CH2

p.31
1 Sketch a diagram of a water molecule and indicate the ends that bear partial
positive and negative charges.

Ans：

2 Compare hydrogen bonding in ice and in liquid water.

Ans：liquid H2O：neighboring H2O molecules orient themselves so that O-H bond of
1 H2O molecule points toward one of the e- pairs of other H2O
molecule.

Ice：each H2O molecule is tetrahedrally surrounded by 4 nearest neighbors

to which it is H bonded.
3 Which of the functional groups listed in Table 1-2 can function as hydrogen bond
donors? As hydrogen bond acceptors?
Ans：Donors：usually H on the strong electronegative atom (e.g. N, O, F).

Acceptors：any lone pair present on O or N in the carbonyl, ether, hydroxyl,

amino, imino & nitrile groups.
ether
4 Describe the nature and relative strength of covalent bonds, ionic interactions, and
van der Waals interactions (hydrogen bonds, dipole–dipole interactions, and London
dispersion forces).
Ans：Covalent bonds：the sharing of electron pairs between atoms.
Ionic interaction：the attraction of ions or molecules with full permanent
charges of opposite signs.
 van der Waals interactions：noncovalent associations between neutral
molecules
H bonds：A largely electrostatic interaction between a weakly acidic donor
group such as O─H or N─H and a weakly basic acceptor atom
such as O or N.
Dipole–dipole interactions：when 2 dipolar molecules interact with each
other through space.
London dispersion forces：The weak attractive forces between electrically
neutral molecules in close proximity, which arise
from electrostatic interactions among their
fluctuating dipoles.

5 What is the relationship between polarity and hydrophobicity?

Ans：─water is polar molecule
─because H2O is polar, polar molecule interact well with it
─nonpolar do not like polar molecules (hydrophobic)
6 Explain why polar substances dissolve in water while nonpolar substances do not.
(i.e., hydration)
Ans：H2O is a polar solvent. It has high dielectric constants, able to weaken the
attraction forces between oppositely charged ions, therefore hold the ions
apart.
An ion immersed in polar solvents attracts oppositely charged ends of the
solvent dipoles.

7 What is the role of entropy in the hydrophobic effect?

Ans：Entropy, or “randomness,” is a measure of the order of a system. If entropy
 increases when a nonpolar molecule leaves an aqueous solution, entropy must
decrease when the molecule enters water. The entropy changes must arise
mainly from ordering of the water itself.
─The aggregation of the nonpolar groups minimizes the surface area of the
cavity
─therefore maximizes the entropy of the entire system.
8 Explain why amphiphiles form micelles or bilayers in water.
Ans：Amphiphile have both polar (or charged) and nonpolar segments, therefore
simultaneously hydrophilic and hydrophobic. Water hydrate the hydrophilic
portion, exclude the hydrophobic portion.
Amphiphiles form structurally ordered aggregates.

