This document provides information on basic chemistry concepts including nitrogen, heat, solutions, acids and bases, organic chemistry, biochemistry, and techniques for purifying organic compounds. Key points covered include properties of nitrogen gas, definitions of heat and temperature, how to calculate solution concentrations, characteristics of acids and bases, classes of organic molecules and reactions, main types of biomolecules, and methods for recrystallization and distillation. Multiple choice and open-ended questions are included for practice applying the concepts.

1. Basic Chemistry in Biology

2. Quiz: True or False
• The valence electron of N is 5.
1. N2 has covalent bonds.
2. N2 has double bonds.
3. N2 is polar.
4. The observation “N2 + 3H2  2NH3” is
quantitative.
5. N2 and H2 can form hydrogen bonds.

3. Heat
• Kinetic energy is the energy of motion.
• Heat or thermal energy is the total kinetic
energy of any matter due to motion of its
molecules.
• Temperature measures the heat intensity or
the average kinetic energy of the molecules.
• Temperature may be measured by the Celsius
scale, Fahrenheit scale, and Kelvin scale.
• Conversions: °F=(9/5)(°C)+32, °C=(5/9)(°F-32),
K=°C-273.15, °C=K+273.15

4. Question
• Convert the following temperatures to the
respective scales.
1. 50°C to °F
2. 113°F to °C
3. 25°C to K
4. 122°F to K

5. Heat
• A calorie is the amount of heat it takes to raise
the temperature of 1g of water by 1°C.
• A kilocalorie (1000 calories) is the amount of
heat required to raise the temperature of 1kg
of water by 1°C.
• Conversions: 1 joule (J)=0.239cal, 1cal=4.184J
• Specific heat is the amount of heat that must
be absorbed or lost for 1g of a substance to
change its temperature by 1°C.

6. Heat
• Heat of vaporization is the quantity of heat a
liquid must absorb for 1g of it to be converted
from the liquid to the gaseous state.
• The molecules with the most kinetic energy
evaporate, leaving the molecules with less
kinetic energy, a phenomenon known as
evaporative cooling.

7. Solution
• A solution is a homogeneous liquid mixture of
two or more substances.
• The dissolving agent is the solvent, while the
substance being dissolved is the solute.
• Hydrophilic substances have an affinity for
water, while hydrophobic substances do not
have an affinity for water.
• A colloid is a stable suspension of particles in a
liquid.

8. Calculating Solution Concentration
• Molecular mass of a compound is the sum of
the atomic masses of the atoms in the
molecule.
• 1 mole (mol)=6.02x1023 molecules
• Molarity(M) is the number of moles solute per
liter of solution.

9. Question
• Calculate the amount of NaCl needed to
produce 1M of a 1L solution. (Na=23g,
Cl=35.5g)
• Solution: 1M=1mol/1L by definition.
• (1mol/1L)(1L)=1mol of NaCl
• Molecular mass of NaCl: 23+35.5=58.5g/1mol
• (1mol)(58.5g/1mol)=58.5g NaCl

10. Question
• Devise a method to separate sand and salt.
• Solution: Put the mixture in water. Salt should
dissolve in water, while the sand will not. Filter
the solution to remove the sand, and
evaporate the water to recover the salt.

11. Acids and Bases
• An acid increases the hydrogen ion (H+)
concentration of a solution.
• A base decreases the hydrogen ion
concentration of a solution, typically by
forming the hydroxide ion (OH-).
• The pH scale measures the acidity or basicity
of a substance and ranges from a value of 0 to
14.
• pH= -log[H+]

12. Acids and Bases
• pH values less than 7 are acidic, pH values
greater than 7 are basic, and pH value equal to
7 is neutral.
• A buffer is a substance that minimizes changes
in H+ or OH- concentrations in the solution.
• Acidity and basicity may be tested by using
litmus paper, pH paper, or pH meter.

13. Acids and Bases
• Red litmus paper will turn blue under basic
conditions, while blue litmus paper will turn
red under acidic conditions.
• pH paper will give an approximation of the
closest whole number of the pH of the
solution by color.
• pH meter will give exact pH to one decimal
point.

