Basic Chemistry in Biology

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.

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

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

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.

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.

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.

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.

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

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.

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+]

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.

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.

Question

• Identify the following as acidic, neutral, or basic.

1. Solution A turns red litmus paper blue.

2. Solution B has pH 3.

Question

0

5

10

15

20

25

30

35

40

45

100 200 300 400

Cal

ciu

m c

arb

on

ate

pre

cip

itat

ion

(p

pb

)

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?

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.

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.

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.

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

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.

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.

Question

• Draw the 3 isomers of C5H12.

• How many isomers does C6H14 have?

CH3 CH3CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3 CH3

CH3CH3 CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

CH3

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.

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

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.

Question

• Identify the following as R or S.

ClCH3

BrF

O

CH3

SH

NH2

CH3

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.

Question

• Identify the functional group(s) in the molecules.

CH3

O

NH2

O

OH

SH

O

P

O

O-

O-OH

NH2

O

OH

Technique: Purification of Organic Compounds

A. Recrystallization1. 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.

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.

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.

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.

Carbohydrates

• Carbohydrates are sugars or polymers of sugars and contain carbonyl and hydroxyl groups.

• Monosaccharides or simple sugars are the monomers.

• Disaccharides contain two monosaccharidesjoined by a covalent bond known as a glycosidic linkage as a result of a dehydration reaction.

• Polysaccharides are the polymers.

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.

Question

• Identify the following as triose, pentose, or hexose.

1. C5H10O5

2. C3H6O3

3. C6H12O6

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.

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.

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.

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.

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.