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QSB #6 CHAPTER 1- 3

Shape and structure of proteins

MBC Chapter 3

interval
Course outline: what, when, and why?

Biochemistry 1 Modeling of biological processes 1 Design 1

introduction, motivation, basic concepts reactions, ODEs, TX/TL, regulation autorepression, toggle switch, AR clock

Biochemistry 2 Modeling of biological processes 2 Design 2

structure, function, reactions, systems post-TX, stochasticity, Gillespie, Langevin chemotaxis, retroactivity

Molecular biology 1 Analysis techniques 1 Design 3

DNA, replication, transcription, translation stability, nullclines, sensitivity, perturbations insulation, shared resources, cell-free extracts

Molecular biology 2 Analysis techniques 2

variations, regulation adaptation, disturbance, 2D limit cycles

Recombinant DNA techniques Analysis techniques 3 Final project

restriction, cloning, libraries nD limit cycles, bifurcation, model reduction write-up, poster, presentation

2
Overview for today
MAIN OBJECTIVE
Get familiar with the basic shape and structure of proteins

1.What are proteins made of?

2.What is primary structure?
3.What is secondary structure?
4.What is tertiary structure?
5.What is quaternary structure?
6.Why and how do proteins fold?
7.Why are domains/modules beneficial?
8.What is the connection between sequence and form?
3
Recap

4
Energy comes
CATALYSIS AND from
THE USEoxidation
OF ENERGY BY of organic molecules
CELLS

PHOTOSYNTHESIS CELLULAR RESPIRATION Figure

CO2 + H2O O2 + SUGARS SUGARS + O2 H2O + CO2 respira
in the
O2 CO2 CO2 O2 conver
sunligh
sugars
Plants,
PLANTS SUGARS AND MOST
H2O H2O the car
ALGAE OTHER ORGANIC LIVING
SOME BACTERIA MOLECULES ORGANISMS purpos
hydrog
as a by
ENERGY USEFUL
CHEMICAL- produc
OF as food
SUNLIGHT BOND
ENERGY organis
a proc
the sam
taken u
by pho
is H2O. A cell is therefore able to obtain energy from sugars or other organic mol- organis
ecules by allowing their carbon and hydrogen atoms to combine with oxygen to bond5 e
 conversi
rier, as illustrated in Figure 2–22. Enzymes are among the most effective catalysts unless c
Enzymes lower the activation energy activatio
b) from it
reaction
This ene
an unusu
activation enzyme lowers molecule
energy for activation X Y, t
a reaction energy for much lar
total energy

total energy
Y X catalyzed this reac
reaction
Y Y
d more rar
Y X
always p
b b
total ene
reactant reactant favorable
minus en
X X (B) Energ
can be lo
c c by the lin
product product
particula
(A) (B) greatly re
uncatalyzed enzyme-catalyzed
reaction pathway reaction pathway reactions

6
 Carrier molecules (ATP) store and transport energy
CATALYSIS AND THE USE OF ENERGY BY CELLS
Chapter 2: Cell Chemistry and Bioenergetics

phosphoanhydride bonds
ENERGY ENERGY
Figure 2–31 Energy transfer and the
role of activated
_ _ carriers
_ in metabolism.
O O O ADENINE
food molecule
By _serving as energy shuttles, activated
molecule
O molecules
carrier P O P Operform
P O their
CH2 function
needed by cell
as go-betweens
O O thatOlink the breakdown ATP
of food molecules and the release of
RIBOSE
energy (catabolism) to the energy-requiring
energetically energetically
favorable unfavorable
biosynthesis
H2O of small and large organic
reaction reaction molecules (anabolism).
ENERGY
_ _ _
O O O ADENINE
_ _
oxidized food activated carrier molecule molecule H+ + O P OH + O P O P O CH2
molecule available in cell
O O O
ADP
CATABOLISM ANABOLISM inorganic RIBOSE
phosphate (Pi)

and two molecules that are closely related to each other, NADH and
energetically
. Cells use such activated carrier molecules like money to favorable reaction, such as the oxidation of foodstuffs, to an en
pay for reac-
at otherwise could not take place. getically unfavorable reaction, such as the generation of an activated carrier7m
MBoC6 m2.55/2.31
 able reaction of rock falling has been directly coupled to the energetically unfavor- only. In (B), the same reaction is coupled
able reaction of lifting the bucket of water. Note that because part of the energy is to a second reaction; this second reaction

Coupling favorable and unfavorable reactions

used to do work in Figure 2–32B, the rocks hit the ground with less velocity than in
Figure 2–32A, and correspondingly less energy is dissipated as heat.
is analogous to the synthesis of activated
carrier molecules. The energy produced in
(B) is in a more useful form than in (A) and
Similar processes occur in cells, where enzymes play the role of the paddle can be used to drive a variety of otherwise
wheel. By mechanisms that we discuss later in this chapter, enzymes couple an energetically unfavorable reactions (C).

