CHAPTER 1
INTRODUCTION TO CELLS
 2009 Garland Science Publishing
Unity and Diversity of Cells
1-1
Living systems are incredibly diverse in size, shape, environment, and behavior. It is
estimated that there are between 10 million and 100 million different species. Despite this
wide variety of organisms, it remains difficult to define what it means to say something is
alive. Which of the following can be described as the smallest living unit?
(a)
DNA
(b)
cell
(c)
organelle
(d)
protein
1-2
Indicate whether the following statements are true or false. If the statement is false,
explain why it is false.
A.
A virus is a living organism.
B.
Cells of different types can have different chemical requirements.
C.
A human white blood cell is larger than a Paramecium cell.
1-3
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
Cells can be very diverse: superficially, they come in various sizes,
ranging from bacterial cells such as Lactobacillus, which is a few
__________________ in length, to larger cells such as a frog’s egg, which
has a diameter of about one __________________. Despite the diversity,
cells resemble each other to an astonishing degree in their chemistry. For
example, the same 20 __________________ are used to make proteins.
Similarly, the genetic information of all cells is stored in their
__________________. Although __________________ contain the same
type of molecules as cells, their inability to reproduce themselves by their
own efforts means that they are not considered living matter.
amino acids
DNA
fatty acids
meter
micrometer(s)
millimeter(s)
plants
plasma membranes
viruses
yeast
1-4
The flow of genetic information is controlled by a series of biochemical reactions that
result in the production of proteins, each with its own specific order of amino acids.
Choose the correct series biochemical reactions from the options presented here.
(a)
replication, transcription, translation
(b)
replication, translation, transcription
(c)
translation, transcription, replication
(d)
translation, replication, transcription
1-5
Proteins are important architectural and catalytic components within the cell, helping to
determine its chemistry, its shape, and its ability to respond to changes in the
environment. Remarkably, all of the different proteins in a cell are made from the same
20 __________. By linking them in different sequences, the cell can make protein
molecules with different conformations and surface chemistries, and therefore different
functions.
(a)
nucleotides
(b)
sugars
(c)
amino acids
(d)
fatty acids
1-6
Changes in DNA sequence from one generation to the next may result in offspring that
are altered in fitness compared with their parents. The process of change and selection
over the course of many generations is the basis of __________.
(a)
mutation
(b)
evolution
(c)
heredity
(d)
reproduction
Cells Under the Microscope
1-7
What unit of length would you generally use to measure a typical human cell?
(a)
centimeters
(b)
nanometers
(c)
millimeters
(d)
micrometers
1-8
Match the type of microscopy on the left with the corresponding description provided
below. There is one best match for each.
A.
confocal
B.
transmission electron
C.
fluorescence
D.
phase contrast
E.
scanning electron
F.
bright-field
____ uses a light microscope with an optical component to take advantage of the different
refractive indexes of light passing through different regions of the cell.
____ employs a light microscope and requires that samples be fixed and stained in order
to reveal cellular details.
____ requires the use of two sets of filters. The first filter narrows the wavelength range
that reaches the specimen and the second blocks out all wavelengths that pass back
up to the eyepiece except for those emitted by the dye in the sample.
____ scans the specimen with a focused laser beam to obtain a series of two-dimensional
optical sections, which can be used to reconstruct an image of the specimen in
three-dimensions. The laser excites a fluorescent dye molecule, and the emitted
light from each illuminated point is captured through a pinhole and recorded by a
detector.
____ has the ability to resolve cellular components a small as 2 nm.
____ requires coating the sample with a thin layer of a heavy metal to produce threedimensional images of the surface of a sample.
1-9
Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both
standard fluorescence microscopy and confocal microscopy to observe specific details in
the cell. Even though fluorescence permits better visualization, the resolving power is
essentially the same as that of a standard light microscope because the resolving power of
a microscope is limited by the __________ of light.
(a)
absorption
(b)
intensity
(c)
filtering
(d)
wavelength
The Procaryotic Cell
1-10
By definition, procaryotic cells do not possess __________.
(a)
a nucleus
(b)
replication machinery
(c)
ribosomes
(d)
membrane bilayers
1-11
Although there are many distinct procaryotic species, most have a small range of shapes,
sizes, and growth rates. Which of the following characteristics are not observed in
procaryotes?
(a)
a highly structured cytoplasm
(b)
endoplasmic reticulum
(c)
the ability to divide rapidly
(d)
a cell wall
1-12
Indicate whether the following statements are true or false. If the statement is false,
explain why it is false.
A.
Oxygen is toxic to certain procaryotic organisms.
B.
Mitochondria are thought to have evolved from anaerobic bacteria.
C.
Although bacteria use a variety of organic substances as food, bacteria are not
able live on inorganic substances.
The Eucaryotic Cell
1-13
Use the list of structures below to label the schematic drawing of an animal cell in Figure
Q1-13.
A.
plasma membrane
B.
nuclear envelope
C.
cytosol
D.
Golgi apparatus
E.
endoplasmic reticulum
F.
mitochondrion
G.
transport vesicles
Figure Q1-13
1-14
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
Eucaryotic cells are bigger and more elaborate than procaryotic cells. By
definition, all eucaryotic cells have a __________________, usually the
most prominent organelle. Another organelle found in essentially all
eucaryotic cells is the __________________, which generates the
chemical energy for the cell. In contrast, the __________________ is a
type of organelle found only in the cells of plants and algae, and performs
photosynthesis. If we were to strip away the plasma membrane from a
eucaryotic cell and remove all of its membrane-enclosed organelles, we
would be left with the __________________, which contains many long,
fine filaments of protein that are responsible for cell shape and structure
and thereby form the cell’s __________________.
chloroplast
chromosome
cytoskeleton
cytosol
endoplasmic reticulum
mitochondrion
nucleus
ribosomes
1-15
The __________ __________ is made up of two concentric membranes and is continuous
with the membrane of the endoplasmic reticulum.
(a)
plasma membrane
(b)
Golgi network
(c)
mitochondrial membrane
(d)
nuclear envelope
1-16
The nucleus, an organelle found in eucaryotic cells, confines the __________, keeping
them separated from other components of the cell.
(a)
lysosomes
(b)
chromosomes
(c)
peroxisomes
(d)
ribosomes
1-17
Which of the following organelles has both an outer and an inner membrane?
(a)
endoplasmic reticulum
(b)
mitochondrion
(c)
lysosome
(d)
peroxisome
1-18
You fertilize egg cells from a healthy plant with pollen (which contains the male germ
cells) that has been treated with DNA-damaging agents. You find that some of the
offspring have defective chloroplasts, and that this characteristic can be passed on to
future generations. This surprises you at first because you happen to know that the male
germ cell in the pollen grain contributes no chloroplasts to the fertilized egg cell and thus
to the offspring. What can you deduce from these results?
1-19
Mitochondria contain their own genome, are able to duplicate, and actually divide on a
different timeline from the rest of the cell. Nevertheless, mitochondria cannot function for
long when isolated from the cell because they are
(a)
viruses.
(b)
parasites.
(c)
endosymbionts.
(d)
anaerobes.
1-20
The mitochondrial proteins found in the inner membrane are involved in the conversion
of ADP to ATP, a source of energy for the cell. This process consumes which of the
following substances?
(a)
oxygen
(b)
nitrogen
(c)
sulfur
(d)
carbon dioxide
1-21
Chloroplasts are found only in eucaryotic cells that carry out photosynthesis: plants and
algae. Plants and algae appear green as a result of the presence of chlorophyll. Where is
chlorophyll located in the chloroplast?
(a)
in the first, outer membrane
(b)
in the space between the first and second membranes
(c)
in the second, inner membrane
(d)
in the third, innermost membrane
1-22
Photosynthesis enables plants to capture the energy from sunlight. In this essential
process, plants incorporate the carbon from CO2 into high-energy __________ molecules,
which the plant cell mitochondria use to produce ATP.
(a)
fat
(b)
sugar
(c)
protein
(d)
fiber
1-23
Indicate whether the following statements are true or false. If the statement is false,
explain why it is false.
A.
Membrane components in the cell are made in the endoplasmic reticulum.
B.
The Golgi apparatus is made up of a series of membrane-enclosed compartments
through which materials destined for secretion must pass.
C.
Lysosomes are small organelles where fatty acid synthesis occurs.
1-24
Circle the appropriate cell type in which the listed structure or molecule can be found.
Note that the structure or molecule can be found in more than one type of cell.
1-25
The protozoan Didinium feeds on other organisms by engulfing them. Why are bacteria,
in general, unable to feed on other cells in this way?
1-26
The cell constantly exchanges materials by bringing nutrients in from the external
environment and shuttling unwanted by-products back out. Which term describes the
process of by which external materials are captured inside vesicles and brought into the
cell?
(a)
degradation
(b)
exocytosis
(c)
(d)
phagocytosis
endocytosis
1-27
__________ are fairly small organelles that provide a safe place within the cell to carry
out certain biochemical reactions that generate harmful, highly reactive oxygen species.
These chemicals are both generated and broken down in the same location.
(a)
nucleosomes
(b)
lysosomes
(c)
peroxisomes
(d)
endosomes
1-28
The cytoskeleton provides support, structure, motility, and organization, and it forms
tracks to direct organelle and vesicle transport. Which of the cytoskeletal elements listed
below is the thickest?