In both micelles and bilayers, the aggregate

is stabilized by the hydrophobic effect, the
tendency of water to exclude hydrophobic
groups.
9 How does osmosis differ from diffusion? Which process occurs during dialysis?
Ans：osmosis：─net movement of solvent across the membrane from a region of
high concentration (pure water) to a region of relatively low
concentration (water containing dissolved solute)
diffusion：─the tendency for solutes to diffuse from an area of high
concentration to an area of low concentration
─fill up container
dialysis：diffusion of solutes
10 Describe the osmotic challenges facing a cell placed in pure water or in a high-salt
solution.
Ans：pure water
─will have H2O coming into cell to try to dilute the content of the cell
─will cause lyse/burst
high-salt solution
─environment has ↑ concentration than contents of cell, water inside the cell
will transfer out.
 ─cause cell to shrivel
p.39
1 What are the products of water’s ionization? How are their concentrations related?
Ans：─ H2O ⇌ H3O+ + OH−
hydronium hydroxide
ion ion
─concentration of the undissociated H2O > concentrations of its component
ions
─[H2O] is considered constant
Kw= [H3O+][OH−]→ the ionization constant of water
2 Predict the pH of a sample of water if Kw were 10−10 or 10−20.
Ans：Kw= [H3O+][OH−], pH=-log [H3O+]
X=[H3O+]
X2=10-10 X2=10-20
X=[H3O+]=10-5 X=[H3O+]=10-10
pH=-log 10-5=5 pH=-log 10-10=10
3 Describe how to calculate pH from the concentration of H+ or OH−.
Ans：Kw= [H3O+][OH−], [H3O+]≒[OH−]
pH=-log [H3O+]
4 Compare the Arrhenius and Bronsted Lowry definitions of acids and bases
Ans：Arrhenius
─acid：dissociates in H2O to form H+
─base：dissociates in H2O to form OH−
Bronsted Lowry
─acid：substance that can donate a proton
─base：substance that can accept a proton
5 Explain why a 1M solution of HCl has a pH of 0.
Ans：HCl ⇌ H3O+ + Cl−
[H3O+]=1, pH=-log 1=0
HCl is a strong acid, we can assume that it ionizes completely
[H3O+] at equil=initial [HCl]
6 Explain why it is more complicated to calculate the pH of a solution of weak acid or
base than to calculate the pH of a solution of strong acid or base.
Ans：they are only partially ionized in aqueous solution
7 List some uses for the Henderson-Hasselbalch equation.
[A− ]
Ans：pH = pK + log
[HA]
─the pH of a solution containing known quantities of a weak acid and its
 conjugate base
─to determine the amount of acid & conjugated base needed to make buffer
of certain pH.
8 What must a buffer solution include in order to resist changes in pH on addition of
acid or base?
Ans：─acidic component, HA, to neutralize OH-
─basic component, A-, to neutralize H+
→weak acid + conjugated base
9 Why is it important to maintain biological molecules in a buffered solution?
Ans：─to stimulate the properties of naturally occurring biological fluid
─maintain fairly constant internal environment

CH3
p.45
1 Identify the purines and pyrimidines commonly found in nucleic acids.
Ans：Purines

Pyrimidines
2 Draw the structures of adenine, adenosine, and adenylate. (The topic of the quiz)

Ans：
3 Differentiate between a ribonucleoside triphosphate and a deoxyribonucleoside
monophosphate. (The topic of the quiz too)
Ans：ribonucleoside triphosphate

deoxyribonucleoside monophosphate

p.50
1 Using Fig. 3-3a as a guide, draw the complete structure of a nucleoside
triphosphate before and after it becomes incorporated into a polynucleotide chain.
Draw the structure that would result if the newly formed phosphodiester bond were
hydrolyzed.
Ans：before

after
 formed phosphodiester bond were hydrolyzed

2 Explain the structural basis for Chargaff’s rules. (p47 & 49)
Ans：─Describe the Base Composition of DNA.
─DNA has equal numbers of adenine and thymine residues (A = T) and equal
numbers of guanine and cytosine residues (G = C).
─structural basis for the rules derives from DNA’s double-stranded nature.
3 Using a three-dimensional computer model of the DNA molecule, identify each of
the following structural features: the 3’ and 5’ end of each strand, the atoms that
make up the sugar-phosphate backbone, the major and minor grooves, the bases in
several base pairs, and the atoms that participate in hydrogen bonding in A · T and
G · C base pairs.
Ans：
4 Describe the Watson-Crick model of DNA. (p48-49)
Ans：─Two polynucleotide chains form a double helix.
─The two strands of DNA are antiparallel
─The surface of the double helix contains the major and minor grooves.
─A=T, C≣G complementary base pairing
p.53
1 Explain why the double-stranded nature of DNA is relevant for copying and
transmitting genetic information when a cell undergoes division (p51-52; Figure 3-11)
Ans：─Each DNA molecule consists of one parental strand and one daughter strand.
─Each strand of parental DNA acts as a template for the synthesis of a
complementary daughter strand.
─Daughter strands are synthesized by the stepwise polymerization of
nucleotides that specifically pair with bases on the parental strands.
─Thus, the resulting double-stranded molecules are identical.
2 Summarize the steps of the central dogma. What role does RNA play in each? (p52-
53)
Ans：

─The link between DNA and enzymes is RNA.

