1. Chapter 02 Lecture Outline
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2. I. Atoms, Ions, and Chemical Bonds
Since physiological processes are based on chemical reactions, a general understanding of chemical principles is necessary.

3. Atoms An atom is the smallest unit of an element. It has:
A nucleus with positively charged protons and uncharged neutrons
Orbiting electrons with negative charges
An atomic mass equal to the number of protons plus the number of neutrons
An atomic number equal to the number of protons

4. Atom Structure Hydrogen 1 proton 1 electron Carbon 6 protons
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Hydrogen
1 proton
1 electron
Carbon
6 protons
6 neutrons
6 electrons
Proton
Neutron
Electron

5. Electron Orbitals
Orbitals (or shells) are energy levels that surround the nucleus of an atom.
Electrons fill the shells, starting with the one closest to the nucleus.
The first shell holds 2 electrons.
Each shell thereafter holds 8 electrons. (Nonbiological elements fill distant shells that hold more than 8.)
Atoms are most stable when the outer shell is filled. Electrons in unfilled outer shells participate in bonding; they are called valence electrons.

6. Common Biological Atoms

7. Isotopes
Atoms of the same element, but with different numbers of neutrons.
Their atomic number is the same, but the atomic mass is different.
Some isotopes are radioactive and used in medical testing and physiological research.
The term chemical element includes all the isotopes of that element

8. Chemical Bonds, Molecules, and Ionic Compounds
Chemical bonds are formed when electrons in atoms interact.
The number of bonds an atom can form is determined by the number of valence electrons.
Hydrogen has one electron; it needs one more to fill the inner shell so that it can form one bond.
Carbon has 6 electrons; 2 fill the inner shell and 4 are valence electrons. It needs 4 more electrons, so that it can form 4 bonds.

9. Covalent Bonds
Valence electrons are shared because energy levels overlap.
Electrons are shared equally form a nonpolar covalent bond; example - 2 hydrogen atoms
Electrons that are not shared equally form a polar covalent bond; they have positive and negative ends; example – between oxygen and hydrogen in water

10. Covalent Bonds
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11. Water Polar molecule Good solvent (substances dissolve in it)
Can form strong hydrogen bonds
Polar molecules (covalent bonds) may dissolve in water and are called hydrophilic
Nonpolar molecules do not dissolve in water and are called hydrophobic

12. Water Molecule – O H O H H H+ (–) OH– (+) (+) Water (H2O) H+
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(–) O H O
OH– H H
(+) H+
(+)
Water (H2O) H+

13. Ionic Bonds
In an ionic bond, one atom gives electrons to another so that both have filled valence shells.
The electron donor becomes positively charged; the atom now called a cation.
The electron receiver becomes negatively charged; the atom now called an anion.
Cations and anions attract each other to form ionic compounds.
Individual ionic bonds are weaker than covalent bonds

14. Ionic Bond – electron transfer
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11P+
17P+
12N
18N
Sodium atom (Na)
Chlorine atom (Cl)
11P+
17P+
12N
18N
Sodium ion (Na+)
Chloride ion (Cl–)

15. Ionic Bonds, cont
Most ionic compounds dissociate (come apart with no reaction) when dissolved in water.
The negative side of water is attracted to the cation, and the positive side of water is attracted to the anion.
This is a strong attraction that pulls the ions apart
Water molecules then surround the ions to form hydration spheres
These free ions are critical to many physiological processes.

16. Sodium chloride dissociates in water
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Na+
Cl–
(–)
Oxygen
Hydrogen
(+)
(+)
Water molecule

17. Hydrogen bond
Weak bond formed between two polar molecules based on opposite charges attracting (not based on electron sharing)
Forms between electropositive H atoms and electronegative O or N atoms
Forms between water molecules; responsible for surface tension and capillarity
Forms between amino acids on a protein to produce the 3D structure of the protein
Holds the two strands of the DNA molecule together.

18. Hydrogen bond between water molecules
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Water molecule O
Hydrogen bonds H + – O – + H H H + – + H O – + – O H – + + – H O – + H

19. Acids, Bases, and pH
Some water molecules ionize to form free hydrogen ions or protons (H+) and hydroxide ions (OH-).
When this happens, there are the same number of H+ ions as OH- ions in solution, so the solution is neutral.
A neutral solution is said to have a pH of 7 (which means 10-7 molar concentration H+).