14. Question
• Identify the following as acidic, neutral, or
basic.
1. Solution A turns red litmus paper blue.
2. Solution B has pH 3.

15. Question
0
5
10
15
20
25
30
35
40
45
100 200 300 400
Calciumcarbonateprecipitation
(ppb)
Carbonate concentration (ppm)
• Suppose that the
following is data based
on the calcification of
ocean coral reefs. The
carbonate ion reacts
with calcium ions to
precipitate as calcium
carbonate. What can be
concluded from this
graph?

16. Question
• It is known that H+ reacts with carbonate ion
to form water and carbon dioxide. Based on
the simulated graph given, explain how ocean
acidification will affect calcification of the
coral reefs.

17. Setting Up an Experiment
• Negative controls are the controls under normal
conditions or the controls that are known to test
negative under the variables to be tested.
• Positive controls are the controls that are known
to test positive under the variables to be tested.
• Independent variables are the variables that are
fixed but being tested in the experiment.
• Dependent variables are the variables that will
vary in the experiment due to the independent
variable.
• Positive and negative controls are not always
available for an experiment, but they should be
included whenever possible.

18. Question
• Devise a method to test whether a certain
plant will grow optimally in basic conditions.
• Solution: Select at least three plants, and plant
one in acidic conditions, one in neutral
conditions, and one in basic conditions.
• Measure the length of the plant daily, and also
note the health of the stems and leaves.

19. Question
• In the previous question, identify the positive
and negative controls (if present), and identify
the dependent and independent variables.
• Positive control: None
• Negative control: Plant in neutral conditions
• Dependent variable: Length of plant, health of
stems and leaves
• Independent variable: Acidic/basic conditions

20. Organic Chemistry
• Organic chemistry is the branch of chemistry that
studies carbon-containing compounds.
• Organic molecules vary by the number of carbons
(length of the molecule), branching, position of
double bonds, and presence of rings.
• Hydrocarbons are organic molecules containing
only carbon and hydrogen.
• Carbon, in the absence of double or triple bonds,
forms a tetrahedral shape with other atoms when
its valence shell is complete.
• Most organic molecules are hydrophobic.

21. Isomers
• Isomers are compounds with the same chemical
formula but with different structure and
properties.
• Structural isomers differ in the arrangement of
the atoms.
• Geometric isomers (cis-trans and E-Z) differ in the
spatial arrangement about a double bond.
• Enantiomers are mirror images of each other and
differ in the arrangement about an asymmetric
carbon (carbon attached to four different atoms).
• Enantiomers are important in pharmaceutical
industry as one enantiomer may be an effective
drug, while the other is not.

22. Question
• Draw the 3 isomers of C5H12.
• How many isomers does C6H14 have?
CH3 CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3 CH3
CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3

23. Cis-Trans/E-Z
• Cis isomers have the same molecule on the
same side of the double bond.
• Trans isomers have the same molecule on
opposite sides of the double bond.
• E isomers have the heavier molecules on
opposite sides of the double bond.
• Z isomers have the heavier molecules on the
same side of the double bond.

24. Question
• Identify the following as cis, trans, E, or Z.
CH3
H
H
CH3
CH3 CH3
H H
F
CH3
Br
Cl
CH3
F Cl
Br

25. R-S Enantiomers
• Dashes indicate projection behind the plane,
while wedges indicate projection toward you.
1. Put the lightest molecule behind the plane. The
other three molecules will be on the plane.
2. If the rotation from lightest to heaviest molecule
of the three remaining molecules is clockwise,
the configuration is R.
3. If the rotation from lightest to heaviest molecule
is counterclockwise, the configuration is S.

26. Question
• Identify the following as R or S.
Cl
CH3
Br
F
O
CH3
SH
NH2
CH3

27. Functional groups
• Functional groups are groups attached to organic
molecules that are chemically reactive.
• The important functional groups are hydroxyl (-
OH), carbonyl (-CO), carboxyl (-COOH), amino (-
NH2), sulfhydryl (-SH), phosphate (-OPO3
2-), and
methyl (-CH3).
• Carboxyl groups act as acids, while amino groups
act as bases.
• Except for the methyl group, functional groups
make organic molecules hydrophilic. The more
functional groups, the more hydrophilic.

