CHAPTER 4

PROTEIN STRUCTURE AND FUNCTION

2009 Garland Science Publisin!
Te Sa"e and S#ruc#ure $% Pr$#eins
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 A. insulin
___ motor B. carboxylase
___ storage C. rhodopsin
___ enzyme D. hemoglobin
___ transport E. ferritin
___ structural . myosin
___ special purpose !. green fluorescent protein
___ receptor ". tubulin
___ signal #. homeodomain proteins
4-2 #ndicate whether the following statements are true or false. #f a statement is false$ explain
why it is false.
A. !enerally$ 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. %he &polypeptide bac'bone( refers to all atoms in a polypeptide chain$ except for
those that form the peptide bonds.
C. %he chemical properties of amino acid side chains include charged$ uncharged
polar$ and nonpolar.
D. %he relati)e distribution of polar and nonpolar amino acids in a folded protein is
determined largely by hydrophobic interactions$ which fa)or the clustering of
nonpolar side chains in the interior.
4-3 ill in the blan' spaces in the table below. %he first row has been completed for
you.
4-4 ully folded proteins typically ha)e 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 sol)ent. #n contrast$ some proteins ha)e a polar
side chain in their hydrophobic interior. *hich 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 bac'bone.
,c- A hydrogen bond forms between a polar side chain and an aromatic side chain.
,d- "ydrogen bonds form between polar side chains and a buried water molecule.
4-5 %o study how proteins fold$ scientists must be able to purify the protein of interest$ use
sol)ents to denature the folded protein$ and obser)e the process of refolding at successi)e
time points. *hat is the effect of the sol)ents used in the denaturation process+
,a- %he sol)ents brea' all co)alent interactions.
,b- %he sol)ents brea' all nonco)alent interactions.
,c- %he sol)ents brea' some of the nonco)alent ineractions$ resulting in a misfolded
protein.
,d- %he sol)ents create a new protein conformation.
4-6 *hich of the following statements is true+
,a- .eptide bonds are the only co)alent bonds that can lin' together two amino acids
in proteins.
,b- %he polypeptide bac'bone is free to rotate about each peptide bond.
,c- /onpolar amino acids tend to be found in the interior of proteins.
,d- %he se0uence of the atoms in the polypeptide bac'bone )aries between different
proteins.
4-7 or each of the following sentences$ fill in the blan's with the best word or phrase
selected from the list below. /ot all words or phrases will be used1 each word or phrase
should be used only once.
A newly synthesized protein generally folds up into a
__________________ conformation. All the information re0uired to
determine a protein2s conformation is contained in its amino acid
__________________. 3n being heated$ a protein molecule will become
__________________ as a result of brea'age of __________________
bonds. 3n remo)al of urea$ an unfolded protein can become
__________________. %he final folded conformation adopted by a
protein is that of __________________ energy.
composition irre)ersible re)ersible
co)alent lowest se0uence
denatured nonco)alent stable
highest renatured unstable
4-8 %he correct folding of proteins is necessary to maintain healthy cells and tissues.
4nfolded proteins are responsible for such neurodegenerati)e disorders as Alzheimer2s$
"untington2s$ and Creutzfeld56acob disease ,the specific faulty protein is different for
each disease-. *hat is the ultimate fate of these disease7causing$ unfolded proteins+
,a- %hey are degraded.
,b- %hey bind a different target protein.
,c- %hey form structured filaments.
,d- %hey form protein aggregates.
4-9 %he three7dimensional coordinates of atoms within a folded protein are determined
experimentally. After researchers obtain a protein2s structural details$ they can use
different techni0ues to highlight particular aspects of the structure. *hat )isual model
best displays a protein2s secondary structures ,8 helices and 9 sheets-+
,a- ribbon
,b- space7filling
,c- bac'bone
,d- wire
4-10 %ypical folded proteins ha)e a stability ranging from : to ;< 'cal=mol at >:?C. @tability is
a measure of the e0uilibrium between the folded ,- and unfolded ,4- forms of the
protein$ with the unfolded form ha)ing a greater free energy. @ee igure AB7;CD for a
protein with a stability of :.; 'cal=mol$ calculate the fraction of protein that would be
unfolded at e0uilibrium at >:?C. %he e0uilibrium constant ,Ke0- is related to the free
energy ,G?- by the e0uation Ke0 E ;C
5G?=;.BF
.