 ─The DNA of a gene is transcribed to produce an RNA molecule that is
complementary to the DNA.
─The RNA sequence is then translated into the corresponding sequence of
amino acids to form a protein.

p.66
1 Explain how restriction enzymes generate either sticky ends or blunt ends.
Ans：

2 How do the smallest fragments of DNA move the farthest during electrophoresis?
Ans：For molecules with a relatively homogeneous composition (such as nucleic
acids), shape and charge density are constant, so the velocity depends
primarily on size. Smaller molecules move more rapidly through the gel and
therefore migrate farther in a given time.
3 List all the components and explain their purpose in the reaction mixture used for
the dideoxy DNA sequencing method.
Ans：─DNA template：supply model of replication
─DNA polymerase I：make complementary copies of the single-stranded DNA
being sequenced.
─primer：initiated Replication, complementary to the 3’ end of the template
DNA, becomes the 5’ end of the new strand.
 ─the four dNTP substrates：pair with bases on the template strand and are
joined to the growing polynucleotide strand in
the 5’ → 3’ direction.
─four fluorescently labeled 2’,3’-dideoxynucleoside triphosphate(ddNTP)：
terminating chain growth, identified according to its laser-stimulated
fluorescence.
4 What proportion of the human genome is transcribed? Translated? (p63)
Ans：─At least 80% of the genome is transcribed to RNA.
─Only ∼1.2% of the genome encodes protein.
5 Summarize what is known about the size and gene content of the human genome.
(p63)
Ans：─About half the human genome consists of repeating sequences of various
types.
─appears to contain only ∼21,000 protein-encoding genes(open reading
frames (ORFs))
─over 3 million genes
─any two people are likely to be ∼99.9% genetically identical.
6 Explain how evolution can result from mutations in DNA. (p63-64)
Ans：─The mispairing of bases during DNA replication can introduce single-
nucleotide errors known as point mutations in the daughter strand
─DNA damage by chemicals or radiation
─Faulty recombination (exchange of DNA between chromosomes)
─The transposition of genes within or between chromosomes
─When a mutated gene is transcribed and the messenger RNA is
subsequently translated, the resulting protein may have properties that confer
some advantage to the individual.
p.76
1 Summarize the steps required to amplify a given segment of DNA in vivo and in
vitro. (p66)
Ans：1. A fragment of DNA of the appropriate size is generated by a restriction
enzyme, by PCR (Section 3-5C), or by chemical synthesis.
2. The fragment is incorporated into another DNA molecule known as a vector,
which contains the sequences necessary to direct DNA replication.
3. The vector—with the DNA of interest—is introduced into cells, in which it is
replicated.
4. Cells containing the desired DNA identified, or selected.
2 Compare the properties of cloning vectors such as pUC18, bacteriophage λ, and
BACs. (p67)
Ans：pUC18：the circular plasmid contains multiple restriction sites
bacteriophage λ：the recombinant DNA is produced in large amounts in easily
purified form.
BACs：for larger DNA segments
3 Describe the activities of the enzymes required to construct a recombinant DNA
molecule. (Fig. 3-26, p69)
Ans：─restriction endonuclease cut vector & foreign DNA
─DNA ligase join stick ends of vector & foreign DNA fragment
4 Explain how cells containing recombinant DNA are selected. Please use pUC18 and
λDNA vectors as the examples. (p68-70)
Ans：pUC18：encodes the enzyme β-galactosidase, which cleaves the colorless
compound X-gal to a blue product

λDNA：
5 What is a DNA library and how can it be screened for a particular gene? (p70-71)
Ans：─DNA library：The cloned set of all DNA fragments from a particular
organism
─by a process known as colony or in situ hybridization
6 What are the advantages of PCR over traditional cloning? (p71-72)
Ans：─faster and more convenient method for amplifying a specific DNA.
─each doubling the amount of the target DNA
─without prior DNA purification
─only need small amount
7 Describe the challenges of expressing a eukaryotic gene in a prokaryotic host cell.
(p72)
Ans：─many eukaryotic genes are large and contain stretches of nucleotides
(introns).
─bacteria lack the machinery to excise the introns.
─many eukaryotic proteins are posttranslationally modified by the addition of
carbohydrates or by other reactions.
8 Explain how site-directed mutagenesis can be used to produce an altered protein in
bacterial cells. (p73-74)
Ans：

9 What is the difference between manipulating a gene for gene therapy and for
producing a transgenic organism? (p74-76)
Ans：gene therapy
 ─the transfer of new genetic material to the cells of an individual to produce a
therapeutic effect.
─be not heritable
transgenic organism
─a genetically modified organism whose genetic material has been altered
using genetic engineering techniques.
─the change to be heritable
CH4
p.88
1 Describe the overall structure of an amino acid and identify itsαcarbon and its
substituents.

