Chemical level

Human Anatomy and Physiology, 7eby Elaine Marieb & Katja Hoehn

Copyright © 2007 Pearson Education, Inc.,publishing as Benjamin Cummings.

Lecture 2

THE CHEMICAL LEVEL

Composition of Matter• Matter – anything that occupies space and has mass

• Matter is composed of elements

• Each element is composed of identical ATOMS

• Atoms are therefore known as the building blocks • There are 112 elements - most of the body’s weight is

made up of four major elements - Carbon, Oxygen, Hydrogen and Nitrogen.

Elements in the Human Body

• Oxygen (65%) • Carbon (18%) • Hydrogen (10%) • Nitrogen (3%) • Calcium (1.5%)

• Phosphorus (1.0%)

• Potassium (0.35%)

• Sulfur (0.25%)

• Sodium (0.15%)

• Magnesium (0.05%)

• Copper, Zinc, Selenium, Molybdenum, Fluorine, Chlorine, Iodine, Manganese, Cobalt, Iron (0.70%)

• Lithium, Strontium, Aluminum, Silicon, Lead, Vanadium, Arsenic, Bromine (trace amounts)

The Structure of an Atom• Each atom is composed of 3 subatomic particles:

1. Protons – positively-charged subatomic particles located in the center of the atom known as the atomic nucleus; number of protons in an atom is specifically referred to as the ATOMIC NUMBER

2. Neutrons – uncharged subatomic particles located inside the atomic nucleus

Therefore, the overall charge of the atomic nucleus is POSITIVE

3. Electrons – negatively-charged subatomic particles located in orbits/shells surrounding the atomic nucleus.

In an atom, the number of protons = the number of electrons; therefore the overall charge of an atom is ZERO – an atom is electrically neutral



Figure 2.1: The structure of an atom, p. 27.

Nucleus

Helium atom2 protons (p+)2 neutrons (n0)2 electrons (e–)

(a) Planetary model

Key:

Helium atom2 protons (p+)2 neutrons (n0)2 electrons (e–)

(b) Orbital model

= Electron

= Electron cloud

= Proton

= Neutron

Nucleus



Figure 2.4: Chemically inert and reactive elements, p. 32.

Helium (He)(2p+; 2n0; 2e–)

Neon (Ne)(10p+; 10n0; 10e–)

He Ne2e 2e

8e

Hydrogen (H)(1p+; 0n0; 1e–)

Carbon (C)(6p+; 6n0; 6e–)

Oxygen (O)(8p+; 8n0; 8e–)

Sodium (Na)(11p+; 12n0; 11e–)

H C

NaO

2e1e4e

2e8e

1e6e

2e

(a) Chemically inert elements (valence shell complete)

(b) Chemically active elements (valence shell incomplete)

Atomic Orbits/Shells• Electrons are located/arranged in the orbits/shells in a specific

manner:

First shell ( closest to the atomic nucleus) – can accommodate a maximum of 2 electrons

Second shell – can accommodate a maximum of 8 electrons

Third shell - can accommodate a maximum of 18 electrons however, the atom is stable with 8 electrons ( “The Octotet rule” )

The outermost shell in an atom is called the VALENCE shell and the electrons located in the valence shells are called VALENCE ELECTRONS

If the valence shell of an atom does not contain the maximum number of electrons, the atom is UNSTABLE, and therefore chemical reactive.

Chemically-Inert and Chemically-reactive Elements

• Inert Elements – atoms with their valence shells complete ( have the maximum number of electron ) and therefore chemically inert, unreactive

• The noble gases are chemically inert

• Chemically-reactive Elements – atoms in the elements have incomplete valence shells and are therefore unstable and they are chemically reactive;

• Such chemically reactive atoms achieve stability by forming CHEMICAL BONDS with other atoms using their valence electrons – result in the formation of Molecules and Compounds

• Molecule – typically involves the same atoms

• Compounds – typically involves different atoms

3 Types of Chemical Bonds• Covalent Bonds – electrons are shared between atoms to attain stability;

2 types of Covalent Bonds: Nonpolar and Polar

Nonpolar covalent Bond – electrons are shared EQUALLY between the atoms involved; Ex. CO2 (Carbon Dioxide)

Polar covalent Bond – UNEQUAL sharing of electrons – one atom pulls the shared electrons closer to itself and such an atom is referred to as an ELECTRONEGATIVE ATOM. The other atom is referred to as an ELECTROPOSITIVE ATOM ; Ex. H2O ( water molecule)

Oxygen = electronegative atom

Hydrogen = electropositive atom

• Ionic Bonds – involve complete transfer of electron from one atom to the other resulting a charged particles called IONS; the atom donating the electrons becomes positively-charged ion called a CATION; the atom accepting electrons becomes a negatively-charged ion called an ANION; Ionic bond therefore forms between the cation and the anion = “opposites attract”

• Hydrogen Bonds – a weaker bond that forms between Hydrogen atoms(electropositive) and electronegative ions; hydrogen bonds form between atoms already involved in Polar Covalent Bond



Figure 2.7b-c: Formation of covalent bonds, p. 35.