(a)
actin filaments
(b)
microtubules
(c)
intermediate filaments
(d)
none of the above (all the same thickness)
1-29
Despite the differences between eucaryotic and procaryotic cells, procaryotes have
proteins that are distantly related to eucaryotic actin filaments and microtubules. What is
likely to be the most ancient function of the cytoskeleton?
(a)
cell motility
(b)
vesicle transport
(c)
membrane support
(d)
cell division
1-30
Which of the following characteristics would not support the idea that the ancestral
eucaryote was a predator cell that captured and consumed other cells?
(a)
dynamic cytoskeleton
(b)
large cell size
(c)
ability to move
(d)
rigid membrane
1-31
Indicate whether the following statements are true or false. If the statement is false,
explain why it is false.
A.
Primitive plant, animal, and fungal cells probably acquired mitochondria after
they diverged from a common ancestor.
B.
Protozoans are single-celled eucaryotes with cell morphologies and behaviors that
can be as complex as those of some multicellular organisms.
C.
Animal, plant, fungal, and bacterial cells all possess cell walls.
Model Organisms
1-32
Given what you know about the differences between procaryotic cells and eucaryotic
cells, rate the following things as “good” or “bad” processes to study in the model
organism, E. coli.
A.
formation of the endoplasmic reticulum
B.
DNA replication
C.
how the actin cytoskeleton contributes to cell shape
D.
how cells decode their genetic instructions to make proteins
E.
how mitochondria get distributed to cells during cell division
1-33
A.
B.
In what way does a fungal cell structurally resemble a plant cell, rather than an
animal cell?
Which principal organelle does a plant cell contain that a fungal cell does not?
1-34
Biologists cannot possibly study all living species. Instead, they try to understand cell
behavior by studying a select subset of them. Which of the following characteristics are
useful in an organism chosen for use as a model in laboratory studies?
(a)
amenability to genetic manipulation
(b)
ability to grow under controlled conditions
(c)
rapid rate of reproduction
(d)
all of the above
1-35
Many of the mechanisms that cells use for maintenance and reproduction were first
studied at the molecular detail in bacteria. Which bacterial species had a central role in
advancing the field of molecular biology?
(a)
E. coli
(b)
D. melanogaster
(c)
S. pombe
(d)
C. elegans
1-36
Brewer’s yeast, apart from being an irreplaceable asset in the brewery and in the bakery,
is an experimental organism used to study eucaryotic cells. However, it does face some
limitations. Which of the processes below cannot be studied with yeast?
(a)
DNA replication
(b)
cell motility
(c)
exocytosis
(d)
cell division
1-37
Circle the simplest model organism best used to study the following processes:
1-38
A. thaliana, or Arabidopsis, is a common weed. Biologists have selected it over hundreds
of thousands of other flowering plant species to serve as an experimental model organism
because __________________.
(a)
it can withstand extremely cold climates
(b)
it can reproduce in 8–10 weeks
(c)
it produces thousands of offspring per plant
(d)
Both (b) and (c) are true.
1-39
Drosophila melanogaster is a/an __________. This type of animal is the most abundant
of all animal species, making it an appropriate choice as an experimental model.
(a)
insect
(b)
bird
(c)
amphibian
(d)
mammal
1-40
C. elegans is a nematode. During its development, it produces more than 1000 cells
However, the adult worm only has 959 somatic cells. The process by which 131 cells are
specifically targeted for destruction is called
(a)
directed cell pruning.
(b)
programmed cell death.
(c)
autophagy.
(d)
necrosis.
1-41
Zebrafish (Danio rerio) are especially useful in the study of early development because
their embryos ______________.
(a)
are exceptionally large
(b)
develop slowly
(c)
are transparent
(d)
are naturally fluorescent
1-42
You wish to explore how mutations in specific genes affecting sugar metabolism might
alter tooth development. Which organism is likely to provide the best model system for
your studies and why?
(a)
horses
(b)
mice
(c)
E. coli
(d)
Arabidopsis
1-43
Genes that have homologues in a variety of species have been discovered through the
analysis of genome sequences. In fact, it is not uncommon to find a family of
homologous genes encoding proteins that are unmistakably similar in amino acid
sequence in organisms as diverse as budding yeast, archaea, plants, and humans. Even
more remarkably, many of these proteins can substitute functionally for their homologues
in other organisms. Explain what it is about the origins of cells that makes it possible for
proteins expressed by homologous genes to be functionally interchangeable in different
organisms.
1-44
Match each biological process with the model organism that is best suited or most
specifically useful for its study, based on information provided in your textbook. You
may list individual processes more than once.
A.
cell division
B.
development (multicellular)
C.
programmed cell death
D.
photosynthesis
E.
immunology
_____ A. thaliana (Arabidopsis)
_____ M. musculus (mouse)
_____ S. pombe
_____ C. elegans
_____ S. cerevisiae
_____ D. rerio (zebrafish)
_____ D. melanogaster
Testing the Concepts
1-45
Evolutionary biologists have always used a broad range of modern organisms to infer the
characteristics that ancestral organisms may have possessed. Genomic sequences are now
available for an increasing number of species, and scientists studying evolutionary
processes can take advantage of this enormous amount of data to bring evolution into the
arena of molecular studies. By aligning the sequences of homologous genes and looking
for regions of similarity and where changes have occurred, it is possible to infer the
sequence of the ancestral gene.
A.
What term is used to describe the changes in gene sequence that have occurred?
How can we use what we know about this process to construct a timeline showing
when various sequence changes occurred and when they lead to the modern
sequences that we know today?
B.
It is possible to express an ancestral gene sequence in modern organisms and
subsequently compare its function with that of the modern protein. Why might
this approach give misleading conclusions?
1-46
The antibiotic streptomycin inhibits protein synthesis in bacteria. If this antibiotic is
added to a culture of animal cells, protein synthesis in the cytosol continues normally.
However, over time the population of mitochondria in the cell becomes depleted.
Specifically, it is observed that the protein synthesis machinery inside the mitochondria is
inhibited.
A.
Explain this observation based on what you know about the origins of the modern
eucaryote.
B.
1-47
What do you expect to observe if, in a new experiment, animal cells are treated
with diphtheria toxin, a compound that is known to block cytosolic protein
synthesis but does not have any impact on bacterial growth?
Your friend has just returned from a deep sea mission and claims to have found a new
single-celled life form. He believes this new life form may not have descended from the
common ancestor that all types of life on Earth share. You are convinced that he must be
wrong, and you manage to extract DNA from the cells he has discovered. He says that the
mere presence of DNA is not enough to prove the point: his cells might have adopted
DNA as a useful molecule quite independently of all other known life forms. What would
you do to persuade him that he was wrong?
CHAPTER 2
CHEMICAL COMPONENTS OF CELLS
 2009 Garland Science Publishing
Chemical Bonds
2-1
Figure Q2-1 depicts the structure of carbon. Use the information in the diagram to choose
the correct atomic number and atomic weight, respectively, for an atom of carbon.
Figure Q2-1
(a)
(b)
(c)
(d)
6, 12
12, 12
6, 18
12, 6
2-2
An element may have more than a one isotope. Isotopes have different atomic weights,
but exhibit the same chemical behavior. Carbon-14 is an unstable isotope of carbon that
decays very slowly. Compared to the common, stable carbon-12 isotope, carbon-14 has
two additional ______________.
(a)
electrons
(b)
neutrons
(c)
protons
(d)
ions
2-3
If the isotope 32S has 16 protons and 16 neutrons, how many protons and how many
neutrons will the isotope 35S have?
2-4
A.
B.
C.
2-5
If 0.5 mole of glucose weighs 90 g, what is the molecular weight of glucose?
What is the concentration, in grams per liter (g/l), of a 0.25 M solution of
glucose?
How many molecules are there in 1 mole of glucose?
Which of the following elements is least abundant in living organisms?
(a)
(b)
(c)
(d)
2-6
sulfur
carbon
oxygen
nitrogen
Your friend learns about Avogadro’s number and thinks it is so huge that there may not
even be a mole of living cells on Earth. You have recently heard that there are about 50
trillion (50 × 1012) human cells in each adult human body, so you bet your friend $5 that
there is more than a mole of cells on Earth. Once you learn that each human contains
more bacterial cells (in the digestive system) than human cells, you are sure that you have
won the bet. The human population is now more than 6 billion (6 × 109). What
calculation can you show your friend to convince him you are right?
2-7 Avogadro’s number, calculated from the atomic weight of hydrogen, tells us how many
atoms or molecules are in mole. The resulting base for all calculations of moles and
molarity (how many molecules are present when you weigh out a substance or measure
from a stock solution) is the following:
1 g of hydrogen atoms = 6  1023 atoms = 1 mole of hydrogen
(a)
(b)
(c)
(d)
2-8
(a)
(b)
(c)
Sulfur has a molecular weight of 32. How many moles and atoms are there in 120
grams of sulfur?
3.75 and 6 × 1023
32 and 6 × 1023
1.75 and 1.05 × 1024
3.75 and 2.25 × 1024
The first task you are assigned in your summer laboratory job is to prepare a concentrated
NaOH stock solution. The molecular weight of NaOH is 40. How many grams of solid
NaOH will you need to weigh out to obtain a 500 ml solution that has a concentration of
10 M?
800 g
200 g
400 g
(d)
160 g
2-9
You have a concentrated stock solution of 10 M NaOH and want to use it to produce a
150 ml solution of 3 M NaOH. What volume of water and stock solutions will you
measure out to make this new solution?
