Chapter 2: The Chemical Level of Organization
Chapter Outline and Objectives
HOW MATTER IS ORGANIZED
1. Identify the principal chemical elements of the human body by their names and chemical
symbols.
2. Describe each component of an atom in terms of its relative position, charge, and mass.
3. Describe valence shell electrons.
4. Define atomic number.
5. Define mass number and atomic mass/weight and how it is related to isotopes.
CHEMICAL BONDS
6. Define molecule and compound.
7. Explain the octet rule.
8. Describe an ionic bond.
9. Explain why and how an atom can lose or gain electrons, and what the resulting balance
between numbers of electrons and protons produces, as with sodium and chlorine.
10. Describe a covalent bond.
11. Distinguish between nonpolar covalent and polar covalent bonds.
12. Describe hydrogen bonds.
CHEMICAL REACTIONS
13. Define a chemical reaction.
14. Explain the differences between substrates and products of a chemical reaction.
15. Distinguish between potential and kinetic energy.
16. Compare and contrast exergonic and endergonic reactions.
17. Describe the role of catalysts/enzymes in chemical reactions.
18. Describe 4 different types of chemical reactions and give examples of each.
WATER AND SOLUTIONS
19. Explain the importance of water in living systems.
20. Explain how hydrogen bonds result in the cohesion and adhesion of water molecules and
how these properties create a high surface tension which is very important to the body.
21. Explain the reason for the high heat capacity of water.
22. Discuss the high heat of vaporization of water.
23. Discuss the properties of frozen water.
24. Explain the properties of water that make it an excellent solvent in a solution.
25. Explain the terms used to designate the constituents of a solution.
26. Define acids and bases.
27. Define pH in terms of hydrogen and base (hydroxide) ion concentration and be able to
recognize acidic and alkaline solutions in terms of pH values.
28. Define a buffer in terms of its ability to prevent large changes in [H+] due to strong acids
and bases, in addition to the general mechanism.
ORGANIC COMPOUNDS
29. Describe the functional groups of organic compounds.
30. Discuss the fact that many organic molecules are macromolecules which are polymers
formed by linking together monomers.
31. Distinguish between hydrolysis and dehydration synthesis.
Carbohydrates
32. List the major forms of carbohydrates (sugars, starches, glycogen, cellulose, and chitin),
and describe their functions.
33. Discuss what is meant by a monosaccharide.
34. Discuss how disaccharides and polysaccharides are formed.
Lipids
35. Discuss the chemical makeup and properties of lipids.
36. Discuss the properties of triglycerides and their function.
37. Discuss the properties of saturated and unsaturated fatty acids.
38. Describe the structure, and role in the body, of phospholipids.
39. Describe the structure of steroids and list members of the steroid class of lipids.
40. Discuss the lipid transport mechanism in the body.
41. Describe the structure and function of eicosanoids.
42. List the “other” lipids.
Proteins
43. Describe the basic amino acid structure, the groups of amino acids, and how amino acids
are joined to form polypeptides.
44. Describe how a chain of amino acids interacts with itself to produce the four levels of
structural organization.
45. List the functional and structural categories of proteins and members of each group.
Nucleic Acids: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA)
46. Note the two general types of nucleic acids (DNA and RNA).
47. List the components of a nucleotide.
48. List the five nitrogenous bases and whether they are in DNA or RNA or both. Explain
how the nitrogenous bases interact in DNA and RNA structure.