igure AB7;C
4-11 Although all protein structures are uni0ue$ there are common structural building bloc's
that are referred to as regular secondary structures. @ome ha)e 8 helices$ some ha)e 9
sheets$ and still others ha)e a combination of both. *hat ma'es it possible for proteins to
ha)e these common structural elements+
,a- specific amino acid se0uences
,b- side7chain interactions
,c- the hydrophobic core interactions
,d- hydrogen bonds along the protein bac'bone
4-12 *hich of the following is not a feature commonly obser)ed in 8 helices+
,a- left7handedness
,b- one helical turn e)ery >.G amino acids
,c- cylindrical shape
,d- amino acid side chains that point outward
4-13 *hich of the following is not a feature commonly obser)ed in 9 sheets+
,a- antiparallel regions
,b- coiled7coil patterns
,c- extended polypeptide bac'bone
,d- parallel regions
4-14 Hou wish to produce a human enzyme$ protein A$ by introducing its gene into bacteria.
%he genetically engineered bacteria ma'e large amounts of protein A$ but it is in the form
of an insoluble aggregate with no enzymatic acti)ity. *hich of the following procedures
might help you to obtain soluble$ enzymatically acti)e protein+ Explain your reasoning.
A. Ma'e the bacteria synthesize protein A in smaller amounts.
B. Dissol)e the protein aggregate in urea$ then dilute the solution and gradually
remo)e the urea.
C. %reat the insoluble aggregate with a protease.
D. Ma'e the bacteria o)erproduce chaperone proteins in addition to protein A.
E. "eat the protein aggregate to denature all proteins$ then cool the mixture.
4-15 .rotein structures ha)e se)eral different le)els of organization. %he primary structure of a
protein is its amino acid se0uence. %he 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 8 helices and 9 sheets
,b- the tertiary structure of a substrate7binding poc'et
,c- a complex of more than one polypeptide chain
,d- a protein segment that folds independently
4-16 %he protein structure in igure AB7;G contains four 8 helices arranged in a
bundle. Iabel each helix by number ,; to B- starting going from the / terminus to
the C terminus$ both of which are labeled. Iist the six possible pairings of these
helices$ and indicate within each pair whether the helices are parallel or
antiparallel.
igure AB7;G
4-17 or each polypeptide se0uence listed$ choose from the options gi)en below to indicate
which secondary structure the se0uence is most li'ely to form upon folding. %he nonpolar
amino acids are italicized.
A. Leu7Gly7Val7Leu7@er7Leu7Phe7@er7Gly7Leu7Met7Trp7Phe7Phe7Trp7Ile
B. Leu7Leu7!ln7@er7Ile7Ala7@er7Val7Leu7!ln7@er7Leu-Leu7Cys7Ala7Ile
C. %hr7Leu7Asn7Ile7@er7Phe7!ln7Met7!lu7Leu7Asp7Val7@er7Ile7Arg7Trp
amphipathic 8 helix hydrophilic 8 helix
hydrophobic 8 helix amphipathic 9 sheet
hydrophilic 9 sheet
4-18 igure AB7;J shows a fatty acid binding protein from two different angles. Apart from its
two short 8 helices$ its structural elements are extended strands that form a cur)ed 9
sheet$ which is called a 9 barrel. Draw arrows on the six top strands in panel ,A- ,those
running horizontally- to determine whether the 9 barrel is made up of parallel or
antiparallel strands. Ioo' at panel ,B- and predict the relati)e distribution of polar and
nonpolar side chains ,inside the barrel or outside the barrel- and explain your answer.
igure AB7;J
4-19 Drawn below are segments of 9 sheets$ which are rigid pleated structures held together by
hydrogen bonds between the peptide bac'bones of adKacent strands ,igure AB7;L-. %he
amino acid side chains attached to the C8 carbons are omitted for clarity.
igure AB7;L
A. or panel ,A- and for panel ,B-$ indicate whether the structure is parallel or
antiparallel.
B. Draw the hydrogen bonds as dashed lines ,7 7 7 7 7 7-.
4-20 or each of the following sentences$ fill in the blan's with the best word or phrase
selected from the list below. /ot all words or phrases will be used1 each word or phrase
should be used only once.
