AP Bio U1
AP Bio U1
Chemistry of life
Ryan Chu
Chemistry of life
• Structure of water and hydrogen bonding
• Elements of life
• Introduction to Biological Macromolecules
• Properties of Biological Macromolecules
• Structure and Function of Biological Macromolecules
• Nucleic Acids
Water
• Water is a polar molecule, meaning the ends have opposite partial charges or
unequal distribution of charge.
• The chemical formula of water H2O tells us that a water molecule is made up of
two hydrogens and one oxygen.
• Water is polar because the hydrogens carry partial positive charges, and oxygen
has a partial negative charge, which we can examine further when we discuss
hydrogen bonding.
Hydrogen Bonding
• Hydrogen bonding (which is NOT a bond) is actually an unusually strong dipole-
dipole attraction and only occurs when hydrogen is directly bonded to F, O, or
N in a molecule.
• It occurs between these molecules because of their high electronegativity
difference and small sizes, which leads to really strong attractions.
• The hydrogen bonded to the F, O, or N is partially positively charged and is
attracted to the neighboring unshared electrons on the F, O, or N.
Water properties
• Capillary action
• Surface tension
• Cohesion and adhesion
• Solvent
• Specific heat
• Evaporative cooling
• Dissociation of Water
Water properties – Cohesion and Adhesion
• Cohesion: the attraction of water molecules.
• Strong cohesive forces are present because they form hydrogen bonds with each other.
• Adhesion: when one substance is attracted to another.
• Water adheres to other molecules and surfaces.
Water properties – Surface Tension
• Difficulty to break the surface of the water because of cohesive forces.
Water properties – Specific Heat
• pH = - log [H+]
Practice!
• Arrange the following solutions in the order of increasing acidity (least acidic to
most acidic):
• (a) pH = 9.8
• (b) pH = 1.2
• (c) pH = 4.7
• (d) pH = 6.4
Practice!
• Calculate the pH for each of the following solutions at 25 oC:
• (a) [H3O+] = 1.3 x 10-2 M
• Hydroxyl group
• H bonded to O (O-H) attached to the carbon skeleton.
• Polar
• Methanol, -ol
• Carbonyl group
• Double bond between C and O
• Aldehyde v.s. Ketone
• Carboxyl group
• Combination of carbonyl and hydroxyl
• Release H+ into solutions, acidic
Functional Groups
• Amino group
• N bonded to 2H and C
• Basic, remove H+ from solution
• Built proteins and nucleic acids
• Phosphate group
• Covalently attached to the carbon skeleton
• Acidic, release H+ into solution
• Built nucleic acids and phospholipids
• Sulfhydryl group
• S bonded to H
• Polar, Acidic, release H+ into solution
Chemical bonds
• Covalent bonds
• Ionic bonds
• Metallic bonds
Polar v.s. non-polar covalent bonds
• Nonpolar covalent bonds
• The equal sharing of electrons and distribution of charge
• Polar covalent bonds
• Unequal sharing of electrons and distribution of charge causes partial positive or partial
negative for each atom or molecule
• InTRAmolecular bonds: Covalent bonds
• InTERmolecular bonds: Hydrogen bonds
Hydrogen bonds
• Hydrogen atom bonded with an electronegative atom is attracted to another
electronegative atom.
• The ability of hydrogen to interact with Fluorine, Nitrogen, and Oxygen (FNO)
Polymers and monomers
• Polymer: a long molecule composed of many molecules bonded together
covalently. (composed of multiple monomers) (Poly-many). Out of the main
biological macromolecules, lipids, do not usually form polymers.
• Monomer: are small building block molecules that, when combined, make a
polymer. (mono-one)
Dehydration and hydration
• Dehydration
• Monomers form a polymer, condensation reaction
• Water is removed (Dehydrate = water lost)
• One donates H+ and another donates OH-
• Requires energy, endergonic reaction, builds complexity
• Hydrolysis
• Polymers break down into monomer
• H2O break down and split into H+ and OH-.
• Releases energy, exergonic reaction, reduces complexity
Properties of Biological Macromolecules
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure
Primary structure
• Simplest level of protein structure
• The sequence of amino acids in a polypeptide chain
Sickle cell anemia
• Single amino acid change
breathlessness, dizziness,
headaches, and abdominal pain.
Secondary structure
• local folded structures that form within a polypeptide due to interactions
between atoms of the backbone.