20. Acids, Bases, and pH, cont
When a solution has more H+ ions than OH- ions, this is called an acid, and its pH is below 7; often called a proton donor
When a solution has more OH- ions than
H+ ions, this is called a base, and its pH is above 7. (Such solutions are also called alkaline.); often called a proton acceptor

21. pH Scale
Runs from 0 to 14, with 0 the strongest acid and 14 the strongest base.
pH is calculated by 1
pH = log
H+ concentration
Pure water has a H+ concentration of 10-7, so the pH is 7. A pH 6 solution actually has 10 times the number of H+ ions.

22. pH Scale

23. Buffers Buffers stabilize pH in a solution.
Has 2 components – a weak acid and a weak base (buffer pair)
In blood, two molecules stabilize pH: bicarbonate ion (HCO3-) and carbonic acid (H2CO3).
HCO H+ ↔ H2CO3
Bicarbonate neutralizes excess acid
Carbonic acid neutralizes excess base

24. Buffers, cont
If blood falls below pH 7.35, the condition is called acidosis.
If blood rises above pH 7.45, the condition is called alkalosis.

25. Organic Molecules Contain carbon and hydrogen
Because carbon must form 4 bonds to satisfy the valence shell, it can form chains and rings of carbons while still bonding with other atoms.
Two carbons can share 1 or 2 pairs of electrons. If 2 pairs are shared, it is a double bond and can bond with 2 additional atoms. If 1 pair of electrons are shared, it can bond with 3 additional atoms

26. Carbon bonding 1P 1P 1P 1P 6P 6P 1P 1P 6P 6P 6N 6N 6N 6N 1P 1P H H 1P
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1P 1P 1P 1P 6P 6P 1P 1P 6P 6P 6N 6N 6N 6N 1P 1P H H 1P 1P H C C H H H C C H H H H
C2H6
C2H4
Ethane (C2H6)
Ethylene (C2H4)

27. Hydrocarbon structures
Carbons are not shown but are understood to be at the corners of the molecule. Some show double bonds.
Carbon chains and rings form backbones for more reactive groups of atoms called functional groups.
Functional groups allow organic compounds to be classified into groups which provides unique chemical properties

28. Hydrocarbon structures
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H
(a) H C C C C C C H
C6H14 (Hexane) H H H H H H
CH2
H2C
CH2
(b) or
C6H12 (Cyclohexane)
H2C
CH2
CH2 H C H H C C
(c) or
C6H6 (Benzene) C C H H C H

29. Functional Groups O O CH3 C CH3 CH3 C O H Ketone Organic acid O H CH3
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O O
Carbonyl (CO) C C C C C C
CH3 C
CH3
CH3 C O H OH
Ketone
Organic acid
Hydroxyl (OH) C C C C C O H SH
Sulfhydryl (SH) C C C C C
CH3 C H
CH3 C O H
NH2 H
Amino (NH2) C C C C C
Aldehyde
Alcohol O
Carboxyl (COOH) C C C C C OH O
Phosphate (H2PO4) C C C C C O P OH OH

30. Stereoisomers
Molecules that have exactly the same atoms arranged in exactly the same sequence, but still differ in the spatial organization of their functional groups.
This characteristic is critical to function. A given enzyme may interact with one stereoisomer but not with another.
The sugars glucose, galactose, and fructose are stereoisomers.

31. Types of stereoisomers
Cis-trans isomers – geometric isomers
Enantiomers (optical isomers) – mirror images; rotate right (D) or left (L)
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H3C
CH3 H
CH3 C C C C H H
H3C H
cis-2-butene
trans-2-butene
(a) H O H O C C H C OH HO C H
CH2OH
CH2OH
D-glyceraldehyde
L-glyceraldehyde
(b)

32. II. Carbohydrates & Lipids

33. Carbohydrates Characteristics
Organic molecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.
Serve as a major source of energy in the body
Includes sugars and starches
-ose suffix of name denotes sugars

34. Classification of Carbohydrates
Monosaccharide: simple sugar, one carbon ring
Examples: glucose, fructose, galactose
Formula is C6H12O6 – structural isomers
Disaccharide: two monosaccharides joined by a covalent bond; examples: sucrose, maltose, lactose