%he 8 helices and 9 sheets are examples of protein __________________
structure. A protein such as hemoglobin$ which is composed of more than
one protein __________________$ has __________________ structure. A
protein2s amino acid se0uence is 'nown as its __________________
structure. A protein __________________ is the modular unit from which
many larger single7chain proteins are constructed. %he three7dimensional
conformation of a protein is its __________________ structure.
allosteric ligand secondary
domain primary subunit
helix 0uaternary tertiary
4-21 #n an attempt to define the protein domains of protein M$ you treat it with a protease and
use polyacrylamide gel electrophoresis to analyze the peptides produced. #n the past$ you
ha)e used chymotrypsin to perform this experiment$ but the stoc' of this enzyme has
been used up . Hou find a stoc' of elastase and decide to use it instead of waiting for a
new stoc' of chymotrypsin to arri)e.
A. !i)e two reasons why elastase is a good substitute for chymotrypsin in this assay.
B. *hy might proteolysis of the same substrate by chymotrypsin or elastase yield
different results+
4-22 Hou are digesting a protein GF< amino acids long with the enzymes actor Ma and
thrombin$ which are proteases that bind to and cut proteins at particular short se0uences
of amino acids. Hou 'now the amino acid se0uence of the protein and so can draw a map
of where actor Ma and thrombin should cut it ,igure AB7FF-. Hou find$ howe)er$ that
treatment with each of these proteases for an hour results in only partial digestion of the
protein$ as summarized under the figure. Iist the segments ,A5E- of the protein that are
most li'ely to be folded into compact$ stable domains.
igure AB7FF
4-23 Calculate how many different amino acid se0uences there are for a polypeptide chain ;C
amino acids long.
4-24 Hou ha)e produced a monoclonal antibody that binds to the protein actin. %o be sure that
the antibody does not cross7react with other proteins$ you test your antibody in a western
blot assay on whole cell lysates that ha)e been subKected to electrophoresis under
nondenaturing conditions ,shown in igure AB7FBA- and denaturing conditions ,shown in
igure AB7FBB-. Does the antibody cross7react with other proteins+ #f so$ does this
explain the results in the two western blots+ #f not$ how do you explain the differences
obser)ed+
igure AB7FB
4-25 Examine the three protein monomers in igure AB7F<. rom 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.
igure AB7F<
4-26 or each of the following indicate whether the indi)idual folded polypeptide chain forms
a globular ,!- or fibrous ,- protein molecule.
A. 'eratin
B. lysozyme
C. elastin
D. collagen
E. hemoglobin
. actin
4-27 !lobular proteins fold up into compact$ spherical structures that ha)e une)en surfaces.
%hey tend to form multisubunit complexes$ which also ha)e a rounded shape. ibrous
proteins$ in contrast$ span relati)ely large distances within the cell and in the extracellular
space. *hich of the proteins below is not classified as a fibrous protein+
,a- elastase
,b- collagen
,c- 'eratin
,d- elastin
4-28 Hou ha)e two purified samples of protein HD the wild7type ,nonmutated- protein and a
mutant )ersion with a single amino acid substitution. *hen washed through the same gel7
filtration column$ mutant protein H runs through the column more slowly than the normal
protein. *hich of the following changes in the mutant protein is most li'ely to explain
this result+
,a- the loss of a binding site on the mutant protein surface through which protein H
normally forms dimers
,b- a change that results in the mutant protein2s ac0uiring an o)erall positi)e instead
of a negati)e charge
,c- a change that results in the mutant protein2s being larger than the wild7type
protein
,d- a change that results in the mutant protein2s ha)ing a slightly different shape from
the wild7type protein
4-29 *hich of the following statements is true+
,a- Disulfide bonds are formed by the cross7lin'ing of methionine residues.
,b- Disulfide bonds are formed mainly in proteins that are retained within the cytosol.
,c- Disulfide bonds stabilize but do not change a protein2s final conformation.
,d- Agents such as mercaptoethanol can brea' disulfide bonds through oxidation.
H$& Pr$#eins '$r(
4-30 or each of the following sentences$ fill in the blan's with the best word or phrase
selected from the list below. /ot all words or phrases will be used1 each word or phrase
should be used only once.