(a)
135 ml of water, 15 ml of NaOH stock
(b)
115 ml of water, 35 ml of NaOH stock
(c)
100 ml of water, 50 ml of NaOH stock
(d)
105 ml of water, 45 ml of NaOH stock
2-10
An ionic bond between two atoms is formed as a result of the ______________.
(a)
sharing of electrons
(d)
(b)
loss of a neutron from one atom
(c)
loss of electrons from both atoms
loss of a proton from one atom
(e)
transfer of electrons from one atom to the other
2-11
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or
phrase should be used only once.
Whereas ionic bonds form a(n) __________________, covalent bonds
between atoms form a(n) __________________. These covalent bonds
have a characteristic bond __________________ and become stronger and
more rigid when two electrons are shared in a(n) __________________.
Equal sharing of electrons yields a(n) __________________ covalent
bond. If one atom participating in the bond has a stronger affinity for the
electron, this produces a partial negative charge on one atom and a partial
positive charge on the other. These __________________ covalent bonds
should not be confused with the weaker __________________ bonds that
are critical for the three-dimensional structure of biological molecules and
for interactions between these molecules.
charge
covalent
double bond
ionic
length
molecule
noncovalent
nonpolar
polar
salt
single bond
weight
2-12
Indicate whether the statements below are true or false. If a statement is false, explain
why it is false.
A.
Electrons are constantly moving around the nucleus of the atom, but they can
move only in discrete regions.
B.
There is no limit to the number of electrons that can occupy the fourth electron
shell.
C.
Atoms with unfilled outer electron shells are especially stable and are therefore
less reactive.
D.
Covalent bonds are formed when electrons are either shared or transferred
between atoms.
2-13
Table Q2-13 indicates the electrons in the first four atomic electron shells for selected
elements. On the basis of the information in the chart and what you know about atomic
structure, which elements are chemically inert?
Table Q2-13
(a)
(b)
(c)
(d)
2-14
carbon, sulfur
helium, neon
sodium, potassium
magnesium, calcium
Table Q2-14 indicates the electrons in the first four atomic electron shells for selected
elements. On the basis of the information in the chart and what you know about atomic
structure, which elements will form ions with a net charge of +1 in solution?
Table Q2-14
(a)
(b)
(c)
(d)
carbon, sulfur
helium, neon
sodium, potassium
magnesium, calcium
2-15
Table Q2-15 indicates the electrons in the first four atomic electron shells for selected
elements. On the basis of the information in the chart and what you know about atomic
structure, which elements will form ions with a net charge of +2 in solution?
Table Q2-15
(a)
(b)
(c)
(d)
2-16
carbon, sulfur
helium, neon
sodium, potassium
magnesium, calcium
Table Q2-16 indicates the electrons in the first four atomic electron shells for selected
elements. On the basis of the information in the chart and what you know about atomic
structure, which elements form stable but reactive diatomic gases?
Table Q2-16
(a)
nitrogen, oxygen
2-17
(b)
(c)
(d)
helium, neon
sodium, potassium
magnesium, calcium
A.
B.
In what scientific units is the strength of a chemical bond usually expressed?
If 0.5 kilocalories of energy is required to break 6 × 1023 bonds of a particular
type, what is the strength of this bond?
2-18
The pH of an aqueous solution is an indication of the concentration of available
protons. However, you should not expect to find lone protons in solution; rather,
the proton is added to a water molecule to form a(n) ______________ ion.
hydroxide
ammonium
chloride
hydronium
(a)
(b)
(c)
(d)
2-19
The relative strengths of covalent bonds and van der Waals interactions remain the same
when tested in a vacuum or in water. However, this is not true of hydrogen bonds or ionic
bonds, whose bond strength is lowered considerably in the presence of water in
comparison with the bond strength observed in a vacuum. Explain these observations.
2-20
Oxygen, hydrogen, carbon, and nitrogen atoms are enriched in the cells and tissues of
living organisms. The covalent bond geometries for these atoms influence their
biomolecular structures. Match the elements on the left with the bond geometries
illustrated on the right. Some elements assume more than one bond geometry.
A.
B.
C.
2-21
oxygen
carbon
nitrogen
Which of the following expressions accurately describes the calculation of pH?
(a)
(b)
(c)
(d)
2-22
pH = –log10[H+]
pH = log10[H+]
pH = –log2[H+]
pH = –log10[OH–]
Larger molecules have hydrogen-bonding networks that contribute to specific, high–
affinity binding. Smaller molecules such as urea can also form these networks. How
many hydrogen bonds can urea (Figure Q2-22) form if dissolved in water?
Figure Q2-22
2-23
(a)
(b)
(c)
(d)
6
5
3
4
A.
Sketch three different ways in which three water molecules could be held together
by hydrogen bonding.
On a sketch of a single water molecule, indicate the distribution of positive and
negative charge (using the symbols δ+ and δ–).
How many hydrogen bonds can a hydrogen atom in a water molecule form? How
many hydrogen bonds can the oxygen atom in a water molecule form?
B.
C.
2-24
A.
B.
C.
What is the pH of pure water?
What concentration of hydronium ions does a solution of pH 8 contain?
Complete the following reaction:
CH3COOH + H2O ↔ __________.
D.
Will the reaction in C occur more readily (be driven to the right) if the pH of the
solution is high?
2-25
Aromatic carbon compounds such as benzene are planar and very stable. Doublebond character extends around the entire ring, which is why it is often drawn as a
hexagon with a circle inside. This characteristic is caused by electron
__________.
resonance
pairing
partial charge
stacking
(a)
(b)
(c)
(d)
2-26
The amino acid histidine is often found in enzymes. Depending on the pH of its
environment, sometimes histidine is neutral and at other times it acquires a proton and
becomes positively charged. Consider an enzyme with a histidine side chain that is
known to have an important role in the function of the enzyme. It is not clear whether this
histidine is required in its protonated or its unprotonated state. To answer this question
you measure enzyme activity over a range of pH, with the results shown in Figure Q2-26.
Which form of histidine is necessary for the active enzyme?
Figure Q2-26
2-27
Silicon is an element that, like carbon, has four vacancies in its outer electron shell and
therefore has the same bonding chemistry as carbon. Silicon is not found to any
significant degree in the molecules found in living systems, however. Does this
difference arise because elemental carbon is more abundant than silicon? What other
explanations are there for the preferential selection of carbon over silicon as the basis for
the molecules of life?
Molecules in Cells
2-28
The variety and arrangement of chemical groups on monomer subunits contribute
to the conformation, reactivity, and surface of the macromolecule into which they
become incorporated. What type of chemical group is circled on the nucleotide
shown in Figure Q2-28?
Figure Q2-28
(a)
(b)
(c)
(d)
pyrophosphate
phosphoryl
carbonyl
carboxyl
2-29
The amino acids glutamine and glutamic acid are shown in Figure Q2-29. They
differ only in the structure of their side chains (circled). At pH 7, glutamic acid
can participate in molecular interactions that are not possible for glutamine. What
types of interaction are these?
Figure Q2-29
(a)
(b)
(c)
(d)
ionic bonds
hydrogen bonds
van der Waals interactions
covalent bonds
2-30
Oligosaccharides are short sugar polymers that can become covalently linked to
proteins and lipids through condensation reactions. These modified proteins and
lipids are called glycoproteins and glycolipids. Within a protein, which of the
amino acids (shown in Figure Q2-30) is the most probable target for this type of
modification?
Figure Q2-30
(a)
(b)
(c)
(d)
serine
glycine
phenylalanine
methionine
2-31
Which of the following are examples of isomers?
(a)
glucose and galactose
(b)
alanine and glycine
(c)
adenine and guanine
(d)
glycogen and cellulose
2-32
A.
B.
C.
How many carbon atoms does the molecule represented in Figure Q2-32 have?
How many hydrogen atoms does it have?
What type of molecule is it?
Figure Q2-32
2-33
Most types of molecule in the cell have asymmetric (chiral) carbons. Consequently there
is the potential to have two different molecules that look much the same but are mirror
images of each other and therefore not equivalent. These special types of isomer are
called stereoisomers. Which of the four carbons circled in Figure Q2-33 is the
asymmetric carbon that determines whether the amino acid (threonine in this case) is a Dor an L- stereoisomer?
Figure Q2-33
(a)
(b)
(c)
(d)
2-34
1
2
3
4
Indicate whether the statements below are true or false. If a statement is false, explain
why it is false.
A.
A disaccharide consists of a sugar covalently linked to another molecule such as
an amino acid or a nucleotide.
B.
The hydroxyl groups on monosaccharides are reaction hotspots and can be
replaced by other functional groups to produce derivatives of the original sugar.
C.
The presence of double bonds in the hydrocarbon tail of a fatty acid does not
greatly influence its structure.
D.
2-35
Glycerol is a three-carbon compound that connects the fatty acid tails with the
polar head group in phospholipids.
On the phospholipid molecule in Figure Q2-35 label each numbered line with a correct
term selected from the list below.