35. Monosaccharides H O C H C OH CH2OH O HO C H H H H (a) H C OH HO OH H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O C H C OH
CH2OH O HO C H H H H
(a) H C OH HO OH H OH H C OH H OH H C OH H
Glucose H O C H C OH
CH2OH O HO C H HO H H
(b) HO C H OH H H OH H C OH H OH H C OH H
Galactose H H C OH C O HO C H
HOCH2 O OH
(c) H C OH H H HO
CH2OH H C OH OH H H C OH H
Fructose

36. Polysaccharides
Polysaccharide: several monosaccharides (generally glucose) joined together
Starch – plant storage of sugar; composed of thousands of glucose molecules
Glycogen – sugar storage in an animal cell; glycogen does not pull in water via osmosis as simple sugars do.
Cellulose – makes up cell walls of plants; cellulose is not digestible by humans.

37. Glycogen O CH2OH OH O OH O CH2OH OH O Glycogen OH O CH2OH OH O O OH
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O
CH2OH OH O OH O
CH2OH OH O
Glycogen OH O
CH2OH OH O O OH
CH2OH
CH2OH
CH2
CH2OH O O O O OH O OH O OH O OH O OH OH OH OH

38. Dehydration Synthesis and Hydrolysis
Covalent bonds that hold monosaccharides together are formed via dehydration synthesis where a hydrogen atom is removed from one molecule, and a hydroxyl group is removed from another to form water.
Hydrolysis breaks bonds between monosaccharides; add water and split the molecule
These processes are also used to build/break fats, proteins, and nucleic acids.

39. Dehydration Synthesis
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CH2OH
CH2OH
CH2OH
CH2OH O O O O H H H H H H H H H H H H + +
H2O
(a) OH H OH H O H H O OH H HO OH HO OH HO OH H OH H OH H OH H OH
Glucose +
Glucose =
Maltose +
Water
CH2OH O H H H
CH2OH O H
CH2OH O OH OH HO H H H + H OH +
H2O OH H H OH
(b) HO O H O H
CH2OH
CH2OH O H OH OH H
Water H OH
Glucose
Fructose H
CH2OH OH H
Sucrose

40. Hydrolysis O O O O H H H H H H H H O O O O etc. + H2O HO (a) Starch
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O O O H H H H H H H H O O O O
etc. +
H2O HO
(a)
Starch
Water O O O O H H H H H H H H + O O HO OH HO OH
etc.
Maltose O O O O H H H H H H H H
(b) +
H2O + O HO OH HO OH HO OH
Maltose +
Water
Glucose +
Glucose

41. Lipids Characteristics
Lipids consist of nonpolar hydrocarbon chains and rings that make them hydrophobic (insoluble in water).
There are several categories of lipids.

42. Triglycerides (Triacylglycerols)
Include fats (solids) and oils (liquids)
Composed of one molecule of glycerol and three molecules of fatty acids
Glycerol is a 3-carbon alcohol
Fatty acid – long, nonpolar hydrocarbon chain with a carbonyl (COOH) at one end
If every carbon on the fatty acid chain shares a single pair, the fatty acid is saturated.
If there are double bonds between carbons, the fatty acid is unsaturated.
Also called neutral fats when stored in adipose tissue

43. Triglycerides (Triacylglycerols)
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Fatty acids
Triglyceride
Carboxylic
acid R
Hydrocarbon chain
Ester
bond
Hydrocarbon
chain
Glycerol
Glycerol H O H H H H H H H O H C OH HO C C C C C C C H C O C R H H H H H H O H H H H H H O H C OH HO C C C C C C C H C O C R +
3H2O H H H H H H O H H H H H H O H C OH HO C C C C C C C H C O C R H H H H H H H H

44. an unsaturated fatty acid
Saturated and Unsaturated Fats
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H H H H H H H H H H H O H C C C C C C C C C C C C C C C C C OH H H H H H H H H H H H H H H H H
Palmitic acid,
a saturated fatty acid
(a) H H H H H H H H H H H H H H H H H H H O H C C C C C C C C C C C C C C C C C C C C OH H H H H H H H H H H H H H
Linolenic acid,
an unsaturated fatty acid
(b)

45. Cis – trans fats Figure 2.19 Structural formulas for fatty acids
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Figure Structural formulas for fatty acids
Oleic Acid
Elaidic Acid
Carbon
Hydrogen
Oxygen
Cis double bond
Trans double bond

46. Ketone Bodies
Hydrolysis of triglycerides forms free fatty acids in the blood. These can be used for energy or converted into ketone bodies by the liver.
Strict low-carbohydrate diets and uncontrolled diabetes can result in elevated ketone levels, called ketosis.
Ketone levels high enough to lower pH can cause ketoacidosis, which can lead to coma and death.