28. Question
• Identify the functional group(s) in the
molecules.
CH3
O
NH2
O
OH
SH
O
P
O
O
-
O
-OH
NH2
O
OH

29. Technique: Purification of Organic
Compounds
A. Recrystallization
1. A solvent is chosen that will dissolve the
compound at high temperatures but not at low
temperatures.
2. The solvent is heated to dissolve the compound
of interest.
3. Any insoluble impurities are then filtered out of
the solution.
4. The compound will then crystallize out of the
solution once the solvent cools down, leaving
the soluble impurities in the solution.

30. Technique: Purification of Organic
Compounds
B. Distillation
1. The compound of interest has a lower boiling
point than the impurities.
2. Using an instrument known as condenser, the
compound is boiled at a certain temperature to
evaporate as gas, which then condenses back to
liquid as it passes through the condenser.
3. The impurities are not boiled off and remain in
the original solution.

31. Biochemistry
• Biochemistry is the chemistry of molecules
associated with biology.
• Macromolecules are large organic molecules.
• Polymers are long molecules consisting of similar
or identical building blocks called monomers
linked by covalent bonds.
• Four types of molecules are important in
biochemistry: lipids, proteins, nucleic acids, and
carbohydrates. Only lipids are not polymers.

32. Polymer Reactions
• Enzymes are specialized macromolecules that
speed up chemical reactions.
• Dehydration reaction occurs when two
molecules become covalently bonded to each
other due to loss of a molecule of water.
• Hydrolysis occurs when two molecules lose
their covalent bonding by the addition of a
molecule of water.

33. Carbohydrates
• Carbohydrates are sugars or polymers of
sugars and contain carbonyl and hydroxyl
groups.
• Monosaccharides or simple sugars are the
monomers.
• Disaccharides contain two monosaccharides
joined by a covalent bond known as a
glycosidic linkage as a result of a dehydration
reaction.
• Polysaccharides are the polymers.

34. Monosaccharides
• Monosaccharides may be classified as aldoses
and ketoses depending on the location of the
carbonyl group.
• Monosaccharides may be classified as trioses,
pentoses, or hexoses depending on the
number of carbons present.

35. Question
• Identify the following as triose, pentose, or
hexose.
1. C5H10O5
2. C3H6O3
3. C6H12O6

36. Polysaccharides
A. Storage polysaccharides
1. Starch is a polymer of glucose found as
granules in plastids of plants.
a. Amylose is a form of starch that is
unbranched.
b. Amylopectin is a form of starch that is
branched.
2. Glycogen is a polymer of glucose found in
muscle and liver cells of animals.

37. Polysaccharides
B. Structural polysaccharides
1. Cellulose is a polymer of glucose found in cell
walls of plants.
-Some microorganisms (bacteria, protists, fungi)
can digest cellulose, but animals cannot.
2. Chitin is a polymer found in the exoskeleton
of arthropods and the cell walls of fungi.
-An exoskeleton covers the soft parts of
arthropods.

38. Question
• Herbivorous animals mainly eat plants as their
diet. Explain how they are able to digest
cellulose.
• Solution: Their digestive system contains
microorganisms that can digest cellulose.

39. Lipids
• Fats, triacylglycerols, or triglycerides are
constructed from glycerol and three fatty
acids.
• Phospholipids are constructed from glycerol,
two fatty acids, and a phosphate group and
are found in cell membranes.
• Steroids contain four fused rings.
• Cholesterol is a steroid that is found in animal
cell membranes and blood and synthesized in
the liver or obtained from the diet.

40. Fats
• A fatty acid contains about 16-18 carbons and a
carboxyl group.
• Glycerol has three carbons, all with hydroxyl
groups.
• The carboxyl group of the fatty acid reacts with
the hydroxyl group of the glycerol through a
dehydration reaction to form an ester linkage.
• Saturated fats have no double bond and are
solids at room temperature.
• Unsaturated fats or oils have one or more double
bonds and are liquids at room temperature.
• The major function of fats is energy storage.