+ or

Oxygen atom Oxygen atom Molecule of oxygen gas (O2)

or

Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2)

+

(b) Formation of a double covalent bond

(c) Formation of a triple covalent bond

O O OO O O

N NN N N N



Figure 2.7a: Formation of covalent bonds, p. 35.

Hydrogen atoms Carbon atom Molecule of methane gas (CH4)

or+

(a) Formation of four single covalent bonds

H

H

H

H

H

H

H

H

C C C

H

H

H H



Figure 2.5: Formation of an ionic bond, p. 33.+

Sodium atom (Na)(11p+; 12n0; 11e–)

Chlorine atom (Cl)(17p+; 18n0; 17e–)

Sodium ion (Na+) Chloride ion (Cl–)

Sodium chloride (NaCl)

CI–

Na+

(a)

(b)

ClNaClNa

–



Figure 2.10a: Hydrogen bonding between polar water molecules, p. 37.

(a)

–

–

–

–

–

+

+

+

+

+

+

HH

H

H

H

O

O

O

O

O

HH

H

H

H

Hydrogen bonds



Figure 2.9: Comparison of ionic, polar covalent, and nonpolar covalent bonds, p. 36.

Ionicbond

Completetransfer ofelectrons

Separateions(chargedparticles)form

Na+ Cl–

Sodiumchloride

Water Carbondioxide

Polarcovalentbond

Unequalsharing ofelectrons

Nonpolarcovalentbond

Equalsharing ofelectrons

Chargebalancedamongatoms

H HO

O OC

Slight negativecharge (–) atone end of molecule, slight positivecharge (+) atother end

+ +

–

Hydrogen bond

weakest strongest

Important Compounds in the Human Body

• Fall into 2 categories: Inorganic compounds and Organic Compounds

• Inorganic Compounds – do not contain Carbon

( except Carbon dioxide and Carbon Monoxide)

Water, Acids, Bases Salts

• Organic Compounds – Contain Carbon; covalently bonded

Carbohydrates, Lipids, Proteins, Nucleic Acids

WATER – Polar Covalent Molecule

1. Most abundant compound in the body – 70% of the volume of cells

2. Known as the UNIVERSAL SOLVENT - involved in all biochemical reactions occurring in the body

3. High heat capacity – absorbs body heat

4. High heat of Vaporization – water evaporates from body using large amounts of heat – cools the body

5. For cushioning around body organs such as the brain

ACIDS and BASES• ACIDS - Substances that release HYDROGEN IONS ( H+) = Protons.

Hence, acids are also known as “PROTON DONORS

Ex. HCl, H2CO3

• Negative log of the H+ concentration = pH;

• The H+ concentration is inversely proportional to the pH; the higher the H+ concentration, the lower the pH and vice versa (refer the pH scale on the next page)

• The blood pH is strictly maintained between 7.35-7.45 – the optimum pH for the actions of enzymes involved in physiological processes

• BASES – substances that accept H+; Bases are “PROTON

ACCEPTORS”Ex. HCO3-, NaOH

• Acid-base balance is regulated by BUFFERS – chemicals that resist abrupt changes in pH by binding H+ when the pH falls and by releasing H+ when the pH rises



Figure 2.13: The pH scale and pH values of representative substances, p. 42.

Concentration in moles/liter

[OH–]

10–14

10–13

10–12

10–11

10–10

10–9

10–8

10–7

10–6

10–5

10–4

10–3

10–2

10–1

100

10–5

10–6

10–7

10–8

10–9

10–10

10–11

10–12

10–13

10–14

10–4

10–3

10–2

10–1

100

5

6

7

8

9

10

11

12

13

14

4

3

2

1

0

[H+] pH Examples

Lemon juice; gastricjuice (pH 2)Grapefruit juice (pH 3)

Sauerkraut (pH 3.5)Tomato juice (pH 4.2)

Coffee (pH 5.0)

Urine (pH 5–8)Saliva; milk (pH 6.5)Distilled water (pH 7)Human blood; semen (pH 7.4)Egg white (pH 8)