47. Ketone Bodies O H C O H H C H H C H + CO2 O C O C H C H H C H H H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O H C O H H C H H C H +
CO2 O C O C H C H H C H H H
Acetoacetic
acid
Acetone

48. Phospholipids Lipids with a phosphate group, which makes them polar.
Major component of cell membranes as a double layer, with hydrophilic phosphates pointing outward on each side and hydrophobic fatty acids and glycerol pointing inward.
As micelles, phospholipids can act as surfactants. The polar nature of the molecule decreases the surface tension of water.
Surfactant keeps lungs from collapsing.

49. Phospholipids O H C O C R Fatty acid chains bonded to glycerol
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Fatty acid
chains bonded
to glycerol
(nonpolar) O H C O C R O
Phosphate
group
(polar) –O P O C H2 O
CH2
CH2
Nitrogen-containing
choline group (polar)
H3C +N
CH3
CH3
Polar
(hydrophilic)
portion
Nonpolar (hydrophobic) portion

50. Micelles and Water

51. Steroids
A steroid is structurally very different from a triglyceride but is nonpolar, so considered a lipid.
3 six-carbon rings + 1 five-carbon ring + functional groups
Cholesterol is a steroid used (1) as a precursor to steroid hormones, such as testosterone, estrogen, and corticosteroids, and (2) to make molecules such as vitamin D and bile salts.

52. Steroids C27 Cholesterol HO CH2OH C O CH3 HO OH CH3 C21 Cortisol
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 21 22 24 26 20 23 25 18 12 17 27 11 13 16 19 14 15 1 9 2 10 8 3 5 7
C27
Cholesterol HO 4 6
CH2OH C O
CH3 HO OH
CH3
C21
Cortisol
(hydrocortisone) O OH
CH3
CH3
C19
Testosterone O OH
CH3
CH3
C18
Estradiol HO

53. Prostaglandins Type of fatty acid with a cyclic hydrocarbon group
Serve as communication molecules between cells in the same organ
Help regulate blood vessel diameter, ovulation, uterine contractions, inflammatory reactions, blood clotting, etc.

54. Prostaglandins O COOH OH OH Prostaglandin E1 OH COOH OH OH
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COOH OH OH
Prostaglandin E1 OH
COOH OH OH
Prostaglandin F1 O
COOH OH OH
Prostaglandin E2 OH
COOH OH OH
Prostaglandin F2

55. Proteins

56. Characteristics Composed of an amino acid chain
An amino acid has an amino group, a carboxyl group, and a functional group.
There are 20 different amino acids that can be combined in an endless number of ways.
The functional group is what differentiates the 20 amino acids.
Amino acids are charged, so they attract each other to form kinks and folds in the protein.
The sequence of amino acids in a chain is determined by DNA.

57. Amino Acids Functional group R H O N C C H OH H Amino group
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Functional group R H O N C C H OH H
Amino group
Carboxyl group
Nonpolar amino acids OH C HC CH HC CH
H3C
CH3 C CH CH H O H O N C C N C C H OH H OH H H
Valine
Tyrosine
Polar amino acids
Basic
Sulfur-containing
Acidic
H2N C NH O OH NH SH C
(CH2)3
CH2
CH2 H O H O H O N C C N C C N C C H OH H OH H OH H H H
Arginine
Cysteine
Aspartic acid

58. Making a Protein
When amino acids are joined, a H is stripped from the amino end and a OH is stripped from the carboxyl end in dehydration synthesis. This is called a peptide bond.
When amino acids are added together to form a chain, it is the primary structure of a protein

59. Making the primary structure of a protein

60. Protein Structure
A chain of amino acids is called a polypeptide chain.
The chain varies in length from 3 to 4,500 amino acids.
The chain is called the primary structure of the protein.
Weak hydrogen bonds may form between neighboring amino acids.
This may form an alpha helix or a beta fold.
This is called the secondary structure of the protein.

