Unsaturated FA lack some H atoms due to presence of > 1 double bond– Monounsaturated fatty acids have one double bond

• olive oil, canola oil, & avocados (yum!!)– Polyunsaturated fatty acids contain > 2 double bonds

• corn, safflower, soybean oils– Double bonds form kink in structure of fatty acid

• fluid rather than solid

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Clinical Application• Essential fatty acids (EFA’s) are essential to human health

and cannot be made by the human body. They must be obtained from foods or supplements.

– ω-3 fatty acids anti-inflammatory– ω-6 fatty acids pro-inflammatory

• Not all inflammation is bad!

– Balance is important

– Conjugated fatty acids (CFA’s) some implications for weight loss…

• trans-fatty acids ↑ risk factors for CVD

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Phospholipids

• Important membrane components

• Amphipathic– polar head

• a phosphate group (PO4-3) & glycerol molecule

• forms hydrogen bonds with water– 2 nonpolar fatty acid tails

• interact only with lipids• hydrophobic

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Steroids• Four rings of carbon atoms

• Include – cholesterol

• important component of cell membranes • starting material for synthesizing other steroids

– sex hormones– bile salts– vitamin D– cortisol

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Other Lipids• Eicosanoids include prostaglandins and leukotrienes.

– derived from 20-C fatty acids AA (ω-6) or EPA (ω-3)– prostaglandins have wide variety of functions

• modify responses to hormones• contribute to inflammatory response• dilate airways• regulate body temperature• influence formation of blood clots

– leukotrienes = allergy & inflammatory responses

• PG & LT derived from EPA are biologically inactive

• Fatty acids; fat-soluble vitamins (D, E, K); and lipoproteins

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Proteins• Contain C, H, O, N & sometimes S

• 12-18% of body weight

• Functions:– Give structure to body (primary role)– Regulate processes– Provide protection– Help muscles contract– Transport substances– Enzymes

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Proteins

• Constructed from combinations of 20 amino acids– dipeptide formed from 2 amino acids joined by

peptide bond (covalent bond)– polypeptide chains formed from 10 to 2000

amino acids

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Amino Acid Structure

• Central carbon atom

• Amino terminus (NH2)

• Carboxyl terminus (COOH)

• Side chains (R groups) vary between amino acids– Amino acids identified by

side chain

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Levels of Protein Structure• Primary = sequence of amino acids• Secondary = twisting & folding

– Alpha helices– Beta pleated sheets

• Tertiary = 3-D shape of folded protein– **Determines function**– Disulfide bridges– Hydrophobic domains in core of folded protein

• Quaternary = structure resulting from linkage of 2 polypeptides

• Shape influences its ability to recognize & bind other molecules

• Denaturation causes loss of characteristic shape and function

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Bonds of Tertiary Structure• Hydrophobic interaxn on

inside of folded protein

• Disulfide bridges stabilize– covalent bond btwn S—H

groups of 2 cysteine a.a.

• H-bonds

• Loss of 3-D structure (denaturation) loss of function– Salts – Heat– Acid

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Enzymes• Biological catalysts• Names generally end in “ase”

– Sucrose is digested by enzyme sucrase• Properties:

– Highly specific in terms of substrate & reaction– Highly efficient– Highly regulated by variety of cellular controls

• Genes• Active & inactive conformations

• Speed up chemical reactions by:– Increasing frequency of collisions– Lowering the activation energy– Properly orienting colliding molecules (Figure 2.23)

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Enzymes as Catalysts

Example:• Normal body temperatures & concentrations are low

enough that rxns are effectively blocked by Ea barrier

– Lactose reacts very slowly w/ water to yield glc & gal

– Lactase (enzyme) orients lactose & water properly

– Thousands of lactose/water reactions may be catalyzed by one lactase enzyme

– Without lactase, lactose remains undigested in intestines • causes diarrhea and cramping condition known as

lactose intolerance (NOT an allergy!!!)

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Nucleic Acids: DNA and RNA

• Huge organic molecules containing C, H, O, N, P• Deoxyribonucleic acid (DNA)

– genetic code inside each cell – regulates most cellular activities

• Ribonucleic acid (RNA)– relays instructions from genes in cell’s nucleus – guides assembly of proteins by ribosomes

• Basic units of nucleic acids are nucleotides– nitrogenous base– pentose sugar

• deoxyribose• ribose

– phosphate group (Figures 2.24a,b)

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RNA Structure

• Differs from DNA– single stranded– ribose sugar not deoxyribose sugar– uracil replaces thymine

• Three types of RNA– messenger RNA– ribosomal RNA– transfer RNA

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Adenosine Triphosphate (ATP)

• Energy currency of cells• Generated from exergonic catabolic reactions

– Breakdown of fats, glucose • Energy liberated upon hydrolysis

– ATP ADP + Pi + energy

• Structure

– 3 PO4-3 groups

– adenine – 5-carbon sugar (ribose)

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Formation & Usage of ATP

• Hydrolysis of ATP (removal of terminal PO4-3 by ATPase)

– releases energy– leaves ADP (adenosine diphosphate)

• Synthesis of ATP

– ATP synthase catalyzes add’n of terminal PO4-3 to ADP

– energy from 1 glc molecule generates up to 36 net molecules of ATP