• The most common types of secondary structures
• α helix
• β pleated sheet
Secondary structure -- α helix
Secondary structure -- β pleated sheet
Tertiary structure
• The three-dimensional structure of a polypeptide
• Interactions between the R groups of the amino acids that make up the protein
• Hydrogen bonding
• Ionic bonding
• Dipole-dipole interaction
• London dispersion forces (LDFs)
• Disulfide bonds
• Hydrophobic/hydrophilic interaction
Quaternary structure
• Dehydration reaction
List three conditions under which proteins may be denatured
• Temperature
• pH
• Salt
Nucleic Acids
• Function: store hereditary info
Nucleotides: monomer of DNA/RNA
• Nucleotide = Sugar + Phosphate + Nitrogen Base
Purines Pyrimidines
•Adenine •Cytosine
•Guanine •Thymine (DNA)
•Uracil (RNA)
•Double ring •Single ring
Chargaff’s Rule
【2015-37】
• Bacteriophages are viruses that infect bacteria. In an experiment,
bacteriophages were labeled with either radioactive phosphorus or radioactive
sulfur. The labeled bacteriophages were incubated with bacteria for a brief
amount of time and then removed. The infected bacteria cells were found to
contain significant amounts of radioactive phosphorus but not radioactive
sulfur. Based on the results of the experiment, which of the following types of
molecules did the bacteriophages most likely inject into the bacteria cells?
A) Simple carbohydrate
B) Amino acid
C) DNA
D) Polypeptide
【2017-8】
• A student analyzed a viral genome and found that the genome had the
following nucleotide composition.
• • 28% adenine • 20% thymine • 35% cytosine • 17% guanine
• Which of the following best describes the structure of the viral genome?
A) Double-stranded DNA
B) Single-stranded DNA
C) Double-stranded RNA
D) Single-stranded RNA
【2015-25】
• The secondary compound cyanide (Figure 1) is a toxic, bitter-tasting chemical
that is found in apple seeds. Cyanide in seeds is only released and tasted if the
seed is crushed. When animals eat apples, they typically eat the sweet fleshy
part of the fruit and spit out the seeds or swallow them whole.
• (a) Based on the chemical structure of cyanide, identify ONE type of biological
macromolecule that could serve as a chemical precursor for the production of
cyanide in a plant. Justify your choice.
• (b) It has been proposed that apple trees are in a mutualistic relationship with
the animals who eat the apples. Describe ONE benefit to each organism in the
mutualistic relationship.
【2017-4】
• Sickle-cell anemia is associated with a mutation in the gene encoding the beta
subunit of hemoglobin that results in a change from glutamic acid to valine at
position 6. All other amino acids are identical to a normal hemoglobin
molecule.
• Based on the information above, which of the following mutations is the most
likely cause of sickle-cell anemia?
A) A single base-pair substitution in the gene encoding the beta subunit
B) A single base-pair insertion in the gene encoding the beta subunit
C) A single base-pair deletion in the gene encoding the beta subunit
D) A translocation of DNA from one chromosome to another
【2016-3】
• In the “RNA world” model for the origin of life, the first protocells (probionts)
relied on RNA, not DNA, for information storage and transmission. Which of
the following could best be considered evidence in support of the RNA world
model?
A) DNA is more stable than is RNA.
B) Some RNA molecules in contemporary cells have catalytic function.
C) RNA is so complex in both structure and function that it must have preceded DNA.
D) RNA has secondary structure whereas DNA does not.
【2015-35】
• Mutations in DNA are usually caused by chemical or radiation damage to DNA
molecules, followed by imperfect repair of the damage. Immediately after this
kind of imperfect repair, there may be a mismatched base pair in the DNA. The
illustration below shows an example of a is match, with the relevant pair bases
in bold.
• In the 1950s, the scientists Alfred Hershey and Martha Chase carried out an
experiment using bacteriophages, which are viruses that infect bacteria.
During the experiment, the scientists allowed bacteriophages that had been
labeled with either radioactive phosphorus or radioactive sulfur to infect
bacterial cells. After the infection process occurred, the scientists determined
the locations of the radioactive elements.
• After carrying out their experiment, the scientists concluded that
bacteriophages inject DNA (a type of nucleic acid), but not protein, into host
bacterial cells during infection.
• Based on the scientists’ conclusion, which of the following describes the
most likely result of the experiment?
A) Infected bacterial cells did not contain any radioactive elements.
B) Infected bacterial cells contained significant amounts of radioactive phosphorus, but not radioactive
sulfur.
C) Infected bacterial cells contained significant amounts of both radioactive phosphorus and sulfur.
D) Infected bacterial cells contained significant amounts of radioactive sulfur, but not radioactive
phosphorus.
• Which of the following best explains water's ability to dissolve certain
substances such as glucose, but remain separate from other substances such
as oils?
A) Due to hydrogen bonding, water is more dense as a liquid than a solid.
B) Water molecules can form ionic bonds with polar molecules, such as glucose.
C) Water has an overall negative charge, which allows it to easily dissolve nonpolar
substances like glucose.
D) Water molecules are polar, consisting of two partially positive hydrogen atoms, and
one partially negative oxygen atom.