(A) (B) (C)

hydraulic USEFUL
machines WORK

heat heat

kinetic energy of falling rocks is part of the kinetic energy is used to lift the potential kinetic energy stored in
transformed into heat energy only a bucket of water, and a correspondingly the raised bucket of water can be
smaller amount is transformed into heat used to drive hydraulic machines that
carry out a variety of useful tasks

8
synthesis of nucleic acids (polynucleotides) from nucleoside triphosphates, as

Building polymers by repetitive condensation

illustrated on the right side of Figure 2–43.
Note that the repetitive condensation reactions that produce macromolecules
can be oriented in one of two ways, giving rise to either the head polymerization
HOW CELLS OBTAIN ENERGY FROM FOOD

or the tail polymerization of monomers. In so-called head polymerization, the

reactive bond required for the condensation reaction is carried on the end of the HEAD POLYMERIZATION (e.g., PROTEINS, FATTY ACIDS)
MBoC6 m2.66/2.42
base
3
P P P O 6 + 7
sugar
base
1
OH each monomer carries a high-energy
high-energy intermediate P O
sugar bond that will be used for the
base 6 addition of the next monomer
2
2 ATP
P O
P Pi sugar

H O 7
OH
HOW CELLS OBTAIN ENERGY
2
FROM FOOD
polynucleotide 73
base chain containing
3 2 ADP 2 Pi two nucleotides
P O
sugar products of base
HEAD POLYMERIZATION
ATP hydrolysis
1
(e.g., PROTEINS, FATTY ACIDS) growing polymer, and it must
TAIL POLYMERIZATION therefore
(e.g., DNA, be regenerated each time
RNA, POLYSACCHARIDES)
OH P O
sugar
is added. In this case, each monomer brings with it the reactive
nucleoside base used in adding the next monomer in the series. In tail polymeriza
monophosphate 2
6 + 7 1
bond carried by each monomer is instead + used
7 immediately for
P O
sugar
base
(Figure 2–44).
polynucleotide chain
each monomer carries a3 high-energy We shall see in later chapters that both
each of these
monomer carriestypes of po
containing three nucleotides
bond that will be used for the a high-energy bond
6
P O
addition of the next monomer
sugar
used. The synthesis of polynucleotides
7 and some simple polysa
for its own addition
by tail polymerization, for example, whereas the synthesis of pro
MBoC6 m2.68/
OH head polymerization process.
Figure 2–43 Synthesis of a polynucleotide, RNA or DNA, is a multistep process driven by ATP
7 1
hydrolysis. In the first step, a nucleoside monophosphate is activated by the sequential transfer of
the terminal phosphate groups from two ATP molecules. The high-energy intermediate formed—a Summary 9
 sugar in a cell, compared with Energy-yielding
ordinary pathways like these, in which organic molecules both donate
The glycolytic pathway is outlined in Figure 2–46 and shown in more detail in andoxidized
burning. (A) If the sugar were accepttoelectrons (and which are often, as in these cases, anaerobic), are called
el 2–8 (pp. 104–105) and Movie 2.5. Glycolysis involves a sequence of 10 sep- CO2 and H2O in a single step, it would

Breakdown of sugar
e reactions, each producing a different sugar intermediate and each catalyzed
different enzyme. Like most enzymes, these have names ending in ase—such
somerase and dehydrogenase—to indicate the type of reaction they catalyze.
release an amount of energy much larger
than could be captured for useful purposes.
(B) In the cell, enzymes catalyze oxidation
via a series of small steps in which free one molecule
CH2OH
O