%he 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 __________________. %he hyper)ariable structural
element that forms the ligand7binding site is comprised of se)eral
__________________. .urified antibodies are useful for a )ariety of
experimental purposes$ including protein purification using
__________________ chromatography.
affinity billions ligands
antibodies coiled coils loops
antigens hundreds size7exclusion
9 strands ion7exchange
4-31 .roteins bind selecti)ely to small molecule targets called ligands. %he selection of one
ligand out of a mixture of possible ligands depends on the number of wea'$ nonco)alent
interactions in the protein2s ligand7binding site. *here is the binding site typically
located in the protein structure+
,a- on the surface of the protein
,b- inside a ca)ity 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 #ndicate whether the following statements are true or false. #f a statement is false$ explain
why it is false.
A. %he amino acids in the interior of a protein do not interact with the ligand and do
not play a role in selecti)e binding.
B. Antibodies are H shaped and are composed of six different polypeptide chains.
C. A%.ases generate A%. for the cell.
D. "exo'inase recognizes and phosphorylates only one of the glucose stereoisomers.
4-33 ill in the blan's with the labels in the list below to identify )arious parts of the antibody
structure in igure AB7>>.
A. constant domain of the light chain
B. constant domain of the hea)y chain
C. antigen7binding site
D. )ariable domain of the hea)y chain
E. )ariable domain of the light chain
igure AB7>>
4-34 %he process of generating monoclonal antibodies is labor7intensi)e and
expensi)e. An alternati)e is to use polyclonal antibodies. A subpopulation of
purified polyclonal antibodies that recognize a particular antigen can be isolated
by chromatography. *hich type of chromatography is used for this purpose+
,a- affinity
,b- ion7exchange
,c- gel7filtration
,d- any of the abo)e
4-35 Iysozyme is an enzyme that specifically recognizes bacterial polysaccharides$ which
renders it an effecti)e antibacterial agent. #nto what classification of enzymes does
lysozyme fall+
,a- isomerase
,b- protease
,c- nuclease
,d- hydrolase
4-36 *hich of the following mechanisms best describes the manner in which lysozyme
lowers the energy re0uired for its substrate to reach its transition state
conformation+
,a- by binding two molecules and orienting them in a way that fa)ors a reaction
between them
,b- by altering the shape of the substrate to mimic the conformation of the transition
state
,c- by speeding up the rate at which water molecules collide with the substrate
,d- by binding irre)ersibly to the substrate so that it cannot dissociate
4-37 @tudies conducted with a lysozyme mutant that contains an AspNAsn change at position
<F and a !luN!ln change at position >< exhibited almost a complete loss in enzymatic
acti)ity. *hat is the most li'ely explanation for the decrease in enzyme acti)ity in the
mutant+
,a- increased affinity for substrate
,b- absence of negati)e charges in the acti)e site
,c- change in the acti)e site scaffold
,d- larger amino acids in the acti)e site decrease the affinity for substrate
4-38 or some proteins$ small molecules are integral to their structure and function. Enzymes
can synthesize some of these small molecules$ whereas others$ called )itamins$ must be
ingested in the food we eat. *hich of the following molecules is not classified as a
)itamin but does re0uire the ingestion of a )itamin for its production+
,a- retinal
,b- biotin
,c- zinc
,d- heme
4-39 or each of the following sentences$ fill in the blan's with the best word or phrase
selected from the list below. /ot all words or phrases will be used1 each word or phrase
should be used only once.
Any substance that will bind to a protein is 'nown as its
__________________. Enzymes bind their __________________ at the
__________________. %he enzyme hexo'inase is so specific that it reacts
with only one of the two __________________ of glucose. Enzymes
catalyze a chemical reaction by lowering the __________________$
because they pro)ide conditions fa)orable for the formation of a
__________________ intermediate called the __________________.
3nce the reaction is completed$ the enzyme releases the
__________________ of the reaction.
acti)ation energy inhibitors products
acti)e site isomers substrates
free energy ligand transition state
high7energy low7energy
4-40 3ne way in which an enzyme can lower the acti)ation energy re0uired 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. %his mechanism will be facilitated if the shape and
chemical properties of the enzyme2s acti)e site are more complementary to the transition
state than to the undistorted substrate1 in other words$ if the enzyme were to ha)e a higher
affinity for the transition state than for the substrate. Onowing this$ your friend loo'ed in
an organic chemistry textboo' to identify a stable chemical that closely resembles the
transition state of a reaction that con)erts M into H. @he generated an antibody against this
transition state analog and mixed the antibody with chemical M. *hat do you thin' might
happen+
H$& Pr$#eins Are C$n#r$lled
4-41 %he biosynthetic pathway for the two amino acids E and " is shown schematically in
igure AB7B;. Hou are able to show that E inhibits enzyme P$ and " inhibits enzyme M.