• A team of virologists has isolated a nucleic acid sample from a newly
discovered virus. In order to classify the virus, they need to figure out whether
the viral nucleic acid is DNA or RNA.
• Which of the following characteristics of the nucleic acid sample would best
help classify the viral nucleic acid as DNA or RNA?
A) The nucleotides of the virus contain a five-carbon sugar.
B) The nucleotides of the virus contain uracil.
C) The nucleotides of the virus contain phosphate groups.
D) The nucleotides of the virus contain covalent bonds.
• In the reaction below, two glucose monomers combine to form the dimer
maltose.
• Which of the following best explains the process of this reaction?
A) Water is added to the reaction to promote the formation of a covalent bond between
the glucose monomers.
B) A covalent bond forms through dehydration synthesis, which results in the formation
of maltose and water.
C) To form a covalent bond, the monomers underwent a hydrolysis reaction.
D) An ionic bond forms through dehydration synthesis, which combines the two glucose
monomers and forms the maltose dimer.
• In order to develop antibiotics, scientists need to understand how bacteria
grow and reproduce. One factor that is essential for bacterial growth and
reproduction is protein synthesis. By understanding how bacteria synthesize
proteins, scientists can then attempt to develop antibiotics that block bacterial
protein synthesis during an infection.
• Which of the following questions will best direct an investigation on how to
develop an antibiotic that inhibits protein synthesis in bacteria?
A) How can the formation of covalent bonds between amino acids be blocked?
B) How can the hydroxyl end of the growing polypeptide chain be blocked?
C) How can the formation of hydrogen bonds between amino acids be blocked?
D) How can the phosphate end of the growing polypeptide chain be blocked?
• The human body is capable of digesting the complex polymer starch into
simpler subunits. This digestive process requires the presence of water and the
enzyme amylase in order to break down starch into maltose. This is depicted
below.
• Which of the following statements best describes the digestion of starch into
maltose?
A) This is a hydrolysis reaction that requires water to break
down a complex polymer into simpler subunits.
B) This is a dehydration synthesis reaction that produces
water when forming a complex polymer from simpler
subunits.
C) This is a dehydration synthesis reaction that requires
water to form a complex polymer from simpler subunits.
D) This is a hydrolysis reaction that forms water by breaking
down a complex polymer into simpler subunits.
• Consider the following molecular model.
• Based on its elemental composition, which of the following molecules does
the model most likely represent?
A) Glucose, a simple carbohydrate
B) Cytidine, a building block of the nucleic acid DNA
C) Phenylalanine, a building block of proteins
D) Cellulose, a complex carbohydrate
• Which of the following statements accurately describes a similarity between
the nucleotides of DNA and RNA?
A) The nucleotides of DNA and RNA contain the same nitrogenous bases.
B) The nucleotides of DNA and RNA contain a five-carbon sugar bonded to a phosphate
group and a nitrogenous base.
C) The nucleotides of DNA and RNA are connected through hydrogen bonds to form the
sugar-phosphate backbone.
D) The nucleotides of DNA and RNA contain the same five-carbon sugar.
• The air temperature ranges of several Southern California cities in August are
shown in the table below.
A) The cohesive tendency of water molecules causes high surface tension, so heat is
unable to penetrate the top layer of the ocean and escape into the air.
B) Because water is less dense as a solid than as a liquid, it easily vaporizes, causing
excess heat to escape into the air near coastal cities.
C) The adhesive properties of ocean water allow the water molecules to stick to one
another, preventing temperature change of the air above it.
D) The high heat capacity of water allows the ocean to moderate the temperature of
nearby air and land.
Distance from Pacific Average daily Average nightly
City
Ocean (km) temperature (∘C) temperature (∘C)
San Diego <1 25 22
Santa Ana 25 29 17
Palm Springs 181 42 25
• A researcher wants to identify a newly isolated DNA strand. The first step in
identifying the DNA strand is to measure its length. To do this, the researcher
wants to develop a fluorescent tag that emits light once it binds to both ends
of the strand.
• Which of the following best describes how the researcher should develop a
fluorescent tag with an ability to bind to both ends of the strand?
A) The tag should have an affinity to bind only adenine (A) and thymine (T) nitrogenous
bases.
B) The tag should have an affinity to bind only free amino (–NH2) and carboxyl (–COOH)
functional groups.
C) The tag should have an affinity to bind only guanine (G) and cytosine (C) nitrogenous
bases.
D) The tag should have an affinity to bind only free 3’ hydroxyl (–OH) and 5’ phosphate (–
PO4) functional groups.
• Human immunodeficiency virus (HIV) is classified as an RNA virus because its
genome, or genetic material, consists of a single strand of RNA.
• Which of the following claims is best supported by the information above?