61. Protein Structure, cont
Attraction to amino acids further away produces bends and folds, creating a specific 3D shape.
This is the tertiary structure of the protein.
This structure dictates function.
Since weak bonds hold tertiary structure together, a protein is easily denatured (unfolded) by changes in pH or temperature.

62. Tertiary Protein Structure
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+NH3
Ionic bond –O C O
van der Waals
forces
Hydrogen
bond HO C O H O H C S
Disulfide bond
(covalent)
H3C
CH2
CH3 S
H3C
H2C
CH3 C H

63. Protein Structure, cont
Some functional proteins are composed of multiple polypeptide chains covalently bonded together.
This is called the quaternary structure of the protein.
Examples are the hemoglobin (4 polypeptides) in blood and the hormone insulin (2 polypeptides).

64. Protein Structure Amino acid 3 Amino acid 2 Amino acid 1
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Amino acid 3
Amino acid 2
Amino acid 1 H O R H H C C N C N C C R R H H O
(a) Primary structure
(polypeptide strand)
(b) Secondary structure
(α helix)
(c) Secondary structure (β pleated sheet)
α helix
Heme
group
(d) Tertiary structure
(e) Quaternary structure
(hemoglobin)

65. Conjugated Proteins
Sometimes proteins are combined with other molecules to become functional
Glycoprotein = Protein + Carbohydrate
Examples: some hormones, in cell membranes
Lipoprotein = Protein + Lipid
Example: in cell membranes, carrier molecules in blood

66. Conjugated Proteins

67. Protein Functions
Structural: collagen fibers in connective tissues; keratin in skin
Enzymes: assist every chemical process in the body
Antibodies: part of the immune system
Receptors: receive communication from other cells for regulation of cell activity
Carriers: across cell membranes or in blood

68. Nucleic Acids

69. Nucleotides Building blocks for nucleic acids
Composed of a five-carbon sugar, a phosphate group, and a nitrogenous base
Nitrogenous bases fall into two categories:
Pyrimidine: a single carbon ring + nitrogen
Cytosine, thymine, uracil
Purine: 2 carbon rings + nitrogen
Guanine, adenine
Pentose sugars are deoxyribose or ribose

70. Deoxyribonucleic Acid (DNA)
The sugar in this molecule is called deoxyribose and can bind to one of four nitrogenous bases:
Guanine
Thymine
Cytosine
Adenine
Deoxyribose bonds with a phosphate group (via dehydration synthesis) to form a long chain, which serves as the backbone of the molecule.

71. DNA Structure, cont
Each nitrogenous base can form a hydrogen bond with another to result in a double-stranded molecule.
Cytosine can only bind with guanine.
Tyrosine can only bind with adenine.
This is the Law of Complementary base pairs
The two chains of DNA are twisted, forming a double helix.
DNA is the basis of the genetic code – the sequence of bases codes for amino acids to make a protein

72. Deoxyribonucleic Acid (DNA)
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Phosphate
group O
Base
Five-carbon
sugar
Nucleotide
Bases O G
Guanine O T
Thymine O C
Cytosine O A
Adenine

73. DNA Structure – base pairings
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H
Phosphate O H N H H N C C
CH2 C C C N H N C H O N C C N N C N H O O
Deoxyribose H
H2C
Guanine
Cytosine H H H C O H N H N H C C C C C
CH2 H C N H N C N O N C C N H O O
H2C
Thymine
Adenine

74. DNA Structure – double helix
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Sugar-phosphate
backbone
Complementary
base pairing
Sugar-phosphate
backbone A T G C C G T A A T C G C G T A G C T A A T C G C G A C G
Hydrogen
bond A T

75. Ribonucleic Acid (RNA)
Similar to DNA except:
Has ribose sugar instead of deoxyribose
Is single-stranded instead of double-stranded
Has uracil instead of thymine

76. DNA vs RNA DNA nucleotides contain RNA nucleotides contain HOCH2 OH
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DNA nucleotides contain
RNA nucleotides contain
HOCH2 OH
HOCH2 O H O O H H
instead of H H H H H H O H H OH OH
Deoxyribose
Ribose O O H
CH3 H H N N
instead of O N H O N H H H
Thymine
Uracil

77. Types of RNA
Three types of RNA are used to take information for assembling a protein out of the nucleus and to actually assemble it:
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
Other RNA-related molecules serve important functions in the body
ATP, GTP – energy carriers
cAMP - regulation
NAD, FAD – co-enzymes