Ans：

2 Classify the 20 standard amino acids by polarity, structure, type of functional

group, and acid–base properties.
Ans：─nonpolar：Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine,
Proline, Phenylalanine, Tryptophan
─uncharged polar：Serine, Threonine, Asparagine, Glutamine, Tyrosine,
Cysteine
─charged polar：Lysine, Arginine, Histidine, Aspartic acid, Glutamic acid
3 Draw a Cys–Gly–Asn tripeptide. Identify the peptide bond and the N- and C-
termini, and determine the peptide’s net charge at neutral pH.
Ans：

4 Draw the structure of pentapeptide Glu-Ser-Cys-Lys-Asp. Identify the peptide

bonds, amino acid residues, and the N- and C-termini of this polypeptide.
Ans：
5 Why do the pK values of ionizable groups differ between free amino acids and
amino acid residues in polypeptides? (p86-87)
Ans：amino acid residues
─in the interior of a polypeptide chain do not have free α-amino and
α-carboxyl groups that can ionize
• Draw the structures of the 20 standard amino acids and give their one- and
three-letter abbreviations

p.91
1 Describe why all the amino acids except for glycine are chiral.
Ans：─chiral：have 4 different substituents

∵It has 2 H group

∴non chiral
2 Identify all the chiral carbons in the amino acids shown in Table 4-1.
Ans：
3 Explain how the Fischer convention describes the (relative) absolute configuration
of a chiral molecule.
Ans：horizontal lines represent bonds that extend above the page and vertical lines
represent bonds that extend below the page.

4 Discuss why an enzyme can catalyze a chemical reaction involving just one
enantiomer of a compound. (p90)
Ans：─because most biological molecules are chiral
─molecule present in a single enantiomeric form—will bind to or react with
only a single enantiomer of another compound
p.94
1 List some covalent modifications of amino acids in proteins. (p92)
Ans：
2 Cover the labels in Figs. 4-14 and 4-15 and identify each parent amino acid and the
type of chemical modification that has occurred.
Ans：

3 Discuss important functions of amino acid derivatives. (P92-94)

Ans：─to function independently
─for the function of the protein
─function as chemical messengers with amino acid for communication
between cells

CH5
p.99
1 Explain why polypeptides have such variable sequences.
Ans：─there are 20 different amino acid
─For a protein of n residues, there are 20n possible sequences.
2 What factors limit the size and compositions of polypeptides? (P98-99)
Ans：─40 residues is minimum for the polypeptide chain to fold into a discrete and
stable shape that allows it to carry out a particular function.
 ─ > 1000 residues may approach the limits of efficiency of the protein
synthetic machinery
─The longer the polypeptide, the more likely to introduce error.
─The 20 standard amino acids do not appear with equal frequencies in
proteins.
─each amino acid residue has characteristic chemical and physical properties,
its presence at a particular position in a protein influences the properties of
that protein.
p.109
1 List some factors that influence the stability of purified proteins. (p100-101)
Ans：(1)pH
─Biological materials are routinely dissolved in buffer solutions effective in
the pH range over which the materials are stable.
─Failure to do so could cause their denaturation (structural disruption)
(2)Temperature
─The thermal stability of proteins varies.
─some proteins denature at low temperatures, most proteins denature at
high temperatures
(3)Presence of degradative enzymes.
─Destroying tissues to liberate the molecule of interest also releases
degradative enzymes, e.g. proteases, nucleases.
─inhibited by adjusting the pH or temperature to values that inactivate them
or by adding compounds that specifically block their action.
(4)Adsorption to surfaces.
─denatured by contact with the air–water interface or with glass or plastic
surfaces.
─should minimize foaming and kept relatively concentrated.
(5)Long-term storage.
─keep in nitrogen or argon gas and/or are frozen at –80°C or–196°C (the
temperature of liquid nitrogen)
─processes such as slow oxidation and microbial contamination must be
prevented.
2 Describe how a protein may be quantified by an assay or by absorbance
spectroscopy. (p101-102)
Ans：Assay：
─enzymes that catalyze reactions with readily detected products.
─Substances with colored or fluorescent products e.g. RIA, ELISA
Spectroscopy：
 ─measure protein concentration
─aromatic side chains absorb strongly in the UV region of the spectrum
─use Beer–Lambert law
3 Explain how salting out is used in protein fractionation. (p102-103)
Ans：─more salt added, the solubility of the protein↓
─At very high salt concentrations, many added ions are solvated that there is
significantly less bulk solvent available to dissolve other substances
─different proteins have different ionic and hydrophobic compositions
─protein fractionated according to solubility
4 Explain how an antibody could be useful for purifying a protein and for determining
its concentration. (p101 and 106)
Ans：─Antibodies will bind to an antigen (in this case foreign protein of interest
that has been introduced)
─protien can be indirectly detected & quantified by using RIA/ELISA
─In immunoaffinity chromatography, an antibody is attached to the matrix to
purify the protein against which the antibody was raised.
5 Describe the basis for separating proteins by ion exchange, hydrophobic
interaction, gel filtration, and affinity chromatography. (p103-106)
Ans：