Seawater (pH 8.4)

Milk of magnesia (pH 10.5)

Household ammonia (pH 11.5–11.9)Household bleach (pH 12)

Oven cleaner (pH 13.5)Incr

easi

ng

alk

alin

ity

(bas

icit

y)In

crea

sin

g a

cid

ity

Neutral[H+] = [OH–]



Figure 2.12: Dissociation of a salt in water, p. 40.

olecule

Saltcrystal

Ions insolution

H

HO

Na+

Cl–

Na+

Cl–

– +

+

Salts are ionic compounds that dissociate completely in water to give CATIONS and ANIONS

Ex. NaCl, KCl



ORGANIC COMPOUNDS

• Carbohydrates – Monosaccharides, Disaccharides,

Polysaccharides

• Lipids – neutral fats( =triglycerides=triacylglycerol), phospholipids, Steroids, Eicosanoids

• Proteins – Fibrous and Globular Proteins

• Nucleic Acids – DNA, RNA



Carbohydrates • Monosaccharides – General formula (CH2O)n; sweet and soluble in water

2 types of Monosaccharides: - Hexose = (CH2O)6 – Glucose, Fructose, Galactose

- Pentose = (CH2O)5 – Deoxyribose, Ribose

• Disaccharides – composed of 2 hexose sugars; sweet and soluble in water

3 types of disaccharides:Maltose ( “Grain sugar) = Glucose + Glucose

Sucrose ( “Table sugar”) = Glucose + Fructose Lactose ( “Milk sugar”) = Glucose + Galactose

• Polysaccharides – composed of long chains of glucose = storage form of glucose; known as starch in plant cells and as GLYCOGEN in animal cells; not sweet, insoluble in water



Figure 2.14a-b: Carbohydrate molecules, p. 45.

Glucose Fructose Galactose Deoxyribose Ribose

Glucose Fructose

Dehydrationsynthesis

Hydrolysis

Glucose Glucose

Maltose

Sucrose

Galactose Glucose

Lactose

(a) Monosaccharides- monomers or building blocks of Carbohydrates

CH2OH

H OH H

CH2OH

H OH H OH OHOH OH

O

HOHOH

H

HO

HH

O

HOHCH2OH

H

HO

HOCH2 O

HOHH

OH

H

HOH

OHOCH2

HHH

OH

H

OHOCH2

HHH

OH

H

+O

CH2OH

H

H

OH

OH

H

HO

HH

OH

O

OH

HO

H

HCH2OH

H

HO

H2O

H2O

HOCH2

O

HOCH2

H

H

OH

OH

H

HO

HH

O

HOCH2

H

HH

OH

OH

OHHH

(b) Disaccharides – composed of 2 monosaccharides – hexose sugars

CH2OH

H

O

O

HOCH2

HOCH2

H OH

HOCH2

H OH

O

HOHHH

HOH

O

HHOH

OHHH

O

O

H

H

OH

OHHO

HH

O

OH

HO

H

HCH2OH

H



Figure 2.14c: Carbohydrate molecules, p. 45.

Glycogen

(c) Portion of a polysaccharide molecule (glycogen)

OO

OO

O

O O

O

O

CH2

O

O

OO

O O

O



LIPIDS• Hydrophobic substances insoluble in water• 4 types:• Neutral fats – composed of a glycerol backbone and 3 free fatty

acid chains attached ( looks like the letter “E”)

• Phospholipids – Composed of a glycerol backbone, 2 free fatty acid chains and a phosphorous-containing group

• steroids – derived from Cholesterol

• Eicosanoids – derived from Arachidonic acids



Figure 2.15a: Lipids, p. 47.

Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 watermolecules

(a) Formation of a triglyceride

H

H

H

C

C

C

O

O

O

H

H

H C

O

CH2 CH2 CH2 CH2 CH3

C

O

CH2 CH2 CH2 CH2 CH3

CH2 CH2 CH2 CH2 CH3

HO

HO

HO

H

H

H

H

H

C

C

C

O

O

O

H

H

CH2 CH2 CH2 CH2 CH3

CH2 CH2 CH2 CH2 CH3

CH2 CH2 CH2 CH2 CH3

3H2O

C

O

C

O

C

O

C

O

++



Neutral Fats = Triglycerides = Triacyglycerol• Most abundant form of fat in the human diet• Known as FATS when solid and OILS when liquid.• 2 types of Neutral Fats – Saturated and Unsaturated

Unsaturated Fats – at least one double covalent bond in the carbon chain; liquid at room temperature; plant sources – olive oil

Saturated Fats – single covalent bonds exist between all the carbons in the chain; solid at room temperature; animal sources – butter

Saturated fats increase Low Density Lipoproteins ( LDL ) – increase myocardial infarction and stroke

Types of Lipoproteins: Very low Density Lipoproteins (vLDL )

Low Density Lipoprotein ( LDL ) = “BAD CHOLESTEROL”

High Density Lipoproteins ( HDL ) = “GOOD CHOLESTEROL”

TRANS FATS – Unsaturated fats + H+ = Saturated ( solid) fats; margarine



Figure 2.15b-c: Lipids, p. 47.

