1. Human Anatomy and Physiology I
CHEMISTRY COMES ALIVE
Chapter 2

2. Chapter 2 Outline Basic Chemistry
Review of Matter, Energy, Atomic Structure,
Elements, Molecules, and Chemical Bonds
Biochemistry
Inorganic Compounds
Water, Salts, Acids and Bases
Organic Compounds
Carbohydrates, Lipids, Proteins,
Nucleic Acids

3. Composition of Matter Elements Atoms Atomic symbol
Cannot be broken down by ordinary chemical means
Atoms
Unique building blocks for each element
Smallest unit of an element
Atomic symbol
One- or two-letter chemical shorthand for each element

4. Major Elements of the Human Body
Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)
About 96% of body mass

5. Lesser Elements of the Human Body
About 3.9% of body mass
Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe)
< 0.01% of body mass
Part of enzymes
chromium (Cr), manganese (Mn), and zinc (Zn)

6. Atomic Structure Determined by numbers of subatomic particles
Nucleus consists of neutrons and protons
Neutrons
No charge
Mass = 1 atomic mass unit (amu)
Protons
Positive charge
Mass = 1 amu

7. Atomic Structure Electrons Orbit nucleus
Equal in number to protons in atom
Negative charge
1/2000 the mass of a proton (0 amu)

8. Helium atom Helium atom Nucleus Nucleus 2 protons (p+) 2 neutrons (n0)
2 electrons (e–)
2 protons (p+)
2 neutrons (n0)
2 electrons (e–)
(a) Planetary model
(b) Orbital model
Proton
Neutron
Electron
Electron
cloud

9. Proton Neutron Electron Hydrogen (H) (1p+; 0n0; 1e–) Helium (He)
Lithium (Li)
(3p+; 4n0; 3e–)

10. Identifying Elements Atomic number = number of protons in nucleus
Mass number = mass of the protons and neutrons
Atomic weight = average of mass numbers of all isotopes

11. Isotopes of Hydrogen Proton Neutron Electron Hydrogen (1H)
(1p+; 0n0; 1e–)
Deuterium (2H)
(1p+; 1n0; 1e–)
Tritium (3H)
(1p+; 2n0; 1e–)

12. Radioisotopes Valuable tools for biological research and medicine
Cause damage to living tissue
Useful against localized cancers
Radon from uranium decay causes lung cancer

13. Molecules and Compounds
Most atoms combine chemically with other atoms to form molecules and compounds
Molecule—two or more of the same type of atoms bonded together
H2, O2
Compound—two or more different kinds of atoms bonded together
C6H12O6

14. Chemical Bonds
Electrons occupy up to seven electron shells (energy levels) around nucleus
Octet rule
Except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their outermost energy level (valence shell)

15. Chemically inert elements
Outermost energy level (valence shell) complete 8e 2e 2e
Helium (He)
(2p+; 2n0; 2e–)
Neon (Ne)
(10p+; 10n0; 10e–)

16. Chemically Reactive Elements
Outermost energy level not fully occupied by electrons
Tend to gain, lose, or share electrons (form bonds) with other atoms to achieve stability

17. Chemically reactive elements
Outermost energy level (valence shell) incomplete 4e 1e 2e
Hydrogen (H)
(1p+; 0n0; 1e–)
Carbon (C)
(6p+; 6n0; 6e–) 1e 6e 8e 2e 2e
Oxygen (O)
(8p+; 8n0; 8e–)
Sodium (Na)
(11p+; 12n0; 11e–)

18. Types of Chemical Bonds
Ionic
Covalent
Hydrogen

19. Ionic Bonds
Ions are formed by transfer of valence shell electrons between atoms
Attraction of opposite charges results in an ionic bond
Sodium atom (Na)
(11p+; 12n0; 11e–)
Chlorine atom (Cl)
(17p+; 18n0; 17e–)
Sodium ion (Na+)
Chloride ion (Cl–)
Sodium chloride (NaCl) + –
(a) Sodium gains stability by losing one electron, and
chlorine becomes stable by gaining one electron.
(b) After electron transfer, the oppositely
charged ions formed attract each other.

20. CI–
Na+
(c) Large numbers of Na+ and Cl– ions
associate to form salt (NaCl) crystals.

21. Covalent Bonds
Formed by sharing of two or more valence shell electrons
Allows each atom to fill its valence shell at least part of the time

22. Single Covalent Bonds Reacting atoms Resulting molecules or Structural+ or
Structural
formula
shows
single
bonds.
Hydrogen
atoms
Carbon
atom
Molecule of
methane gas (CH4)
(a) Formation of four single covalent bonds:
carbon shares four electron pairs with four
hydrogen atoms.

23. Double Covalent Bonds Reacting atoms Resulting molecules or Structural+ or
Structural
formula
shows
double
bond.
Oxygen
atom
Oxygen
atom
Molecule of
oxygen gas (O2)
(b) Formation of a double covalent bond: Two
oxygen atoms share two electron pairs.

24. Triple Covalent Bonds Reacting atoms Resulting molecules or Structural+ or
Structural
formula
shows
triple
bond.
Nitrogen
atom
Nitrogen
atom
Molecule of
nitrogen gas (N2)
(c) Formation of a triple covalent bond: Two
nitrogen atoms share three electron pairs.

25. Hydrogen Bonds
Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule

26. Hydrogen bond (indicated by dotted line)+ –
Hydrogen bond
(indicated by
dotted line) + + – – – + + + –
The slightly positive ends (+) of the water molecules become aligned with the slightly negative ends (–) of other water molecules.

