Chapter 3

Question 1

stupid textbook isnt working

Answer 1

oh no

Question 2

Substances having this dual (acid-base) nature are amphoteric and are o

Answer 2

led ampholytes
(from “amphoteric electrolytes”). A simple monoamino monocarboxylic α-amino acid, such as
alanine, is a diprotic acid when fully protonated; it has two groups, the —COOH group and the
—NH
+
3 group, that can yield protons

Question 3

good pics on pg 373

Answer 3

kk

Question 4

The 20 amino acids commonly found as residues in proteins contain an \and thus amino acids can exist in at least two
stereoisomeric forms.
378
Only the L stereoisomers of amino acids, with a configuration related to the absolute
configuration of the reference molecule L-glyceraldehyde, are found in proteins.
Amino acids can be classified into five types on the basis of the polarity and charge (at pH 7) of
their R groups.
Other, less common amino acids also occur, either as constituents of proteins (usually through
modification of common amino acid residues a

Answer 4

α-carboxyl group, an αamino group, and a distinctive R group substituted on the α-carbon atom.

Question 5

The α-carbon atom of
all amino acids except glycine is asymmetric,

Answer 5

\and thus amino acids can exist in at least two
stereoisomeric forms.

Question 6

Only the L stereoisomers of amino acids, with a configuration related to the absolute
configuration of the reference molecule L-glyceraldehyde, are found in

Answer 6

proteins

Question 7

Amino acids can be classified into five types on the basis of

Answer 7

the polarity and charge (at pH 7) of
their R groups.

Question 8

Other, less common amino acids also occur, either as

Answer 8

s constituents of proteins (usually through
modification of common amino acid residues a

Question 9

Amino acids vary in their acid-base properties and have characteristic

Answer 9

titration curves.
Monoamino monocarboxylic amino acids (with nonionizable R groups) are diprotic acids
(+H3NCH(R)COOH) at low pH and exist in several different ionic forms as the pH is increase

Question 10

Amino acids with ionizable R groups have additional

Answer 10

ionic species, depending on the pH of the
medium and the pKa of the R group

Question 11

Ionizable R groups in a peptide (Table 3-1) also
contribute to

Answer 11

the overall acid-base properties of the molecule

Question 12

Many small peptides exert their effects at

Answer 12

very low
concentrations. For example, a number of vertebrate hormones
(Chapter 23) are small peptides. These include oxytocin (nine
amino acid residues), which is secreted by the posterior pituitary
gland and stimulates uterine contractions, and thyrotropinreleasing factor (three residues), which is formed in the
hypothalamus and stimulates the release of another hormone,
thyrotropin, from the anterior pituitary gland. Some extremely
toxic mushroom poisons, such as amanitin, are also small
peptides, as are many antibiotics.

Question 13

Amino acids can be

Answer 13

joined covalently through peptide bonds to
form peptides and proteins. Cells generally contain thousands of
different proteins, each with a different biological activity.

Question 14

The ionization behavior of peptides reflects their ionizable side
chains as well as

Answer 14

the terminal α-amino and α-carboxyl groups.

Question 15

Proteins can be very long polypeptide chains of

Answer 15

100 to several
thousand amino acid residues. However, some naturally
occurring peptides have only a few amino acid residues. Some
proteins are composed of several noncovalently associated
polypeptide chains, called subunits.

Question 16

Simple proteins yield only amino acids on

Answer 16

hydrolysis;
conjugated proteins contain in addition some other component,
such as a metal or organic prosthetic group.

Question 17

Ion-exchange chromatography

Answer 17

exploits differences in the sign
and magnitude of the net electric charge of proteins at a given pH

Question 18

Affinity chromatography

Answer 18

is based on binding affinity (Fig. 3-17c).
The beads in the column have a covalently attached chemical
group called a ligand — a group or molecule that binds to a
macromolecule such as a protein.

Question 19

Protein purification protocols o

Answer 19

fuse additional amino acids or peptides (tags) to the target
protein. Affinity chromatography can be used to bind this tag,
achieving a large increase in purity in a single step (see Fig. 9-11).
In many cases, the tag can be subsequently removed, fully
restoring the function of the native protein.

Question 20

electrophoresis

Answer 20

Protein purification is usually complemented by electrophoresis,
an analytical process that allows researchers to visualize and
characterize proteins as they are purified.

Question 21

The electrophoretic method commonly employed for estimation
of purity and molecular weight makes use of the detergent

Answer 21

sodium dodecyl sulfate (SDS) (“dodecyl” denoting a 12-carbon
chain).

Question 22

Isoelectric focusing

Answer 22

is a procedure used to determine the
isoelectric point (pI) of a protein (Fig. 3-20).

Question 23

A pH gradient is
established by

Answer 23

y allowing a mixture of low molecular weight
organic acids and bases (ampholytes; p. 77) to distribute
407
themselves in an electric field generated across the gel. When a
protein mixture is applied, each protein migrates until it reaches
the pH that matches its pI. Proteins with different isoelectric
points are thus distributed differently throughout the gel.

Question 24

Combining isoelectric focusing and SDS electrophoresis
sequentially in a process called

Answer 24

two-dimensional electrophoresis
permits the resolution of complex mixtures of proteins (Fig. 3-
21). This is a more sensitive analytical method than either
electrophoretic method alone. Two-dimensional electrophoresis
408
separates proteins of identical molecular weight that differ in pI,
or proteins with similar pI values but different molecular weights.