Although no molecular oxygen is used in glycolysis, oxidation occurs, in that energy is transferred in conveniently sized of glucose OH
trons are removed by NAD+ (producing NADH) from some of the carbons packets to carrier molecules—most often HO OH energy
ATP and NADH. At each step, an enzyme investment
ved from the glucose molecule. The stepwise nature of the process releases OH to be
energy of oxidation in small packets, so that much of it can be stored in acti- controls the reaction by reducing the
ATP STEP 1 recouped
activation-energy barrier that has to be later
ed carrier molecules rather than all of it being released as heat (see Figure surmounted before the specific reaction
5). Thus, some of the energy released by oxidation drives the direct synthesis can occur. The total free energy released is STEP 2
ATP molecules from ADP and Pi, and some remains with the electrons in the exactly the same in (A) and (B).
tron carrier NADH. ATP STEP 3

(A) DIRECT BURNING OF SUGAR (B) STEPWISE OXIDATION OF SUGAR IN CELLS P OH2C O CH2O P
IN NONLIVING SYSTEM fructose 1,6-
bisphosphate HO
OH
large activation
small activation energies OH
energy overcome
by the heat from overcome by enzymes that cleavage of
work at body temperature STEP 4
a fire six-carbon
sugar to two
SUGAR + O2 SUGAR + O2
three-carbon
STEP 5 sugars
free energy

CHO CHO
some free two molecules of
all free energy is glyceraldehyde
energy stored in CHOH CHOH
released as heat; 3-phosphate
activated carrier
none is stored molecules CH2O P CH2O P
NADH STEP 6 NADH
Figure
ATP STEP 7 ATP Each o
CO2 + H2O CO2 + H2O
by a dif
STEP 8
cleaves
carbon
STEP 9 energy
generation
molecu
As indic
ATP STEP 10 ATP generat
COO– COO– two mo
early, e
two molecules C O C O results
of pyruvate
NADH
CH3 CH3 (see
10als
MBoC6 m2.69/2.45
 account for the net yield of two ATP molecules and two NADH molecules per mol-

S
phosphogl
ecule of glucose
HO (seeO Panel 2–8, pp. 104–105). (A) STEPS 6 AND 7 OF GYCOLYSIS
As we have just seen, ATP can be formed readily from ADP when a reaction
C

Oxidation for energy storage

intermediate is formed with a phosphate bond of higher energy than the terminal H O
phosphate bond
H Cin ATP.
OH Phosphate bonds can be ordered in energy by comparing
3-phosphoglycerate C
the standard free-energy
CH2O P
change (∆G°) for the breakage of each bond by hydroly- glyceraldehyde
sis. Figure 2–50 compares the high-energy phosphoanhydride bonds in ATP with H C OH 3-phosphate

the energy of some other phosphate bonds, several of which are generated during CH2O P
glycolysis.
A short-lived covalent bond is
(B) HS ENZYME formed between glyceraldehyde
SUMMARY OF STEPS 6 AND 7
Organisms Store Food Molecules in Special Reservoirs NAD+
3-phosphate and the –SH group of
a cysteine side chain of the enzyme
H O HO O
The oxidation of an aldehyde to a glyceraldehyde 3-phosphate
All organisms need to maintain a high ATP/ADP
NADH ratio to maintain biological order
carboxylic acid releases energy, dehydrogenase. The enzyme also
C C

glyceraldehyde 3-phosphate dehydrogenase

in their cells. Yet animals have only periodicmuchaccess to food,
of which andinplants
is captured the need to ENZYME S
binds noncovalently to NAD+.
survive aldehyde
overnight without sunlight, activated carriers ATP and NADH.
carboxylic when they are unable to produce sugar from
H C OH
photosynthesis. For this reason,acidboth plants and animals convert sugars and fats
to special forms for storage
ATP (Figure 2–51). H C OH Glyceraldehyde 3-phosphate is
To compensate for long periods of fasting, animals store fatty acids as fat oxidized as the enzyme removes a
CH2O P hydrogen atom (yellow) and
droplets composed of water-insoluble triacylglycerols (also called triglycerides).

STEP 6
transfers it, along with an electron,
The triacylglycerols in animals are mostly stored in the cytoplasm of specialized to NAD+, forming NADH (see
Figure 2–37). Part of the energy
fat cells called adipocytes. For shorter-term storage, sugar is stored as glucose NADH + H
+
released by the oxidation of the
aldehyde is thus stored in NADH,
MBoC6 e13.05/2.48 and part is stored in the high-
ENZYME S high-energy
thioester bond energy thioester bond that links
glyceraldehyde 3-phosphate to the
P O O P O O C O enzyme.
1,3-bisphosphoglycerate
C C
H C OH
ATP
CH2O P
NADH
high-energy A molecule of inorganic phosphate
inorganic
phosphate Pi displaces the high-energy thioester
formation of hydrolysis of phosphate
bond bond to create 1,3-bisphospho-
high-energy bond high-energy bond glycerate, which contains a
free energy

high-energy phosphate bond.