Figure Q2-35
2-36
(a)
(b)
(c)
(d)
2-37
(a)
(b)
(c)
(d)
2-38
Biological membranes are composed of specialized lipids that form bilayers.
Which of the following is formed by unmodified fatty acids?
fat droplets
bilayers
micelles
planar lipid patches
Choose the answer that best fits the statement. Cholesterol is an essential
component of biological membranes. Although it is much smaller than the typical
phospholipids and glycoplipids in the membrane, it is a(n) _________________
molecule, having both hydrophilic and hydrophobic regions.
polar
oxygen-containing
hydrophobic
amphipathic
DNA and RNA are different types of nucleic acid polymer. Which of the following is
true of DNA but not true of RNA?
(a)
It contains uracil.
(b)
It contains thymine.
(c)
It is single stranded.
(d)
It has 5′-to-3′ directionality.
2-39
A.
B.
C.
D.
E.
F.
G.
H.
I.
Match each term related to the structure of nucleic acids (A–I) with one of the
descriptions provided.
base
glycosidic bond
nucleoside
nucleotide
phosphoanyhydride bond
phosphoester bond
ribose
phosphodiester bond
deoxyribose
____
____
____
____
____
____
____
____
____
the linkage between two nucleotides
the linkage between the 5′ sugar hydroxyl and a phosphate group
the nitrogen-containing aromatic ring
five-carbon sugar found in DNA
sugar unit linked to a base
linkage between the sugar and the base
linkages between phosphate groups
sugar linked to a base and a phosphate
five-carbon sugar found in RNA
2-40 A.
Write out the sequence of amino acids in the following peptide, using the full
names of the amino acids.
Pro-Val-Thr-Gly-Lys-Cys-Glu
B.
C.
Write the same sequence with the single-letter code for amino acids.
According to the conventional way of writing the sequence of a peptide or a
protein, which is the C-terminal amino acid and which is the N-terminal amino
acid in the above peptide?
2-41
Which of the following statements about amino acids is true?
(a)
Twenty-two amino acids are commonly found in proteins.
(b)
Most of the amino acids used in protein biosynthesis have charged side chains.
(c)
Amino acids are often linked together to form branched polymers.
(d)
All amino acids contain an NH2 and a COOH group
2-42
Which of the following statements is false?
(a)
ATP contains high-energy phosphoanhydride bonds.
(b)
ATP is sometimes called the “universal currency” in the energy economy of cells.
(c)
ATP can be incorporated into DNA.
(d)
ATP can be hydrolyzed to release energy to power hundreds of reactions in cells.
(e)
ATP comprises a sugar, phosphate groups, and a nitrogenous base.
Macromolecules in Cells
2-43
Both DNA and RNA are synthesized by covalently linking a nucleotide triphosphate to
the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the
new strand becomes part of a stable helix. The two strands are complementary in
sequence and antiparallel in directionality. What is the principal force that holds these
two strands together?
(a)
ionic interactions
(b)
hydrogen bonds
(c)
covalent bonds
(d)
van der Waals interactions
2-44
(a)
(b)
(c)
(d)
2-45
(a)
(b)
(c)
(d)
Each nucleotide in DNA and RNA has an aromatic base. What is the principal
force that keeps the bases in a polymer from interacting with water?
hydrophobic interactions
hydrogen bonds
covalent bonds
van der Waals interactions
Because there are four different monomer building blocks that can be used to
assemble RNA polymers, the number of possible sequence combinations that can
be created for a RNA molecule made of 100 nucleotides is _______.
1004
4100
4 × 100
100/4
2-46
There are 20100 different possible sequence combinations for a protein chain with 100
amino acids. In addition to the amino acid sequence of protein, what other factors
increase the potential for diversity in these macromolecules?
(a)
free rotation around single bonds during synthesis
(b)
noncovalent interactions sampled as protein folds
(c)
the directionality of amino acids being added
(d)
the planar nature of the peptide bond
2-47
Indicate whether the statements below are true or false. If a statement is false, explain
why it is false.
A.
“Nonpolar interactions” is simply another way of saying “van der Waals
attractions.”
B.
Condensation reactions occur in the synthesis of all the macromolecules found in
cells.
C.
All proteins and RNAs pass through many unstable conformations as they are
folded, finally settling on one single, preferred conformation.
D.
When nonpolar molecules are placed in an aqueous solution, the water molecules
surrounding the nonpolar surface become completely disordered.
2-48
(a)
(b)
(c)
(d)
2-49
(a)
(b)
(c)
(d)
Macromolecules in the cell can often interact transiently as a result of noncovalent
interactions. These weak interactions also produce stable, highly specific
interactions between molecules. Which of the factors below is the most significant
in determining whether the interaction will be transient or stable?
the size of each molecule
the concentration of each molecule
the rate of synthesis
surface complementarity between molecules
In a folded protein, most of the nonpolar amino acids are buried inside the protein
fold, whereas the polar and charged side chains are exposed to the components in
the cytosol. This fold is more stable because of the expulsion of nonpolar atoms
from contact with water, favoring the interaction of nonpolar atoms with each
other. What is this fourth type of noncovalent interaction called?
hydrophobic interaction
hydrophilic interaction
apolar interaction
hydrocarbon interaction
2-50
You are trying to make a synthetic copy of a particular protein but accidentally join the
amino acids together in exactly the reverse order. One of your classmates says the two
proteins must be identical, and bets you $20 that your synthetic protein will have exactly
the same biological activity as the original. After having read this chapter, you have no
hesitation in staking your $20 that it won’t. What particular feature of a polypeptide chain
makes you sure your $20 is safe and that your project will have to be redone.
2-51
A protein chain folds into its stable and unique three-dimensional structure, or
conformation, by making many noncovalent bonds between different parts of the chain.
Such noncovalent bonds are also critical for interactions with other proteins and cellular
molecules. From the list provided, choose the class(es) of amino acids that are most
important for the interactions detailed below.
A.
forming ionic bonds with negatively charged DNA
B.
forming hydrogen bonds to aid solubility in water
C.
binding to another water-soluble protein
D.
localizing an “integral membrane” protein that spans a lipid bilayer
E.
tightly packing the hydrophobic interior core of a globular protein
acidic
basic
2-52
nonpolar
uncharged polar
It is now a routine task to determine the exact order in which individual subunits have
been linked together in polynucleotides (DNA) and polypeptides (proteins). However, it
remains difficult to determine the arrangement of monomers in a polysaccharide. Explain
why this is the case.
2-53
Your lab director requests that you add new growth medium to the mammalian cell
cultures before heading home from the lab on a Friday night. Unfortunately, you need to
make fresh medium because all the pre-mixed bottles of medium have been used. One of
the ingredients you know you need to add is a mix of the essential amino acids (those that
cannot be made by the cells, but are needed in proteins). On the shelf of dry chemicals
you find the amino acids you need, and you mix them into your medium, along with all
the other necessary nutrients and replace the old medium with your new medium. On
Sunday, you come in to the lab just to check on your cells and find that the cells have not
grown. You are sure you made the medium correctly, but on checking you see that
somebody wrote a note on the dry mixture of amino acids you used: “Note: this mixture
contains only D-amino acids.”
A.
What is the meaning of the note and how does it explain the lack of cell growth in
your culture?
B.
Are there any organisms that could grow using this mixture? Justify your answer.
2-54
Eucaryotic cells have their DNA molecules inside their nuclei. However, to package the
DNA all into such a small volume requires the cell to use specialized proteins called
histones. Histones have amino acid sequences enriched for lysines and arginines.
A.
What problem might a cell face in trying to package DNA into a small volume
without histones, and how do these special packaging proteins alleviate the
problem?
B.
Lysine side chains are substrates for enzymes called acetylases. A diagram of an
acetylated lysine side chain is shown in Figure Q2-54. How do you think the
acetylation of lysines in histone proteins will affect the ability of a histone to
perform its role (refer to your answer in part A)?
Figure Q2-54
CHAPTER 3
ENERGY, CATALYSIS, AND BIOSYNTHESIS
 2009 Garland Science Publishing
Catalysis and the Use of Energy by Cells
3-1
Chemical reactions carried out by living systems depend on the ability of some organisms
to capture and use atoms from nonliving sources in the environment. The specific subset
of these reactions that breakdown nutrients in food can be described as _____________.
(a)
metabolic
(b)
catabolic
(c)
anabolic
(d)
biosynthetic
3-2
The second law of thermodynamics states that the disorder in any system is always
increasing. In simple terms, you can think about dropping NaCl crystals into a glass of
water. The solvation and diffusion of ions is favored because there is an increase in
_____________.
(a)
pH
(b)
entropy
(c)
ionic structure
(d)
stored energy
3-3
The energy used by the cell to generate specific biological molecules and highly ordered
structures is stored in the form of _____________.
(a)
Brownian motion
(b)
heat
(c)
light waves
(d)
chemical bonds
3-4
At first glance, it may seem that living systems are able to defy the second law of
thermodynamics. However, on closer examination it becomes clear that although cells
create organization from raw materials in the environment, they also contribute to
disorder in the environment by releasing _____________.
(a)
water
(b)
radiation
(c)
heat
(d)
proteins
3-5
If you weigh yourself on a scale one morning then eat four pounds of food during the
day, will you weigh four pounds more the next morning? Why or why not? Hint: What
happens to the atoms contained in the food as useful energy is derived from metabolizing
the food molecules?