Adenosine Triphosphate
49. Discuss the structure and function of ATP.
Chapter Lecture Notes
Elements
Elements – cannot be reduced to simpler substances by normal chemical means (Table 2.1)
Atoms – smallest complete unit of an element
Subatomic particles – building blocks of atoms (Fig 2.1)
Protons (+)
Neutrons (neutral)
Electrons (-)
Nucleus of an atom is comprised of neutrons and protons and therefore has a + charge;
electrons (-) are attracted to the nucleus and move around the nucleus in orbitals
which are grouped into shells
1st shell – holds 2 e2nd shell – holds 8 e3rd shell – holds 8 eouter shell = valence shell (valence is = number of extra or deficient e- in outermost
shell)
Arranged in periodic table by symbols, along with atomic number and atomic mass/weight
(Fig 2.2)
Atomic number = number of protons = number of electrons (in a neutral atom)
atomic number determines which element is in question
Mass number = number of protons + number of neutrons (whole number)
mass (weight) of protons or neutrons is 1840 x larger than that of e-, so number of
electrons is ignored
Isotopes - elements with the same # of protons but a varying # of neutrons
element with the same atomic number but a different mass number
Radioisotopes – unstable isotopes that emit energetic particles
All elements with atomic number > 84 are radioactive but these elements are not
normally present in biological material
Atomic Mass (Weight) = a ratio of the average mass of isotopes of an element from a single
given sample (number with decimals)
Molecules & Compounds
Molecules - chemical combination of 2 or more atoms of one or more elements chemically
bonded together (Fig 2.5)
atoms don't have to be different
H2 is a molecule as is H2O
Compounds - 2 or more different elements joined together
Chemical Bonding
Electrons are the part of an atom that actively participates in a chemical reaction (never the
nucleus) (Fig 2.5)
Chemical behavior of atoms can be explained by behavior of electrons
Octet rule: atoms react with one another to achieve 8 e- in outer shell (except 1st shell)
Atoms with fewer than 8 electrons in valence shell may transfer or share electrons to
complete outer shell
When atoms transfer or share electrons in their valence shells, they are attracted to each other
by chemical bonds
Types of Chemical Bonding
Ions - atoms that are electrically charged either by gaining or losing electrons (Table 2.2)
Ionic bond – formed when electrons are transferred from one atom to another; the bond is
therefore the electrical attraction between 2 oppositely charged ions (Fig 2.4)
compounds containing ionic bonds readily separate (dissociate) into ions in water and are
called electrolytes because as charged particles they can conduct an electric current
examples of electrolytes are acids, bases, and salts
if outer (valence) shell has 1,2, or 3 e-, the atoms tend to lose the electron and become + ions,
which are called cations
if outer (valence) shell has 6 or 7 e-, the atoms tend to gain electrons and become – ions,
which are called anions
if outer (valence) shell has 4 or 5 e-, they don't tend to form ions; they tend to share electrons
and form covalent bonds
Covalent bond – results from sharing valence electrons (Fig 2.5)
covalent compounds tend to be nonelectrolytes
carbon has 4 electrons in outer shell and needs 4 more electrons so it normally forms
covalent bonds
More different compounds containing carbon than any other element
Nonpolar covalent - equal sharing of electrons; no charged regions (Fig 2.5a-d)
Polar Covalent - electrons are not equally shared; results in charged regions (Fig 2.5e)
water is a good example of a polar covalent compound
oxygen is more electronegative (tendency to attract electrons) than hydrogen
Hydrogen or H bonds - weak attraction between a slightly + hydrogen and a slightly - oxygen or
nitrogen
H bonds can be between molecules (intermolecular; as in water) or within molecules
(intramolecular; as in DNA and protein) (Fig 2.6)
H bonds are significantly weaker than covalent or ionic bonds
Chemical Reactions
Chemical Reactions – the making and breaking of chemical bonds (Fig 2.7)
Reactants – starting materials in a reaction
Products – ending materials in a reaction
Energy - the capacity to do work
Kinetic energy – the energy of motion
Potential energy - the energy that matter possesses because of its location or structure, stored
energy
Exergonic reaction - a reaction that proceeds with a net release of energy (Fig 2.8)
Endergonic reaction - a reaction that absorbs energy from its surroundings
Catalyst - a chemical agent that changes the rate of a reaction without being consumed by the
reaction (Fig 2.9)
lowers the activation energy needed for a reaction to occur
Enzymes - catalytic proteins (Fig 2.23)
substrate - the material or substance on which an enzyme acts
active site - area of enzyme where substrate attaches
enzyme + substrate = product + enzyme
Types of Chemical Reactions
Anabolism (Synthesis reaction) - reactions that consume energy to build complicated
molecules from simpler ones
Catabolism (Decomposition reaction) - reactions that break down complex molecules into
simpler compounds
Reversible reactions
Exchange reactions
Water
Water - extraordinary liquid because of its intermolecular hydrogen bonds