A) Deoxyribose is a five-carbon sugar within the nucleic acid structure of HIV.
B) The structure of HIV forms a double-stranded nucleic acid.
C) Uracil nucleotides are present in the HIV genome.
D) The nucleotides of HIV form an antiparallel nucleic acid structure.
• Most species of shark are strict carnivores. However, bonnethead sharks
(Sphyrna tiburo) have been observed consuming seagrass within their natural
habitat. Like other plants, seagrasses contain cellulose within their cell walls.
• Based on the information above, which of the following best supports the
claim that bonnethead sharks are capable of hydrolyzing cellulose during
digestion?
A) Cellulose is consumed as a linear polysaccharide and is broken down into glucose
monosaccharides during digestion.
B) Cellulose is consumed as a linear polysaccharide and is converted into branched
glucose monosaccharides during digestion.
C) Cellulose is consumed as glucose monosaccharides and is converted into a linear
polysaccharide during digestion.
D) Cellulose is consumed as a linear polysaccharide and remains as a linear
polysaccharide during digestion.
• Which of the following diagrams shows the most likely way that two water
molecules will bond with each other?
• Based on the reaction depicted below, which of the following statements is
true?
A) The reverse of this reaction requires the addition of water in order to build the dimer.
B) If water is not added to the reaction, dehydration synthesis will not occur.
C) If water is not added to the reaction, hydrolysis will not occur.
D) The reverse of this reaction requires the removal of water from the reaction in order
to break down the dimer.
• A scientist grew Chlorella, a single-celled photosynthetic algae, for 3 weeks in a
laboratory culture. The culture medium contained dissolved carbon dioxide
and other nutrients.
• At the beginning and end of the 3-week period, the scientist measured the
rate of synthesis for certain biological molecules. The results are shown in the
following graph.
• Based on the experimental results, which of the following is most likely true
about the Chlorella culture medium?
A) The culture medium contained a sufficient level of phosphates, but
lacked nitrogen-containing compounds.
B) The culture medium contained a sufficient level of nitrogen-
containing compounds, but lacked phosphates.
C) The culture medium contained both nitrogen-containing
compounds and phosphates.
D) The culture medium lacked both nitrogen-containing compounds
and phosphates.
• The following excerpt describes a potential origin of the first living cells on
earth.
• We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell
membrane that defines a spatially localized compartment, and an informational polymer that allows for the
replication and inheritance of functional information.
• Schrum, J. P., Zhu, T. F., & Szostak, J. W. (2010). The Origins of Cellular Life. Cold Spring Harbor Perspectives in
Biology, 2(9), a002212. http://doi.org/10.1101/cshperspect.a002212
• Based on this excerpt, which of the following questions would best direct an
investigation on whether the "informational polymer" is DNA or RNA?
A) Which purines are present in the structure of the informational polymer?
B) Which phosphate group is present in the structure of the informational polymer?
C) Which functional groups are located at the 3’ and 5’ ends of informational polymer?
D) Which five-carbon sugar is present in the structure of the informational polymer?
• Bodies of water, such as ponds, freeze from top to bottom, forming a floating
sheet of ice. This can help aquatic organisms survive during cold winter
months.
• Which of the following statements explains why the ice floats on the surface
of the pond?
A) The ice molecules have higher kinetic energy than the liquid water molecules, causing
them to float.
B) The increased number of hydrogen bonds in ice compared to liquid water causes the
water molecules in ice to be closer together
C) The crystalline structure of solid ice makes it less dense than liquid water.
D) As water freezes, ionic bonds form between water molecules, preventing the ice from
sinking below the surface.
• In order to develop antibiotics, scientists need to understand how bacteria
grow and reproduce. One factor that is essential for bacterial growth and
reproduction is protein synthesis. By understanding how bacteria synthesize
proteins, scientists can then attempt to develop antibiotics that block bacterial
protein synthesis during an infection.
• Which of the following questions will best direct an investigation on how to
develop an antibiotic that inhibits protein synthesis in bacteria?
A) How can the 5’ end of the growing polypeptide chain be blocked?
B) How can the carboxyl (–COOH) terminus of a growing polypeptide chain be blocked?
C) How can the 3’ end of the growing polypeptide chain be blocked?
D) How can the amino (–NH2) terminus of a growing polypeptide chain be blocked?
• The following table shows the relative percentages of elements in a certain
biological molecule.
Element Percentage of total
Carbon (C) 54%
Nitrogen (N) 17%
Phosphorus (P) 0%
Oxygen (O) 21%
Sulfur (S) 1%
Hydrogen (H) 7%
• Which of the following best describes the biological molecule?
A) The molecule is a phospholipid.
B) The molecule is a complex carbohydrate.
C) The molecule is a nucleic acid.
D) The molecule is a protein.