Enzyme % is most li'ely to be subKect to feedbac' inhibition by __________________
alone.
igure AB7B;
,a- "
,b- B
,c- C
,d- E
4-42 #ndicate whether the following statements are true or false. #f a statement is false$ explain
why it is false.
A. eedbac' inhibition is defined as a mechanism of down7regulating enzyme
acti)ity by the accumulation of a product earlier in the pathway.
B. #f an enzyme2s allosteric binding site is occupied$ the enzyme may adopt an
alternati)e conformation that is not optimal for catalysis.
C. .rotein phosphorylation is another way to alter the conformation of an enzyme
and ser)es exclusi)ely as a mechanism to increase enzyme acti)ity.
D. !%. binding proteins typically ha)e !%.ase acti)ity$ and the hydrolysis of !%.
transforms them to the &off( conformation.
4-43 %he Qas protein is a !%.ase that functions in many growth7factor signaling pathways. #n
its acti)e form$ with !%. bound$ it transmits a downstream signal that leads to cell
proliferation1 in its inacti)e form$ with !D. bound$ the signal is not transmitted.
Mutations in the gene for Qas are found in many cancers. 3f the choices below$ which
alteration of Qas acti)ity is most li'ely to contribute to the uncontrolled growth of cancer
cells+
,a- a change that pre)ents Qas from being made
,b- a change that increases the affinity of Qas for !D.
,c- a change that decreases the affinity of Qas for !%.
,d- a change that decreases the rate of hydrolysis of !%. by Qas
4-44 Motor proteins use the energy in A%. to transport organelles$ rearrange elements of the
cytos'eleton during cell migration$ and mo)e chromosomes during cell di)ision. *hich
of the following mechanisms is sufficient to ensure the unidirectional mo)ement of a
motor protein along its substrate+
,a- A conformational change is coupled to the release of a phosphate ,.i-.
,b- %he substrate on which the motor mo)es has a conformational polarity.
,c- A conformational change is coupled to the binding of AD..
,d- A conformational change is lin'ed to A%. hydrolysis.
4-45 %he phosphorylation of a protein is typically associated with a change in acti)ity$ the
assembly of a protein complex$ or the triggering of a downstream signaling cascade. %he
addition of ubi0uitin$ a small polypeptide$ is another type of co)alent modification that
can affect the protein function. 4bi0uitylation often results in ______________.
,a- membrane association
,b- protein degradation
,c- protein secretion
,d- nuclear translocation
4-46 Energy re0uired by the cell is generated in the form of A%.. A%. is hydrolyzed to power
many of the cellular processes$ increasing the pool of AD.. AD. molecules then bind to
glycolytic enzymes$ which will lead to the production of more A%.. %he best way to
describe how oxidation energy is con)erted to A%. energy during glycolysis is by
___________.
,a- feedbac' inhibition
,b- allosteric conformation
,c- allosteric acti)ation
,d- substrate7le)el phosphorylation
4-47 @ome of the enzymes that oxidize sugars to yield usable cellular energy ,for example$
A%.- are regulated by phosphorylation. or these enzymes$ would you expect the inacti)e
form to be the phosphorylated form or the dephosphorylated form+ Explain your answer.
4-48 *hich of the following methods used to study proteins is limited to proteins with a
molecular weight of <C 'D or less+
,a- x7ray crystallography
,b- fingerprinting
,c- nuclear magnetic resonance
,d- mass spectroscopy
4-49 Determining a protein2s se0uence$ site of co)alent modification$ or entire three7
dimensional structure re0uires the careful analysis of complex data sets. *hich of the
data sets below would you ha)e to interpret to sol)e the structure of a protein by using x7
ray crystallography+
4-50 #nstead of studying one or two proteins or protein complexes present in the cell at any
gi)en time$ we can now loo' at a snapshot of all proteins being expressed in cells being
grown in specific conditions. %his large7scale$ systematic approach to the study of
proteins is called _______________.
,a- proteomics
,b- structural biology
,c- systems biology
,d- genomics
4-51 4sing the example of the p<> protein$ explain how different combinations of co)alent
modifications can lead to a wide )ariety of protein functions.