P O
ADP
C O
NAD+ 1,3-bisphosphoglycerate
H C OH
H O HO O
glyceraldehyde CH2O P
3-phosphoglycerate
C 3-phosphate C
Figure 2–49 Schematic view of the

phosphoglycerate kinase
C–H bond P P A ADP
oxidation coupled reactions that form NADH and The high-energy phosphate group
ATP in steps 6 and 7 of glycolysis. The is transferred to ADP to form ATP.
C–H bond oxidation energy drives the

STEP 7
P P P A ATP
formation of both NADH and a high-energy
STEP 6 STEP 7
phosphate bond. The breakage of the high-
TOTAL ENERGY CHANGE for step 6 followed by step 7 is a favorable –12.5 kJ/mole energy bond then drives ATP formation. HO O
C

H C OH
3-phosphoglycerate
CH2O P 11
Shape and structure
of proteins

12
 Methionine Aspartic acid acid side
Leucine chains. There are three types of these weak bonds: hydrogen bon
Tyrosine
(Met) (Asp) trostatic attractions, and van der Waals attractions, as explained in Chapt
(Leu)
(Tyr)

Proteins are polypeptides

p. 44). Individual noncovalent bonds are 30–300 times weaker than th
covalent bonds that create biological molecules. But many weak bonds
(“water-fearing”), others are negatively or positively charged,
parallel cansome
hold two readily formof a polypeptide chain tightly together. In
regions
covalent bonds, and so on. Panel 3–1 (pp. 112–113)the shows their atomic structures
combined strength of large numbers of such noncovalent bonds det
and Figure 3–2 lists their abbreviations. the stability of each folded shape (Figure 3–4).
As discussed in Chapter 2, atoms behave almost as if they were hard spheres
110 Chapter 3: Proteins with a definite radius (their van der Waals radius). The requirement that no two
AMINO ACID SIDE CHAIN A
atoms overlap plus other constraints limit the possible bond angles in a poly-
peptide chain (Figure 3–3), severely restricting the possible three-dimensional Aspartic acid Asp D negative Alanin
arrangements (or conformations) of atoms. Nevertheless, a longGlutamic
MBoC6 m3.01/3.01 flexible chainacid Glu E negative Glycin
such as OH
a protein can still fold in an enormous Figure
number 3–1ofTheways.components of a protein.
A protein consists Arginine
of different
a polypeptide Arg R positive Valine
O O The folding of a protein chain is also determined by many Lysine
sets of Lys K positive Leucin
weak noncovalent bonds that form betweenbackbone one part withof theattached
chain and sideanother.
chains. Each
C These involve atoms in the polypeptide backbone, type of as protein
well as differs
atoms inHistidine
its sequence
in the amino and
His H positive Isoleuc
polypeptide backbone side chains
acid side chains. There are three types of these number of amino
weak bonds: acids;
hydrogen therefore,
Asparagine
bonds, elec-it is the
Asn N uncharged polar Proline
CH2 CH
trostatic attractions,
2 sequence of the chemicallyGlutamine
and van der Waals attractions, as explained in Chapter 2 (see different side
Gln Q uncharged polar Pheny
chains that makes each protein
Serine distinct.
the typical Ser S uncharged polar Methio
H H O H H O p. 44). Individual O
noncovalent bonds are 30–300 times weaker than
amino covalent bonds that create The two ends of
biological molecules. But many weak bonds
carboxyl
a polypeptide
Threonine chain are
acting in Thr T uncharged polar Trypto
+
terminus H N C C N C C N C C parallel N Ccan hold C two regions
terminus chemically
of a polypeptide different:
chain tightly the end
together. In carrying
this way, the
Tyrosine
+ Tyr Y uncharged polar Cystein
(N-terminus) the combined strength(C-terminus) free amino
of large numbers of such group (NH
noncovalent 3 , also
bonds written NH2)
determines
H H O O is the amino terminus, or N-terminus,
H theHstability
H of each folded shape (Figure 3–4). POLAR AMINO ACIDS
and that carrying the free carboxyl group
CH2 CH2
(COO–, also written COOH) Figure 3–2 is the
The carboxyl
20 amino acids commonly found in proteins. Each am
peptide peptide bond AMINO ACID SIDE CHAIN letter AMINO ACID
abbreviation. SIDE CHAIN
There are equal numbers of polar and nonpolar side c
CH2 bonds CH terminus or C-terminus. The amino acid
here as polar are large enough to have some nonpolar properties (for exa
Aspartic acid Asp D sequence of a proteinstructures,
negative is always
Alanine presented
see Panel 3–1Ala (pp.A112–113).
nonpolar
S H 3C CH 3 Glutamic acid Glu E in the N-to-C direction,Glycine
negative reading from left Gly G nonpolar
side chains Arginine Arg R to right.
positive Valine Val V nonpolar MBoC6 m3.02/3.02
CH3
Lysine Lys K positive Leucine Leu L nonpolar
Histidine His H positive Isoleucine Ile I nonpolar
Methionine Aspartic acid Leucine Asparagine
Tyrosine Asn N uncharged polar Proline Pro P nonpolar
(Met) (Asp) (Leu) (Tyr)Glutamine Gln Q uncharged polar Phenylalanine Phe F nonpolar
Serine Ser S uncharged polar Methionine Met M nonpolar
Threonine Thr T uncharged polar Tryptophan Trp W nonpolar
Tyrosine Tyr Y uncharged polar Cysteine Cys C nonpolar
(“water-fearing”), others are negatively or positively charged, some readily form
covalent bonds, and so on. Panel 3–1 (pp. 112–113) shows their atomicPOLAR structures
AMINO ACIDS NONPOLAR AMINO ACIDS
and Figure 3–2 lists their abbreviations.
Figure 3–2 The 20 amino acids commonly found in proteins. Each amino acid has a three-letter and a one- 13
As discussed in Chapter 2, atoms behave almost as if they were
letter hard There
abbreviation. spheres
are equal numbers of polar and nonpolar side chains; however, some side chains listed
 Proteins twist and
THE SHAPE AND STRUCTURE OF PROTEINS
turn 111