27. A water strider can walk on a pond because of the high surface tension of water, a result of the combined strength of its hydrogen bonds

28. What type of chemical bonds do we find in salt?
Hydrogen
Complex
Covalent
Ionic

29. Chemical Reactions
Occur when chemical bonds are formed, rearranged, or broken
Represented as chemical equations
Chemical equations contain:
Molecular formula for each reactant and product
Relative amounts of reactants and products, which should balance
2H + O H2O

30. Synthesis reactions Smaller particles are bonded
together to form larger,
more complex molecules.
Example
Amino acids are joined together to
form a protein molecule.
Amino acid
molecules
Protein
molecule

31. Decomposition reactions
Bonds are broken in larger
molecules, resulting in smaller,
less complex molecules.
Example
Glycogen is broken down to release
glucose units.
Glycogen
Glucose
molecules

32. Exchange reactions Bonds are both made and broken
(also called displacement reactions).
Example
ATP transfers its terminal phosphate
group to glucose to form glucose-phosphate. +
Glucose
Adenosine triphosphate (ATP) +
Glucose
phosphate
Adenosine diphosphate (ADP)

33. Rate of Chemical Reactions
Rate of reaction is influenced by:
 temperature   rate
 particle size   rate
 concentration of reactant   rate
Catalysts:  rate without being chemically changed
Enzymes are biological catalysts

34. Classes of Compounds Inorganic compounds Organic compounds
Water, salts, and many acids and bases
Do not contain carbon
Organic compounds
Carbohydrates, fats, proteins, and nucleic acids
Contain carbon, usually large, and are covalently bonded

35. Water 60% – 80% of the volume of living cells
Most important inorganic compound in living organisms because of its properties
Involved in temperature regulation
Body’s major transport medium
Protects certain organs from physical trauma

36. How many electrons can the second valence shell hold?8 2 10 7

37. Organic Compounds
Contain carbon (except CO2 and CO, which are inorganic)
Unique to living systems
Include carbohydrates, lipids, proteins, and nucleic acids

38. Carbohydrates Sugars and starches Contain C, H, and O [(CH20)n]
Three classes
Monosaccharides
Disaccharides
Polysaccharides
Major source of cellular fuel (e.g., glucose)

41. Lipids Contain C, H, O (less than in carbohydrates), and sometimes P
Insoluble in water
Main types
Neutral fats or triglycerides – energy storage
Phospholipids – cell membrane
Steroids - Cholesterol, vitamin D, steroid hormones
Eicosanoids - Prostaglandins

44. Proteins Polymers of amino acids (20 types)
Joined by peptide bonds
Contain C, H, O, N, and sometimes S and P
Proteins have 4 levels of structure
Primary, Secondary, Tertiary, Quaternary

45. Protein Synthesis + Dehydration synthesis: Hydrolysis: Peptide
Amino acid
Dipeptide
Dehydration synthesis:
The hydroxyl group of one
amino acid is bonded to
the amine group of the
next, with loss of a water
molecule.
Hydrolysis: Peptide
bonds linking amino
acids together are
broken when water is
added to the bond. +
Peptide
bond

46. Protein Structure Amino acid (a) Primary structure
The sequence of amino acids forms the polypeptide chain.
Amino acid
a-Helix: The primary chain is coiled
to form a spiral structure, which is
stabilized by hydrogen bonds.
b-Sheet: The primary chain “zig-zags” back
and forth forming a “pleated” sheet. Adjacent
strands are held together by hydrogen bonds.
(b) Secondary structure
The primary chain forms spirals (a-helices) and sheets (b-sheets).

47. Tertiary structure of prealbumin
(transthyretin), a protein that
transports the thyroid hormone
thyroxine in serum and cerebro-
spinal fluid.
(c) Tertiary structure
Superimposed on secondary structure. a-Helices and/or b-sheets are
folded up to form a compact globular molecule held together by
intramolecular bonds.

48. Quaternary structure of
a functional prealbumin
molecule. Two identical
prealbumin subunits
join head to tail to form
the dimer.
(d) Quaternary structure
Two or more polypeptide chains, each with its own tertiary structure,
combine to form a functional protein.

49. Fibrous and Globular Proteins
Fibrous (structural) proteins
Strandlike, water insoluble, and stable
Examples: keratin, elastin, collagen, and certain contractile fibers
Globular (functional) proteins
Compact, spherical, water-soluble and sensitive to environmental changes
Specific functional regions (active sites)
Examples: antibodies, hormones, molecular chaperones, and enzymes

50. Nucleic Acids DNA and RNA Contain C, O, H, N, and P
Largest molecules in the body
Contain C, O, H, N, and P
Building block = nucleotide
composed of N-containing base, a pentose sugar, and a phosphate group

51. Deoxyribonucleic Acid (DNA)
Four bases
adenine (A), guanine (G), cytosine (C), and thymine (T)
Double-stranded helical molecule in the cell nucleus
Provides instructions for protein synthesis
Replicates before cell division, ensuring genetic continuity

52. Sugar: Deoxyribose Base: Adenine (A)
Phosphate
Thymine (T)
Sugar
Phosphate
Adenine nucleotide
Thymine nucleotide
Hydrogen
bond
(a)
Deoxyribose
sugar
Sugar-phosphate
backbone
Phosphate
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
(b)
(c) Computer-generated image of a DNA molecule

53. Ribonucleic Acid (RNA)
Four bases
adenine (A), guanine (G), cytosine (C), and
uracil (U)
Single-stranded molecule mostly active outside the nucleus
Three main types of RNA carry out the DNA orders for protein synthesis
messenger RNA
transfer RNA
ribosomal RNA