3-6
Which of the following statements are true or false? If a statement is false, explain why it
is false.
A.
The second law of thermodynamics states that the total amount of energy in the
Universe does not change.
B.
The ultimate source of energy for living systems is chlorophyll.
C.
CO2 gas is fixed in a series of reactions that are light-dependent.
D.
H2 is the most stable and abundant form of hydrogen in the environment.
3-7
Two college roommates do not agree on the best way to handle the clutter piled up in
your dorm room. Roommate 1 explains that chaos is inevitable, so why fight it?
Roommate 2 counters that maintaining an organized environment makes life easier in
many ways, and that chaos is not inevitable. What law of thermodynamics drives the
thinking of roommate 1? What thermodynamic argument can be used to support
roommate 2?
3-8
Assume that the average human adult requires 2000 kilocalories per day to sustain all
normal processes and maintain a constant weight. If manufactured solar panels could
somehow provide power directly to the human body, what size solar panel would be
required (in cm2)? Assume there are 10 hours of sunlight per day, and that the usable
energy output for a typical solar panel is 850 kJ/ft2 per hour.
Note: 1 kcal = 4.184 kJ
1 ft2 = 929.03 cm2
3-9
Fill in the blanks, selecting from the choices below.
Light + _________ + _________ → _________ + heat + sugars
CO,
CO2,
O2,
H2,
H2O, N2,
NO
3-10
During respiration, energy is retrieved from the high-energy bonds found in certain
organic molecules. Which of the following, in addition to energy, are the ultimate
products of respiration?
(a)
CO2, H2O
(b)
CH3, H2O
(c)
CH2OH, O2
(d)
CO2, O2
3-13
For each of the pairs A–D in Figure Q3-13, pick the more reduced member of the pair.
Figure Q3-13
3-14
Oxidation is the process by which oxygen atoms are added to a target molecule.
Generally, the atom that is oxidized will experience which of the following with respect
to the electrons in its outer shell?
(a)
a net gain
(b)
a net loss
(c)
no change
(d)
an equal sharing
3-15
When elemental sodium is added to water, the sodium atoms ionize spontaneously.
Uncharged Na becomes Na+. This means that the Na atoms have been _____________.
(a)
protonated
(b)
oxidized
(c)
hydrogenated
(d)
reduced
3-16
Arrange the following molecules in order with respect to their relative levels of oxidation
(assign 5 to the most oxidized and 1 to the most reduced).
_______ CH2O (formaldehyde)
_______ CH4 (methane)
_______ CHOOH (formic acid)
_______ CH3OH (methanol)
_______ CO2 (carbon dioxide)
3-17
Oxidation and reduction states are relatively easy to determine for metal ions, because
there is a measurable net charge. In the case of carbon compounds, oxidation and
reduction depend on the nature of polar covalent bonds. Which of the following is the
best way to describe these types of bond?
(a)
hydrogen bonds in a nonpolar solution
(b)
covalent bonds in an aqueous solution
(c)
unequal sharing of electrons across a covalent bond
(d)
equal sharing of electrons across a covalent bond
3-18
Seed oils are often dehydrogenated and added back into processed foods as partly
unsaturated fatty acids. In comparison with the original oil, the new fatty acids have
additional double carbon–carbon bonds, replacing what were once single bonds. This
process could also be described as _____________.
(a)
isomerization
(b)
oxidation
(c)
reduction
(d)
protonation
3-20
Chemical reactions that lead to a release of free energy are referred to as “energetically
favorable.” Another common way in which these reactions are described is
_____________.
(a)
uphill
(b)
uncatalyzed
(c)
spontaneous
(d)
activated
3-21
ΔG° indicates the change in the standard free energy as a reactant is converted to product.
Given what you know about these values, which reaction below is the most favorable?
(a)
ADP + Pi → ATP
ΔG° = +7.3 kcal/mole
(b)
glucose 1-phosphate → glucose 6-phosphate
ΔG° = –1.7 kcal/mole
(c)
glucose + fructose → sucrose
ΔG° = +5.5 kcal/mole
(d)
glucose → CO2 + H2O
ΔG° = –686 kcal/mole
3-22
Catalysts are molecules that lower the activation energy for a given reaction. Cells
produce their own catalysts called _____________.
(a)
proteins
(b)
enzymes
(c)
cofactors
(d)
complexes
3-23
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
By definition, catalysis allows a reaction to occur more
__________________. Chemical reactions occur only when there is a loss
of __________________ energy. Enzymes act more
__________________ than other catalysts. A catalyst decreases the
__________________ energy of a reaction.
activation
chemical bond
completely
selectively
3-24
free
kinetic
rapidly
slowly
unfavorable
favorable
Figure Q3-24 is an energy diagram for the reaction X→Y. Which equation below
provides the correct calculation for the amount of free-energy change when X is
converted to Y?
(a)
(b)
(c)
(d)
a+b– c
a– b
a– c
c– a
Figure Q3-24
3-25
Enzymes facilitate reactions in living systems. Figure Q3-25 presents an energy diagram
for the reaction X→Y. The solid line in the energy diagram represents changes in energy
as the product is converted to reactant under standard conditions. The dashed line shows
changes observed when the same reaction takes place in the presence of a dedicated
enzyme. Which equation below indicates how the presence of an enzyme affects the
activation energy of the reaction (catalyzed versus uncatalyzed)?
(a)
d – c versus b – c
(b)
d – a versus b – a
(c)
a + d versus a + b
(d)
d – c versus b – a
Figure Q3-25
3-26
Which of the following statements are true or false? If a statement is false, explain why it
is false.
A.
Enzymes lower the free energy released by the reaction that they facilitate.
B.
Enzymes lower the activation energy for a specific reaction.
C.
Enzymes increase the probability that any given reactant molecule will be
converted to product.
D.
Enzymes increase the average energy of reactant molecules.
3-27
ΔG measures the change of free energy in a system as it converts reactant (Y) into
product (X). When [Y] =[X], ΔG is equal to _____________.
(a)
ΔG° + RT
(b)
RT
(c)
ln [X]/[Y]
(d)
ΔG°
3-28
For the reaction Y→X at standard conditions with [Y] = 1 M and [X] = 1 M, ΔG is
initially a large negative number. As the reaction proceeds, [Y] decreases and [X]
increases until the system reaches an equilibrium. How do the values of ΔG and ΔG°
change as the reaction equilibrates?
(a)
ΔG becomes less negative and ΔG° stays the same.
(b)
ΔG becomes positive and ΔG° becomes positive.
(c)
ΔG stays the same and ΔG° becomes less negative.
(d)
ΔG reaches zero and ΔG° becomes more negative.
3-29
The equilibrium constant (K) for the reaction Y→X can be expressed with respect to the
concentrations of the reactant and product molecules. Which of the expressions below
shows the correct relationship between K, [Y], and [X]?
(a)
K = [Y]/[X]
(b)
K = [Y] * [X]
(c)
K = [X]/[Y]
(d)
K = [X] – [Y]
3-30
Isomerization of glucose 1-phosphate to glucose 6-phosphate is energetically favorable.
At 37°C, ΔG° = –1.42 log10K. What is the equilibrium constant for this reaction if ΔG° =
–1.74 kcal/mole at 37°C?
(a)
16.98
(b)
(c)
(d)
3-31
0.09
–0.09
0.39
On the basis of the two reactions below, decide which of the following statements are
true and which are false. If a statement is false, explain why it is false.
1:
2:
ATP + Y → Y-P + ADP
Y-P + A → B
A.
Reaction 1 is favorable because of the large negative ΔG associated with the
hydrolysis of ATP.
Reaction 2 is an example of an unfavorable reaction.
Reactions 1 and 2 are coupled reactions, and when they take place together,
reaction 2 will proceed in the forward direction.
Reaction 2 can be used to drive reaction 1 in the reverse direction.
B.
C.
D.
ΔG = –100 kcal/mole
ΔG = 50 kcal/mole
3-32
The potential energy stored in high-energy bonds is commonly harnessed when the bonds
are split by the addition of _______________ in a process called _____________.
(a)
ATP, phosphorylation
(b)
water, hydrolysis
(c)
hydroxide, hydration
(d)
acetate, acetylation
3-33
When the polymer X-X-X… is broken down into monomers, it is “phosphorylyzed”
rather than hydrolyzed, in the following repeated reaction:
X-X-X… + P → X-P + X-X…
(reaction 1)
Given the ΔG° values of the reactions listed in the following table, what is the expected
ratio of X-phosphate (X-P) to free phosphate (P) at equilibrium for reaction 1?
(a)
(b)
(c)
(d)
(e)
3-34
1:106
1:104
1:1
104:1
106:1
Consider the reaction X→Y in a cell at 37°C. At equilibrium, the concentrations of X and
Y are 50 μM and 5 μM, respectively. Using the equations below and your new
knowledge, answer the following questions.
ΔG° = –0.616 ln Keq
ΔG = ΔG° + 0.616 ln [Y]/[X]
Recall that the natural log of a number z will have a negative value when z < 1, positive
when z > 1, and 0 when z = 1.
A.
B.
C.
D.
E.
What is the value of Keq for this reaction?
Is the standard free-energy change of this reaction positive or negative? Is the
reaction X→Y an energetically favorable or unfavorable reaction under standard
conditions?