Question 25

Proteins are separated and purified on the basis of

Answer 25

f differences
in their properties. Proteins can be selectively precipitated by
changes in pH or temperature, and particularly by the addition of
certain salts. A wide range of chromatographic procedures makes
use of differences in size, binding affinities, charge, and other
properties. These include ion-exchange, size-exclusion, affinity,
and high-performance liquid chromatograph

Question 26

Electrophoresis separates proteins on the basis of

Answer 26

mass or
charge for analytical purposes. SDS gel electrophoresis and
isoelectric focusing can be used separately or in combination for
higher resolution.

Question 27

All purification procedures require

Answer 27

e a method for quantifying or
assaying the protein of interest in the presence of other proteins.
Purification can be monitored by assaying specific activity

Question 28

primary structure

Answer 28

A description of all covalent bonds (mainly
peptide bonds and disulfide bonds) linking amino acid residues in
a polypeptide chain is its primary structure. The most important
element of primary structure is the sequence of amino acid
residues.

Question 29

secondary structure

Answer 29

refers to particularly stable
arrangements of amino acid residues giving rise to recurring
structural patterns.

Question 30

tertiary structure

Answer 30

describes all aspects of the
three-dimensional folding of a polypeptide.

Question 31

quaternary structure

Answer 31

When a protein has
two or more polypeptide subunits, their arrangement in space is
referred to as quaternary structure. Our exploration of proteins
will eventually include complex protein machines consisting of
dozens to thousands of subunits

Question 32

good pic on p 417

Answer 32

kk

Question 33

what does it mean for fxn if a protein has a unique amino acid sequence

Answer 33

this confers a particular threedimensional structure. This structure in turn confers a unique
function.

Question 34

Enzymes called proteases

Answer 34

catalyze the hydrolytic cleavage of
peptide bonds and provide the most common method to break a
protein into parts. Some proteases cleave only the peptide bond
adjacent to particular amino acid residues (Table 3-6) and thus
fragment a polypeptide chain in a predictable and reproducible
way. A

Question 35

. A few chemical reagents also

Answer 35

cleave the peptide bond
adjacent to specific residues. Among proteases, the digestive
enzyme trypsin catalyzes the hydrolysis of only those peptide
bonds in which the carbonyl group is contributed by either a Lys
or an Arg residue, regardless of the length or amino acid
sequence of the chain.

Question 36

Mass spectrometry can

Answer 36

provide a highly accurate measure of the
molecular mass of a protein, readily distinguishing between
single proton differences. it can also do much more

Question 37

what more can mass spectrometry allow for

Answer 37

The sequences of multiple short polypeptide segments (20
426
to 30 amino acid residues each) in a protein sample can be
obtained within seconds.

Question 38

Electrospray ionization mass spectrometry of a protein (this is a pic on p 429)

Answer 38

A
protein solution is dispersed into highly charged droplets by passage
through a needle under the influence of a high-voltage electric field. The
droplets evaporate, and the ions (with added protons in this case) enter the
mass spectrometer for m/z measurement. (b) The spectrum generated is a
family of peaks, with each successive peak (from right to le

Question 39

The analysis of complex mixtures of proteins — even entire
cellular proteomes — is facilitated by

Answer 39

y liquid chromatography (LC)
that is integrated into the instrument (LC-MS/MS). The organism
of interest is generally one in which the genomic sequence is
known. Cellular proteins are first isolated in an extract, then
digested into relatively short peptides by a protease such as
trypsin. The very complex mixture of peptides is subjected to
chromatography, so that resolved peptides are introduced to the
mass spectrometer successively

Question 40

Many peptides are potentially useful as pharmacologic agents,
and their production is of considerable commercial importance.
In addition to its commercial applications, the synthesis of
specific peptide portions of larger proteins is an increasingly
important tool for the study of protein structure and function.
There are three ways to obtain a peptide:

Answer 40

(1) purification from
tissue, a tasok

oomade difficult by the vanishingly low
concentrations of some peptides; (2 (2) genetic engineering
(Chapter 9); and (3) direct chemical synthesis. Powerful
techniques now make direct chemical synthesis an attractive
option in many cases.

Question 41

The complexity of proteins makes the traditional synthetic
approaches of organic chemistry impractical for peptides with
more than four or five amino acid residues. One problem is

Answer 41

the
difficulty of purifying the product after each step

Question 42

Knowledge of the sequence of amino acids in a protein can
offer insights into

Answer 42

its three-dimensional structure and its
function, cellular location, and evolution. Most of these insights
are derived by searching for similarities between a protein of
interest and previously studied proteins. Comparison of a newly
obtained sequence with sequence data in international
repositories often reveals relationships both surprising and enlightening.

Question 43

Much of the functional information encapsulated in protein
sequences comes in the form of consensus sequences. This term
is applied to

Answer 43

such sequences in DNA, RNA, or protein. When a
series of related nucleic acid sequences or protein sequences are
compared, a consensus sequence is the one that reflects the most
common base or amino acid at each position.

Question 44

horizontal gene transfer

Answer 44

Another complicating factor in tracing evolutionary history is the
rare transfer of a gene or a group of genes from one organism to
another, a process called horizontal gene transfer.

Question 45

Differences in protein function result from

Answer 45

differences in
amino acid composition and sequence. The chemical properties
of particular amino acid residues are often critical to the function
of a protein.

Question 46

Most amino acid sequences are deduced from

Answer 46

genomic
sequences and by mass spectrometry. Methods derived from
classical approaches to protein sequencing remain important in
protein chemistry

Question 47

Short proteins and peptides (up to about 100 residues) can be

Answer 47

chemically synthesized. The peptide is built up, one amino acid
residue at a time, while tethered to a solid support

Question 48

Protein sequences are a rich source of

Answer 48

information about
protein structure and function. Bioinformatics can analyze
changes in the amino acid sequences of homologous proteins
over time to trace the evolution of life on Earth.