H2O has an unusually high surface tension because of collective strength of its H bonds
surface tension - measure of how difficult it is to break the surface of a liquid
pins/needles can float on water; certain insects can walk on H2O
Capillary action – H2O moves up a capillary tube or between 2 glass slides because H2O
molecules stick together
Adhesion - molecules sticking to other molecules
Water to glass
Cohesion - holding together of molecules of the same substance
Water to water
Resistance to change in temperature
temperature of water rises and falls more slowly than other liquids
the many H bonds that hold water together help water absorb heat without a change in
temperature
requires 1 calorie of heat energy to raise 1 gram of water 1° C, which is about 2x what
other covalent liquids require
Resistance to change is temperature is an advantage to organisms living in water
High water content of terrestrial plants and animals help them maintain a relatively
constant internal temperature
Has high heat of vaporization
Heat of vaporization - amount of heat a liquid must absorb for 1 gram of it to be
converted from liquid to gas
water - 540 calories
ethyl alcohol - 237 calories
acetone -125 calories
changing from liquid to gas requires that H bonds be broken
the H bonds make it difficult for molecules of water to make exodus from liquid to gas
when water evaporates it takes a lot of heat energy along with it and gives the surface a
cooling effect
evaporation of water from terrestrial plants and animals is chief way these organisms
unload excess heat and stabilize internal temperature
Freezing Water
Motion of molecules slows as temperature decreases and molecules come closer together
so that water molecules can now form H bonds with 4 other molecules
This creates an open latticework which takes up more space so water expands when it
freezes; therefore ice floats on lakes/ponds/rivers
Water freezes from top to bottom and allows life to continue beneath
Adding solutes like NaCl to water decreases the freezing point because salt interferes
with H bonding—it is a physical interference that prevents H bonds from
occurring as readily
Water is one of only a few substances that is less dense as a solid than as a liquid
Water is most dense at 4° C (water expands as temperature decreases below 4° C)
Water is a versatile solvent because of polarity of water molecule
solvent + solute = solution
polar water molecules separate ionic substances such as NaCl into ions (Fig 2.10)
polar molecules (ammonia, some proteins, carbohydrates) tend to dissolve in water
nonpolar (like fats) molecules do not dissolve well in water
H bonds act to exclude nonpolar molecules
Acids - substances that release H+ when they dissociate in water (proton donors)
strong acids - dissociate readily because of electronegativity of anion (Fig 2.11)
HCl→H+ + Clweak acids - don't dissociate readily
H2CO3→ H+ + HCO3- (only 1 % dissociation)
Bases – substances that release OH- or accept H+ when they dissociate in water (proton
acceptors)
may be strong (NaOH) or weak (amino group)
Salts – can be made chemically by an exchange reaction with a strong acid and strong
base
strong acid + strong base→ salt and H2O
pH - measure of H+ concentration (Fig 2.12 & Table 2.4)
Buffers - substances that minimize (resist) change in pH
works by accepting H+ when in excess and donating H+ when depleted
buffers are generally a mixture of weak acid and a weak base
Functional Organic Groups
Functional organic groups - regions of organic molecules most commonly involved in chemical
reactions (Table 2.5)
compounds that contain the functional groups tend to result in a polar compound that
dissolves in water
Hydroxyl – alcohols
Sulfhydryl – thiols
Carbonyl – aldehydes and ketones
Carboxyl – carboxylic acids
Ester
Phosphate
Amino - amines
Organic Compounds
Organic compounds - any substance that contains both carbon and hydrogen
Polymer - long chain of a repeating molecular unit (Fig 2.21)
monomer + monomer → polymer + H2O (dehydration synthesis = condensation)
polymer + H2O → monomer + monomer (digestion reaction = hydrolysis)
Carbohydrates
Carbohydrates (contain C, H, O) = sugars and starches (Table 2.6)
most abundant group of organic compounds in all organisms
provides most readily available source of energy
short term storage of energy in animals
Monosaccharides - generally an aldehyde or ketone with several hydroxyl groups (Fig 2.13 &
2.14)
Pentose - 5 carbon sugar
ribose/deoxyribose of RNA/DNA
Hexose - 6 carbon sugar
The following are isomers:
glucose - (aldehyde) most abundant hexose
galactose - (aldehyde)
fructose - (ketone)
Disaccharides - Monomer + Monomer = disaccharide (Fig 2.15)
sucrose =______________+_____________
maltose =_____________ + _____________
lactose = ______________ + _____________
Polysaccharides (Fig 2.16)
starches - principal storage polysaccharide in plants
potatoes, rice, grain
glucose polymer
glycogen - principal storage polysaccharide in animals
1 pound stored in liver/skeletal muscle
glucose polymer
cellulose - found in plant cell walls; the most abundant carbohydrate; digested by
protozoans in termites and bacteria in cows
constitutes fiber in our diet which stimulates goblet cells to secrete mucus
glucose polymer
chitin - in exoskeleton of arthropods and insects; in cell walls of fungus
modified glucose polymer
Lipids