Glycerolbackbone

Phosphorus-containinggroup (polar end)

2 fatty acid chains (nonpolar end)

Polar “head”

Nonpolar “tail”

(b) Phospholipid molecule (phosphatidylcholine)

(c) Cholesterol

C

O

O C

O

P

O

N+ CH2 CH2 O O

CH3

CH3

O

O

CH3

CH2

CH2

CH

O

CH2 CH2 CH2C

H

CH2

CH2 CH2 CH2 CH2 CH2 CH2 CH3CH2

CH3

CH3

CH3

CH3

H3C

HO

H

CCH

2 CH3



LIPIDS - EICOSANOIDS

Phospholipids - Arachidonic acid ----

Prostaglandins and Leukotrienes; mediate physiological reaction occurring in the body



PROTEINS• Building blocks = AMINO ACIDS

• Each has an AMINO terminal that can act as a base and a CARBOXYL terminal that can act as an acid

• Amino acids are amphoteric molecules – can act as acids and bases

• There are 20 naturally-occurring amino acids



Figure 2.16: Amino acid structures, p. 49.

Aminegroup

Acidgroup

(a) Generalized structure of all amino acids

(b) Glycine (the simplest amino acid)

(d) Lysine (a basic amino acid)

(e) Cysteine (a sulfur-containing amino acid)

(c) Aspartic acid (an acidic amino acid)

R

H

C OHH2N

H

CH2

COOH

CH2

SH

C OHH2N

CH2

NH2H

H

CH2

CH2

C

C OHH2N

H

H

OHH2N

H

C C OHH2N

H

O

CO

C

O

C

O

C

O

C



Figure 2.17: Amino acids are linked together by dehydration synthesis, p. 49.

Amino acid Amino acid

Dehydrationsynthesis

HydrolysisDipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH



4 Structural levels of Proteins

• PRIMARY Structure- linear polypeptide chain indication the type and position of the amino acids

• SECONDARY Structure – twisting/bending to form an alpha HELIX ( coiled) or a beta PLEATED sheet ( polypeptide chains linked side by side)

• TERTIARY Structure – secondary structure fold upon themselves to give a compact, globular molecule;

3-dimensional structure

• QUATERNARY Structure – 2 or more polypeptide chains are held together by disulfide bonds



Figure 2.18a,c: Levels of protein structure, p. 51.

O

O

(c) Secondary structure (-pleated sheet)

(a) Primary structure (polypeptide strand)

C

C

R H

N

N

C

H

C RH

H

C RH

O

O



Figure 2.18b,d,e: Levels of protein structure, p. 51.

Heme group

(b) Secondary structure (-helix)

(d) Tertiary structure (e) Quaternary structure (hemoglobin molecule)

-helix



2 Classes of Protein• 1. Fibrous Proteins:

Extended/strand-likeInsoluble in waterProvide mechanical support and tensile strength as the

main building material in the body hence, the fibrous protein are also known as Structural Proteins

• 2. Globular Proteins:Compact/ball-like

Soluble in water, sensitive to pH and temperature changesChemically active – they mediate all biochemical

reactions occurring in the body hence, the globular proteins are also known as Functional Proteins



Figure 2.19: Denaturation of a globular protein such as an enzyme, p. 53.

Substrate “fits” with active site

Active site

Functionalenzyme

Substrate unable to bind

Denatured enzyme

(a) (b)



4th type of Organic compounds in the body: NUCLEIC

ACIDS - Structure of DNA, p. 56.

(b)

A

A

G

A

T

T

T

C

G C

G C

A

A

G

G

A

(c)

Thymine (T)

Adenine (A)

Cytosine (C)

Guanine (G)

Deoxyribosesugar

Phosphate

Hydrogen bond

Key:

Sugar-phosphatebackbone

Chemical level

Documents

atomeach atom

maximum number of electrons

formation of covalent

shared electrons closer

reactive atoms

atomic number

valence electronsif

charged particles