6 Describe the basis and the processes of gel electrophoresis, SDS-PAGE, and 2D gel
electrophoresis. (p106-108)
Ans：─gel electrophoresis：based on mass, shape & electric charge
─SDS-PAGE：based on mass
─2D gel electrophoresis：use isoelectric focusing & SDS-PAGE
7 List the separation techniques that exploit the following molecular properties:
charge, polarity, size, and specificity. (Table 5-2, p102)
Ans：
p.119
1 Explain the steps involved in sequencing a protein. (p110-118)
Ans：
2 Why is it important to identify the N-terminal residue(s) of a protein? How can it be
identified? (p110-112)
Ans：─establish the number of chemically distinct polypeptides in a protein.
How?
─(1)5-dimethylamino-1-naphthalenesulfonyl chloride (dansyl chloride)
reacts with primary amines to yield dansylated polypeptides. The
treatment of a dansylated polypeptide with aqueous acid at high
temperature hydrolyzes its peptide bonds.
─(2)performing the first step of Edman degradation
3 What are some advantages of sequencing peptides by mass spectrometry rather
than by Edman degradation? (p118)
Ans：─take only a few minutes
─to sequence peptides with chemically blocked N-termini
─to characterize other posttranslational modifications
4 Explain why long polypeptides must be broken into at least two different sets of
peptide fragments for sequencing. (p118)
Ans：Their order in the original polypeptide must be elucidated. It is accomplished
by conducting a second round of protein cleavage with a reagent of different
specificity and then comparing the amino acid sequences of the overlapping
sets of peptide fragments.
5 What types of information can be retrieved from a protein sequence database?
(p118-119)
Ans：─proteins & DNA sequences
 ─ID code that includes information about its source (accession number)
─description of the protein (function, sequence, features, binding sites)
─proteins with similar sequences in various organisms.
─protein sequence provides information about protein structure that is not
revealed by nucleic acid sequencing
─modified proteins
p.126
1 How can sequence comparisons reveal which amino acid residues are essential for
a protein’s function? (p122)
Ans：─the same residue at a particular position in the amino acid sequence of a
series of related proteins suggests that the chemical or structural properties
of that so-called invariant residue uniquely suit it to some essential function
of the protein.
─a particular amino acid position may tolerate many different amino acid
residues, indicating that the functional requirements of that position are
rather nonspecific. Such a position is said to be hypervariable.
2 Using Table 5-6, identify some invariant, conservative, and hypervariable positions.
What types of amino acids appear at conservatively substituted sites? (p122)
Ans：
3 Explain how the number of amino acid differences between homologous proteins
can be used to construct a phylogenetic tree. (p122)
Ans：count the amino acid differences between proteins.
4 Explain the origin of orthologous proteins, paralogous proteins, and multidomain
proteins. (p124-126)
Ans：orthologous proteins─Homologous proteins with the same function in
different species
paralogous proteins─Two independently evolving genes that are derived from
a duplication event
multidomain proteins─domains occur in several other proteins in the same
organism and may be repeated numerous times
within a given protein
5 Why do different proteins appear to evolve at different rates? (p124-125)
Ans：─the rate at which mutations are accepted into a protein varies.
─effect of amino acid changes on the protein’s function
─the protein’s structural stability
─The DNA sequences that control the expression of proteins are also subject
to mutation.