PE AND STRUCTURE OF
(A) PROTEINS (B) 111
amino acid
+180

(A) O R2 H (B)
amino acid
+180
H C Cα N H
O R2 H
Cα N H C Cα
H phi psi
C Cα N H psi 0
R1 H O
R3
Cα N H C Cα
phi psi psi 0
R1 H O bonds
peptide R3

Figure 3–3 Steric limitations on the bond angles in a polypeptide –180

peptide bonds
chain. (A) Each amino acid contributes three bonds (red) to the backbone –180 0 +180
phi
of the chain. The peptide bond is planar (gray shading) and does not permit
beta sheet alpha helix
Figure 3–3 rotation. By contrast,
Steric limitations on rotation
the bond can occurin
angles about the Cα–C bond, whose
a polypeptide –180 (right-handed)
angle of rotation is called psi ( ), and about the
chain. (A) Each amino acid contributes three bonds (red) to the backbone N–C α bond, whose angle of
–180 left-handed
0 +180
phi
helix
of the chain.rotation is called
The peptide bondphiis( planar
). By convention,
(gray shading) an Randgroup
doesisnot
often used to denote
permit
rotation. By an amino rotation
contrast, acid sidecan chain
occur(purple
about the Cα(B)
circles). –C The
bond,conformation
whose of the main- beta sheet alpha helix
chainisatoms (right-handed)
angle of rotation calledinpsia protein
( ), andisabout
determined
the N–C byα one
bond,pair of and
whose angle ofangles for each left-handed
MBoC6 m3.03b/3.
aminophi
rotation is called acid;
( ). because of steric
By convention, ancollisions
R group between atoms
is often used within each amino
to denote helix
an amino acidacid, most
side chainof (purple
the possible pairs
circles). (B)ofTheand angles do
conformation not main-
of the occur. In this so-
chain atomscalled Ramachandran
in a protein is determinedplot, by
eachonedot
pairrepresents
of and ananglesobserved pair of angles in
for each 14
 molecules, including the nonpolar side chains of particular amino acids, tend to
be forced together in an aqueous environment in order to minimize their disrup-
Non-covalent bonds determine twisting and turning
tive effect on the hydrogen-bonded network of water molecules (see Panel 2–2,
pp. 92–93). Therefore, an important factor governing the folding of any protein is
glutamic acid
H O
N C C electrostatic
H attractions
CH2
+ R
CH2