What is the value of the standard free energy? Refer to Table 3-1 in the textbook
or use a calculator.
Imagine circumstances in which the concentration of X is 1000 μM and that of Y
is 1 μM. Is conversion of X to Y favorable? Will it happen quickly?
Imagine starting conditions in which the reaction X→Y is unfavorable, yet the
cell needs to produce more Y. Describe two ways in which this may be
accomplished.
3-35
If proteins A and B have complementary surfaces, they may interact to form the dimeric
complex AB. Which of the following is the correct way to calculate the equilibrium
constant for the association between A and B?
(a)
kon/koff = K
(b)
K = [A][B]/[AB]
(c)
K = [AB]/[A][B]
(d)
(a) and (c)
3-36
Match the following general equations with the energy diagram that best describes the
free-energy transitions along the reaction pathway. Indicate your answer by filling in the
equation number in the box under each respective curve. After you have identified a
match for each equation, indicate the positions of A, B, and C (if applicable) on the freeenergy curves. Not all of the energy diagrams will have a match.
3-37
The net distance a molecule travels as it diffuses through the cytosol is relatively short in
comparison with the total distance it travels. This is because movement governed by
diffusion alone is a ________________ process that is most effective for the dispersion
of small molecules over short distances.
(a)
slow
(b)
random
(c)
regulated
(d)
complicated
3-38
The small molecule cyclic AMP (cAMP) takes about 0.2 second to diffuse 10 μm, on
average, in a cell. Suppose that cAMP is produced near the plasma membrane on one end
of the cell; how long will it take for this cAMP to diffuse through the cytosol and reach
the opposite end of a very large cell, on average? Assume that the cell is 200 μm in
diameter.
(a)
4 seconds
(b)
16 seconds
(c)
80 seconds
(d)
200 seconds
3-39
The graph in Figure Q3-39 illustrates the relationship between reaction rates and
substrate concentration for an enzyme-catalyzed reaction. What does the Km value
indicate with respect to enzyme substrate interactions?
(a)
the maximum rate of catalysis
(b)
the number of enzyme active sites
(c)
the enzyme–substrate binding affinity
(d)
the equilibrium rate of catalysis
Figure Q3-39
3-40
The graph in Figure Q3-40 illustrates the change in the rate of an enzyme-catalyzed
reaction as the concentration of substrate is increased. Which of the values listed below is
used to calculate the enzyme turnover number?
(a)
(b)
(c)
½Vmax
Km
Vmax
(d)
Vmax – Km
Figure Q3-40
3-41
Protein E can bind to two different proteins, S and I. The binding reactions are described
by the following equations and values:
E + S → ES
E + I → EI
Keq for ES = 10
Keq for EI = 2
Given the equilibrium constant values, which one of the following statements is true?
(a)
E binds I more tightly than S.
(b)
When S is present in excess, no I molecules will bind to E.
(c)
The binding energy of the ES interaction is greater than that of the EI interaction.
(d)
Changing an amino acid on the binding surface of I from a basic amino acid to an
acidic one will probably make the free energy of association with E more
negative.
3-42
Indicate whether the following statements about enzymes are true or false. If a statement
is false, explain why it is false.
A.
Enzymes alter the equilibrium point of a reaction.
B.
Vmax can be determined by measuring the amount of product accumulated late in
the reaction.
C.
Competitive inhibitors bind irreversibly to the enzyme active site, lowering Vmax.
3-43
A.
B.
You are measuring the effect of temperature on the rate of an enzyme-catalyzed
reaction. If you plot reaction rate against temperature, which of the graphs in
Figure Q3-43 would you expect your plot to resemble?
Explain why temperature has this effect.
Figure Q3-43
3-44
Consider a description of an enzymatic reaction pathway that begins with the binding of
substrate S to enzyme E, and ends with the release of product P from the enzyme.
E + S → ES → EP → E + P
In many circumstances,
Km = [E] [S] / [ES]
A.
B.
3-45
What proportion of enzyme molecules are bound to substrate when [S] = Km?
Recall that when [S] = Km, the reaction rate is ½Vmax. Does your answer to part A
make sense in the light of this rate information?
Figure Q3-45 illustrates the amount of energy per molecule for a population in a
contained, controlled environment. Most molecules will have the average energy of the
population, shown in region 1. The number of molecules in the population with enough
energy to be converted to product is shown in region 2. The number of molecules with
enough energy to react in the presence of enzyme is shown in region 3. Use this
information to explain how enzymes catalyze reactions.
Figure Q3-45
3-46
Chemical reactions are reversible; they can proceed in both the forward and reverse
directions. If the ΔG° for the reaction Y→X is energetically favorable, how can you
explain the fact that not all of the Y molecules will be converted to X molecules?
3-47
Enzymes A and B catalyze different reactions, but use the same reactant molecule as a
substrate. The graph in Figure Q3-47 presents the reaction rates observed when enzyme
A and enzyme B are mixed together in a single test tube containing molecule X. What are
the Vmax and the apparent Km values for each enzyme under these conditions? How might
these values change for enzyme B if it were analyzed in the absence of enzyme A?
Explain your answer.
Figure Q3-47
Activated Carrier Molecules and Biosynthesis
3-48
Consider an analogy between reaction coupling and money. In a simple economy, barter
provides a means of direct exchange of material goods. For example, the owner of a cow
may have excess milk and need eggs, whereas a chicken owner has excess eggs and
needs milk. Provided that these two people are in close proximity and can communicate,
they may exchange or barter eggs for milk. But in a more complex economy, money
serves as a mediator for the exchanges of goods or services. For instance, the cow owner
with excess milk may not need other goods until three months from now, or may want
goods from someone who does not need milk. In this case, the “energy” from providing
milk to the economy can be temporarily “stored” as money, which is a form of “energy”
used for many transactions in the economy. Using barter and money as analogies,
describe two mechanisms that can serve to drive an unfavorable chemical reaction in the
cell.
3-49
You are studying a biochemical pathway that requires ATP as an energy source. To your
dismay, the reactions soon stop, partly because the ATP is rapidly used up and partly
because an excess of ADP builds up and inhibits the enzymes involved. You are about to
give up when the following table from a biochemistry textbook catches your eye.
Which of the following reagents are most likely to revitalize your reaction?
(a)
a vast excess of ATP
(b)
glucose 6-phosphate and enzyme E
(c)
creatine phosphate and enzyme A
(d)
pyrophosphate
3-50
The anhydride formed between a carboxylic acid and a phosphate (Figure Q3-50A) is a
high-energy intermediate for some reactions in which ATP is the energy source. Arsenate
can also be incorporated into a similar high-energy intermediate in place of the phosphate
(Figure Q3-50B). Figure Q3-50C shows the reaction profiles for the hydrolysis of these
two high-energy intermediates. What is the effect of substituting arsenate for phosphate
in this reaction?
Figure Q3-50
(a)
(b)
(c)
(d)
3-51
It forms a high-energy intermediate of lower energy.
It forms a high-energy intermediate of the same energy.
It decreases the stability of the high-energy intermediate.
It increases the stability of the high-energy intermediate.
The synthesis of glutamine from glutamic acid requires the production of an activated
intermediate followed by a condensation step that completes the process. Both amino
acids are shown in Figure Q3-51.
Figure Q3-51
Which molecule is added to glutamic acid in the activation step?
(a)
phosphate
(b)
(c)
(d)
3-52
NH3
ATP
ADP
The synthesis of glutamine from glutamic acid requires the production of an activated
intermediate followed by a condensation step that completes the process. Both amino
acids are shown in Figure Q3-52.
Figure Q3-52
In the condensation step, _______________ is displaced by ________________.
(a)
OH, NH3
(b)
ADP, NH2
(c)
ATP, NH3
(d)
phosphate, NH3
3-53
NADH and NADPH are activated carrier molecules that function in completely different
metabolic reactions. Both carry two additional ________ and one additional
_____________. This combination can also be referred to as a hydride ion.
(a)
protons, electron
(b)
electrons, phosphate
(c)
hydrogens, electron
(d)
electrons, proton
3-54
The addition of a new deoxynucleotide to a growing DNA chain requires more energy
than can be obtained by the hydrolysis of ATP to ADP + Pi. What alternative series of
reactions is used, and how does this help overcome the energy barrier for DNA
synthesis?
CHAPTER 4
PROTEIN STRUCTURE AND FUNCTION
 2009 Garland Science Publishing
The Shape and Structure of Proteins
4-1
Match the basic protein functions in the left column with a specific example of
that type of protein in the column on the right.
___ gene regulatory
___ motor
___ storage
___ enzyme
___ transport
___ structural
___ special purpose
___ receptor
___ signal
A. insulin
B. carboxylase
C. rhodopsin
D. hemoglobin
E. ferritin
F. myosin
G. green fluorescent protein
H. tubulin
I. homeodomain proteins
4-2
Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A.
Generally, the total number of nonpolar amino acids has a greater effect on
protein structure than the exact order of amino acids in a polypeptide chain.
B.
The “polypeptide backbone” refers to all atoms in a polypeptide chain, except for
those that form the peptide bonds.
C.
The chemical properties of amino acid side chains include charged, uncharged
polar, and nonpolar.
D.
The relative distribution of polar and nonpolar amino acids in a folded protein is
determined largely by hydrophobic interactions, which favor the clustering of
nonpolar side chains in the interior.