Lipids - all tend to be insoluble in water (Table 2.7)
Triglycerides (neutral fats) - largest of class of lipids (Fig 2.17)
Functions
Long term storage - 1 gram of fat stores twice as much energy as 1 gram of carbohydrate
Because plants are immobile, they can function with bulky energy storage in the
form of starch. Animals, however, must carry their energy baggage with them,
so there is an advantage to a more compact storage of fuel
Protect and insulate
Structure
glycerol (monomer) + 3 fatty acids (monomers) → triglyceride
fatty acids have a carboxyl group at one end & a long hydrocarbon chain that is
hydrophobic (often 16-24 carbons long)
glycerol has 3 hydroxyl groups
glycerol’s hydroxyl groups can react with a fatty acid’s carboxyl group and form an
ester linkage
saturated fats – all bonding sites of the fatty acid are filled with hydrogen
saturated fats may cause increased deposits of cholesterol along arterial walls
animal fats - tend to be saturated and solid at room temperature
unsaturated fats - some double bonds present so not all bonding sites are filled with
hydrogen and the fatty acid has a kink in its shape, preventing solidification
plant fats (corn, canola, peanut, olive, sesame) - tend to be unsaturated and oils at
room temperature (exception - palm & coconut)
some vegetable oils are partially hydrogenated to make margarine, Crisco
shortening, peanut butter
Phospholipids - in cell membranes and membranes of organelles (Fig 2.18)
consists of glycerol + 2 fatty acids + phosphate group (- charge)
fatty acid tail - hydrophobic = insoluble in water
phosphate head - hydrophilic = soluble in water
phospholipids are arranged as a bilayer with phosphate heads toward water (outside of
bilayer in contact with aqueous (water) solutions inside and outside the cell) and the
fatty acid tails toward the interior of the membrane
Steroids (Fig 2.19)
Cholesterol
precursor from which most other steroids are synthesized
cholesterol is found in all cell membranes (keeps membranes from dissolving)
consists of 4 fused carbon rings
Sex hormones - estrogen, progesterone, testosterone
Adrenocorticotropic hormones
cortisol - needed for stress control
aldosterone - needed to regulate salt and water balance
Vitamin D
made in skin upon exposure to UV radiation
Vitamin D needed for calcium metabolism
Bile salts - aid in digestion of lipids
Lipid Transport
Cholesterol and triglycerides travel in the blood combined with protein in structures called
lipoproteins.
Lipids are insoluble in water; proteins are soluble.
Lipoproteins are synthesized in liver and contain varying amounts of triglycerides,
phospholipids, cholesterol, and protein.
The more protein, the more dense (HDL); the more lipid, the less dense (LDL)
LDL - delivery trucks - carry dietary cholesterol & newly synthesized cholesterol to cells
which have special receptors—if receptors are absent or damaged, excess
cholesterol can deposit along arterial walls, causing atherosclerosis
HDL - garbage trucks - carry excess cholesterol on one-way trip to liver for degredation
and excretion; exercise increases HDL
Eicosanoids – Prostaglandins and Leukotrienes
produced from fatty acids
mimic hormones (many different kinds with conflicting functions)
has role in blood clotting, fever, pain, and inflammation
aspirin blocks the action of an enzyme involved in prostaglandin formation; therefore,
aspirin helps control pain, fever, inflammation, reduces blood clotting
Other lipids
Vitamin A - in orange pigmented vegetables and fruits; used in vision
carotene → Vitamin A (in liver)
Vitamin E - in plant products like wheat germ/green leafy vegetables
promote wound healing and prevent scarring
prevents saturation of unsaturated fatty acids in cell membranes = antioxidant
Vitamin K - made in intestine by bacteria; needed for blood clotting
Proteins
Protein - contain C, H, O, N and some S
most abundant organic molecule class in humans (makes up 50% of dry weight)
monomer = amino acid (Fig 2.20)
20 different amino acids in proteins
polymer = protein (polypeptide chain)
amino acids are linked by peptide bonds (covalent bonds) (Fig 2.21)
Protein Structure (Fig 2.22)
Primary - unique amino acid sequence
Secondary – alpha helices and beta pleated sheets
Tertiary – hydrophobic interactions and disulfide bridges
Quaternary - aggregation of polypeptide subunits
Functional Categories of Proteins (Table 2.8)
Structural: Collagen (1/3 of protein of body), keratin, microtubules
Regulatory: Hormones
Contractile: actin and myosin in muscle
Immunological
Transport: Hemoglobin, myoglobin
Catalytic: Enzymes
Structural Categories of Proteins
Fibrous protein
Collagen = 1/3 of protein in vertebrates: in bones, cartilage, tendons, ligaments, soft
connective tissue
Keratin = hair, nails, epidermis
Globular protein
Microtubules - spindle fibers, centrioles, cilia
Enzymes - catalysts that regulate chemical reactions
Antibodies
Membrane receptors
Nucleic Acids
DNA and RNA (Fig 2.24 & Table 2.9)
monomer = nucleotide
pentose sugar (5-carbon monosaccharide) = ribose/deoxyribose
phosphate group
nitrogenous base
Pyrimidines – cytosine and thymine in DNA; uracil in RNA only
Purines – adenine and guanine
Adenine pairs with Thymine or Uracil
Cytosine pairs with Guanine
ATP - Adenosine plus three phosphate groups bonded with high energy bonds
Energy currency of the cell (Fig 2.25)