4-3
Fill in the blank spaces in the table below. The first row has been completed for
you.
4-4
Fully folded proteins typically have polar side chains on their surfaces, where
electrostatic attractions and hydrogen bonds can form between the polar group on the
amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar
side chain in their hydrophobic interior. Which of following would not occur to help
accommodate an internal, polar side chain?
(a)
A hydrogen bond forms between two polar side chains.
(b)
A hydrogen bond forms between a polar side chain and protein backbone.
(c)
A hydrogen bond forms between a polar side chain and an aromatic side chain.
(d)
Hydrogen bonds form between polar side chains and a buried water molecule.
4-5
To study how proteins fold, scientists must be able to purify the protein of interest, use
solvents to denature the folded protein, and observe the process of refolding at successive
time points. What is the effect of the solvents used in the denaturation process?
(a)
The solvents break all covalent interactions.
(b)
The solvents break all noncovalent interactions.
(c)
The solvents break some of the noncovalent ineractions, resulting in a misfolded
protein.
(d)
The solvents create a new protein conformation.
4-6
Which of the following statements is true?
(a)
Peptide bonds are the only covalent bonds that can link together two amino acids
in proteins.
(b)
The polypeptide backbone is free to rotate about each peptide bond.
(c)
Nonpolar amino acids tend to be found in the interior of proteins.
(d)
The sequence of the atoms in the polypeptide backbone varies between different
proteins.
4-7
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
A newly synthesized protein generally folds up into a
__________________ conformation. All the information required to
determine a protein’s conformation is contained in its amino acid
__________________. On being heated, a protein molecule will become
__________________ as a result of breakage of __________________
bonds. On removal of urea, an unfolded protein can become
__________________. The final folded conformation adopted by a
protein is that of __________________ energy.
composition
covalent
denatured
highest
irreversible
lowest
noncovalent
renatured
reversible
sequence
stable
unstable
4-8
The correct folding of proteins is necessary to maintain healthy cells and tissues.
Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer’s,
Huntington’s, and Creutzfeld–Jacob disease (the specific faulty protein is different for
each disease). What is the ultimate fate of these disease-causing, unfolded proteins?
(a)
They are degraded.
(b)
They bind a different target protein.
(c)
They form structured filaments.
(d)
They form protein aggregates.
4-9
The three-dimensional coordinates of atoms within a folded protein are determined
experimentally. After researchers obtain a protein’s structural details, they can use
different techniques to highlight particular aspects of the structure. What visual model
best displays a protein’s secondary structures (α helices and β sheets)?
(a)
ribbon
(b)
space-filling
(c)
backbone
(d)
wire
4-10
Typical folded proteins have a stability ranging from 7 to 15 kcal/mol at 37°C. Stability
is a measure of the equilibrium between the folded (F) and unfolded (U) forms of the
protein, with the unfolded form having a greater free energy. See Figure Q4-10: for a
protein with a stability of 7.1 kcal/mol, calculate the fraction of protein that would be
unfolded at equilibrium at 37°C. The equilibrium constant (Keq) is related to the free
energy (G°) by the equation Keq = 10–G°/1.42.
Figure Q4-10
4-11
Although all protein structures are unique, there are common structural building blocks
that are referred to as regular secondary structures. Some have α helices, some have β
sheets, and still others have a combination of both. What makes it possible for proteins to
have these common structural elements?
(a)
specific amino acid sequences
(b)
side-chain interactions
(c)
the hydrophobic core interactions
(d)
hydrogen bonds along the protein backbone
4-12
Which of the following is not a feature commonly observed in α helices?
(a)
left-handedness
(b)
one helical turn every 3.6 amino acids
(c)
cylindrical shape
(d)
amino acid side chains that point outward
4-13
Which of the following is not a feature commonly observed in β sheets?
(a)
antiparallel regions
(b)
coiled-coil patterns
(c)
extended polypeptide backbone
(d)
parallel regions
4-14
You wish to produce a human enzyme, protein A, by introducing its gene into bacteria.
The genetically engineered bacteria make large amounts of protein A, but it is in the form
of an insoluble aggregate with no enzymatic activity. Which of the following procedures
might help you to obtain soluble, enzymatically active protein? Explain your reasoning.
A.
Make the bacteria synthesize protein A in smaller amounts.
B.
Dissolve the protein aggregate in urea, then dilute the solution and gradually
remove the urea.
C.
Treat the insoluble aggregate with a protease.
D.
Make the bacteria overproduce chaperone proteins in addition to protein A.
E.
Heat the protein aggregate to denature all proteins, then cool the mixture.
4-15
Protein structures have several different levels of organization. The primary structure of a
protein is its amino acid sequence. The secondary and tertiary structures are more
complicated. Consider the definitions below and select the one that best fits the term
“protein domain.”
(a)
a small cluster of α helices and β sheets
(b)
the tertiary structure of a substrate-binding pocket
(c)
a complex of more than one polypeptide chain
(d)
a protein segment that folds independently
4-16
The protein structure in Figure Q4-16 contains four α helices arranged in a
bundle. Label each helix by number (1 to 4) starting going from the N terminus to
the C terminus, both of which are labeled. List the six possible pairings of these
helices, and indicate within each pair whether the helices are parallel or
antiparallel.
Figure Q4-16
4-17
For each polypeptide sequence listed, choose from the options given below to indicate
which secondary structure the sequence is most likely to form upon folding. The nonpolar
amino acids are italicized.
A.
B.
C.
Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile
Leu-Leu-Gln-Ser-Ile-Ala-Ser-Val-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile
Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp
amphipathic α helix
hydrophobic α helix
hydrophilic β sheet
4-18
hydrophilic α helix
amphipathic β sheet
Figure Q4-18 shows a fatty acid binding protein from two different angles. Apart from its
two short α helices, its structural elements are extended strands that form a curved β
sheet, which is called a β barrel. Draw arrows on the six top strands in panel (A) (those
running horizontally) to determine whether the β barrel is made up of parallel or
antiparallel strands. Look at panel (B) and predict the relative distribution of polar and
nonpolar side chains (inside the barrel or outside the barrel) and explain your answer.
Figure Q4-18
4-19
Drawn below are segments of β sheets, which are rigid pleated structures held together by
hydrogen bonds between the peptide backbones of adjacent strands (Figure Q4-19). The
amino acid side chains attached to the Cα carbons are omitted for clarity.
Figure Q4-19
A.
For panel (A) and for panel (B), indicate whether the structure is parallel or antiparallel.
B.
Draw the hydrogen bonds as dashed lines (- - - - - -).
4-20
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
The α helices and β sheets are examples of protein __________________
structure. A protein such as hemoglobin, which is composed of more than
one protein __________________, has __________________ structure. A
protein’s amino acid sequence is known as its __________________
structure. A protein __________________ is the modular unit from which
many larger single-chain proteins are constructed. The three-dimensional
conformation of a protein is its __________________ structure.
allosteric
domain
helix
4-21
ligand
primary
quaternary
secondary
subunit
tertiary
In an attempt to define the protein domains of protein X, you treat it with a protease and
use polyacrylamide gel electrophoresis to analyze the peptides produced. In the past, you
have used chymotrypsin to perform this experiment, but the stock of this enzyme has
been used up . You find a stock of elastase and decide to use it instead of waiting for a
new stock of chymotrypsin to arrive.
A.
Give two reasons why elastase is a good substitute for chymotrypsin in this assay.
B.
Why might proteolysis of the same substrate by chymotrypsin or elastase yield
different results?
4-22
You are digesting a protein 625 amino acids long with the enzymes Factor Xa and
thrombin, which are proteases that bind to and cut proteins at particular short sequences
of amino acids. You know the amino acid sequence of the protein and so can draw a map
of where Factor Xa and thrombin should cut it (Figure Q4-22). You find, however, that
treatment with each of these proteases for an hour results in only partial digestion of the
protein, as summarized under the figure. List the segments (A–E) of the protein that are
most likely to be folded into compact, stable domains.
Figure Q4-22
4-23
Calculate how many different amino acid sequences there are for a polypeptide chain 10
amino acids long.
4-24
You have produced a monoclonal antibody that binds to the protein actin. To be sure that
the antibody does not cross-react with other proteins, you test your antibody in a western
blot assay on whole cell lysates that have been subjected to electrophoresis under
nondenaturing conditions (shown in Figure Q4-24A) and denaturing conditions (shown in
Figure Q4-24B). Does the antibody cross-react with other proteins? If so, does this
explain the results in the two western blots? If not, how do you explain the differences
observed?
Figure Q4-24
4-25
Examine the three protein monomers in Figure Q4-25. From the arrangement of
complementary binding surfaces, which are indicated by similarly shaped protrusions and
indentations, decide whether each monomer could assemble into a defined multimer, a
filament, or a sheet.
Figure Q4-25
4-26
For each of the following indicate whether the individual folded polypeptide chain forms
a globular (G) or fibrous (F) protein molecule.
A.
keratin
B.
lysozyme
C.
elastin
D.
collagen
E.
hemoglobin
F.
actin
4-27
Globular proteins fold up into compact, spherical structures that have uneven surfaces.
They tend to form multisubunit complexes, which also have a rounded shape. Fibrous
proteins, in contrast, span relatively large distances within the cell and in the extracellular
space. Which of the proteins below is not classified as a fibrous protein?
(a)
elastase
(b)
collagen
(c)
keratin
(d)
elastin
4-28
You have two purified samples of protein Y: the wild-type (nonmutated) protein and a
mutant version with a single amino acid substitution. When washed through the same gelfiltration column, mutant protein Y runs through the column more slowly than the normal
protein. Which of the following changes in the mutant protein is most likely to explain
this result?
(a)
the loss of a binding site on the mutant protein surface through which protein Y
normally forms dimers
(b)
a change that results in the mutant protein’s acquiring an overall positive instead
of a negative charge
(c)
a change that results in the mutant protein’s being larger than the wild-type
protein
(d)
a change that results in the mutant protein’s having a slightly different shape from
the wild-type protein
4-29
Which of the following statements is true?
(a)
Disulfide bonds are formed by the cross-linking of methionine residues.
(b)
(c)
(d)
Disulfide bonds are formed mainly in proteins that are retained within the cytosol.
Disulfide bonds stabilize but do not change a protein’s final conformation.
Agents such as mercaptoethanol can break disulfide bonds through oxidation.
How Proteins Work
4-30
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
The human immune system produces __________________ of different
immunoglobulins, also called __________________, which enable the
immune system to recognize and fight germs by specifically binding one
or a few related __________________. The hypervariable structural
element that forms the ligand-binding site is comprised of several
__________________. Purified antibodies are useful for a variety of
experimental purposes, including protein purification using
__________________ chromatography.
affinity
antibodies
antigens
β strands
billions
coiled coils
hundreds
ion-exchange
ligands
loops
size-exclusion
4-31
Proteins bind selectively to small molecule targets called ligands. The selection of one
ligand out of a mixture of possible ligands depends on the number of weak, noncovalent
interactions in the protein’s ligand-binding site. Where is the binding site typically
located in the protein structure?
(a)
on the surface of the protein
(b)
inside a cavity on the protein surface
(c)
buried in the interior of the protein
(d)
forms on the surface of the protein in the presence of ligand
4-32
Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A.
The amino acids in the interior of a protein do not interact with the ligand and do
not play a role in selective binding.
B.
Antibodies are Y shaped and are composed of six different polypeptide chains.
C.
ATPases generate ATP for the cell.
D.
Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.
4-33
Fill in the blanks with the labels in the list below to identify various parts of the antibody
structure in Figure Q4-33.
A. constant domain of the light chain
B. constant domain of the heavy chain
C. antigen-binding site
D. variable domain of the heavy chain
E. variable domain of the light chain
Figure Q4-33
4-34
The process of generating monoclonal antibodies is labor-intensive and
expensive. An alternative is to use polyclonal antibodies. A subpopulation of
purified polyclonal antibodies that recognize a particular antigen can be isolated
by chromatography. Which type of chromatography is used for this purpose?
(a)
affinity
(b)
ion-exchange
(c)
gel-filtration
(d)
any of the above
4-35
Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which
renders it an effective antibacterial agent. Into what classification of enzymes does
lysozyme fall?
(a)
isomerase
(b)
protease
(c)
nuclease
(d)
hydrolase
4-36
Which of the following mechanisms best describes the manner in which lysozyme
lowers the energy required for its substrate to reach its transition state
conformation?
(a)
by binding two molecules and orienting them in a way that favors a reaction
between them
(b)
(c)
(d)
by altering the shape of the substrate to mimic the conformation of the transition
state
by speeding up the rate at which water molecules collide with the substrate
by binding irreversibly to the substrate so that it cannot dissociate
4-37
Studies conducted with a lysozyme mutant that contains an Asp→Asn change at position
52 and a Glu→Gln change at position 35 exhibited almost a complete loss in enzymatic
activity. What is the most likely explanation for the decrease in enzyme activity in the
mutant?
(a)
increased affinity for substrate
(b)
absence of negative charges in the active site
(c)
change in the active site scaffold
(d)
larger amino acids in the active site decrease the affinity for substrate
4-38
For some proteins, small molecules are integral to their structure and function. Enzymes
can synthesize some of these small molecules, whereas others, called vitamins, must be
ingested in the food we eat. Which of the following molecules is not classified as a
vitamin but does require the ingestion of a vitamin for its production?
(a)
retinal
(b)
biotin
(c)
zinc
(d)
heme
4-39
For each of the following sentences, fill in the blanks with the best word or phrase
selected from the list below. Not all words or phrases will be used; each word or phrase
should be used only once.
Any substance that will bind to a protein is known as its
__________________. Enzymes bind their __________________ at the
__________________. The enzyme hexokinase is so specific that it reacts
with only one of the two __________________ of glucose. Enzymes
catalyze a chemical reaction by lowering the __________________,
because they provide conditions favorable for the formation of a
__________________ intermediate called the __________________.
Once the reaction is completed, the enzyme releases the
__________________ of the reaction.
activation energy
active site
free energy
high-energy
4-40
inhibitors
isomers
ligand
low-energy
products
substrates
transition state
One way in which an enzyme can lower the activation energy required for a reaction is to
bind the substrate(s) and distort its structure so that the substrate more closely resembles
the transition state of the reaction. This mechanism will be facilitated if the shape and
chemical properties of the enzyme’s active site are more complementary to the transition
state than to the undistorted substrate; in other words, if the enzyme were to have a higher
affinity for the transition state than for the substrate. Knowing this, your friend looked in
an organic chemistry textbook to identify a stable chemical that closely resembles the
transition state of a reaction that converts X into Y. She generated an antibody against
this transition state analog and mixed the antibody with chemical X. What do you think
might happen?
How Proteins Are Controlled
4-41
The biosynthetic pathway for the two amino acids E and H is shown schematically in
Figure Q4-41. You are able to show that E inhibits enzyme V, and H inhibits enzyme X.
Enzyme T is most likely to be subject to feedback inhibition by __________________
alone.
Figure Q4-41
(a)
(b)
(c)
(d)
H
B
C
E
4-42
Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A.
Feedback inhibition is defined as a mechanism of down-regulating enzyme
activity by the accumulation of a product earlier in the pathway.
B.
If an enzyme’s allosteric binding site is occupied, the enzyme may adopt an
alternative conformation that is not optimal for catalysis.
C.
Protein phosphorylation is another way to alter the conformation of an enzyme
and serves exclusively as a mechanism to increase enzyme activity.
D.
GTP binding proteins typically have GTPase activity, and the hydrolysis of GTP
transforms them to the “off” conformation.
4-43
The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In
its active form, with GTP bound, it transmits a downstream signal that leads to cell
proliferation; in its inactive form, with GDP bound, the signal is not transmitted.
Mutations in the gene for Ras are found in many cancers. Of the choices below, which
alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer
cells?
(a)
a change that prevents Ras from being made
(b)
(c)
(d)
a change that increases the affinity of Ras for GDP
a change that decreases the affinity of Ras for GTP
a change that decreases the rate of hydrolysis of GTP by Ras
4-44
Motor proteins use the energy in ATP to transport organelles, rearrange elements of the
cytoskeleton during cell migration, and move chromosomes during cell division. Which
of the following mechanisms is sufficient to ensure the unidirectional movement of a
motor protein along its substrate?
(a)
A conformational change is coupled to the release of a phosphate (Pi).
(b)
The substrate on which the motor moves has a conformational polarity.
(c)
A conformational change is coupled to the binding of ADP.
(d)
A conformational change is linked to ATP hydrolysis.
4-45
The phosphorylation of a protein is typically associated with a change in activity, the
assembly of a protein complex, or the triggering of a downstream signaling cascade. The
addition of ubiquitin, a small polypeptide, is another type of covalent modification that
can affect the protein function. Ubiquitylation often results in ______________.
(a)
membrane association
(b)
protein degradation
(c)
protein secretion
(d)
nuclear translocation
4-46
Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power
many of the cellular processes, increasing the pool of ADP. ADP molecules then bind to
glycolytic enzymes, which will lead to the production of more ATP. The best way to
describe how oxidation energy is converted to ATP energy during glycolysis is by
___________.
(a)
feedback inhibition
(b)
allosteric conformation
(c)
allosteric activation
(d)
substrate-level phosphorylation
4-47
Some of the enzymes that oxidize sugars to yield usable cellular energy (for example,
ATP) are regulated by phosphorylation. For these enzymes, would you expect the
inactive form to be the phosphorylated form or the dephosphorylated form? Explain your
answer.
4-48
Which of the following methods used to study proteins is limited to proteins with a
molecular weight of 50 kD or less?
(a)
x-ray crystallography
(b)
fingerprinting
(c)
nuclear magnetic resonance
(d)
mass spectroscopy
4-49
Determining a protein’s sequence, site of covalent modification, or entire threedimensional structure requires the careful analysis of complex data sets. Which of the
data sets below would you have to interpret to solve the structure of a protein by using xray crystallography?
4-50
Instead of studying one or two proteins or protein complexes present in the cell at any
given time, we can now look at a snapshot of all proteins being expressed in cells being
grown in specific conditions. This large-scale, systematic approach to the study of
proteins is called _______________.
(a)
proteomics
(b)
structural biology
(c)
systems biology
(d)
genomics
4-51
Using the example of the p53 protein, explain how different combinations of covalent
modifications can lead to a wide variety of protein functions.