C C H
hydrogen bonds H
O O H C
N
H H O C
O
N H
+ C H
H CH2 C R
N
CH2 van der Waals attractions C
CH2 R O
CH2
H C O
H CH3 CH3
C C C C H
N CH3 CH3 valine
O H H HN
C CH3
N
lysine
H C H C C
C N O
H H
O
valine
alanine
15
Twisting
114 and turning
Chapter 3: Proteins means proteins are folded

unfolded polypeptide Figure 3–5 How a pro

compact conformatio
acid side chains tend t
of the protein, where th
water; the nonpolar am
are buried on the insid
packed hydrophobic c
nonpolar polar polypeptide are hidden from water.
side chains side backbone drawing, the protein co
chains 35 amino acids.

polar side chain on the hydrophobic core region

outside of the molecule contains nonpolar
can form hydrogen side chains
bonds to water

folded conformation in aqueous environment

16
Secondary structure: alpha-helix and beta-sheet
116 Chapter 3: Proteins

amino acid
H-bond side chain
amino acid hydrogen
R
R side chain
carbon
R
R
R
R nitrogen R 0.7 nm
carbon
oxygen
R R
H-bond 0.54 nm
R
R
carbon peptide
bond R
R hydrogen
R
R
R oxygen
carbon
R nitrogen
nitrogen R
R
R R

R R R
(A) (B)

(C) (D)

Figure 3–7 The regular conformation of the polypeptide backbone in the helix and the sheet. The α helix is shown in
(A) and (B). The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four peptide
bonds away in the same chain. Note that all of the N–H groups point up in this diagram and that all of the C=O groups point
down (toward the C-terminus); this gives a polarity to the helix, with the C-terminus having a partial negative and the N-terminus 17
 Studies of the conformation, function, and evolution of proteins have also structures. (A) An antiparallel β sheet (see
revealed the central importance of a unit of organization distinct from these four. Figure 3–7C). (B) A parallel β sheet. Both of
This is the protein domain, a substructure produced by any contiguous part of these structures are common in proteins.

Tertiary structure: 3D structure of polypeptide

a polypeptide chain that can fold independently of the rest of the protein into a
compact, stable structure. A domain usually contains between 40 and 350 amino
acids, and it is the modular unit from which many larger proteins are constructed.
The different domains of a protein are often associated with different func-
MBoC6 m3.08/3.08

tions. Figure 3–10 shows an example—the Src protein kinase, which functions in
signaling pathways inside vertebrate cells (Src is pronounced “sarc”). This protein

a NH 2 118 Chapter 3: Proteins

e
THE
d SHAPE AND STRUCTURE OF PROTEINS 117

a SH3 domain
framework for many elongated proteins. Examples are α-keratin, NH2 whichNH
forms the (A)
2
intracellular
e fibers that reinforce the outer layer of the skin and its appendages,
d
and the myosin molecules responsible for muscle contraction.
a Figure 3–9 A coiled-coil. (A) A single α
Protein
g Domains Are Modular Units from Which Larger Proteins helix, with successive amino acid side
ATP
stripe of
chains labeled in a sevenfold sequence,
Are Built
hydrophobic
“abcdefg” (from bottom to top). Amino
d “a” and “d”
aminoprotein
Even a small acids molecule is built from thousands of atoms linked together by acids “a” and “d” in such a sequence lie
close together on the cylinder surface,
precisely
a oriented covalent and noncovalent bonds. Biologists are aided in visu- forming a “stripe” (green) that winds
g
alizing these extremely complicated structures11by nm
various graphic and comput- (B)
slowly around the α helix. Proteins that
er-based three-dimensional displays. The student resource site that accompanies form coiled-coils typically have nonpolar
d
this
c book contains computer-generated images of selected proteins, displayed amino acids at positions “a” and “d.”
and rotated on the screen in a variety of formats. Consequently, as shown in (B), the two α
a helices can wrap around each other with
g Scientists distinguish four levels of organization in the structure of a protein. the nonpolar side chains of one α helix
The amino acid sequence is known as the primary structure. Stretches of poly- interacting with the nonpolar side chains
peptided chain that form
helices αaround
wrap helices and
each β to
other sheets constitute the protein’s second-
minimize of the other. (C) The atomic structure
c
ary structure. The full three-dimensional
exposure organization
of hydrophobic amino acid of a polypeptide chain is of a coiled-coil determined by x-ray
side chains to aqueous environment crystallography. The alpha helical backbone
sometimes referred to as the tertiary structure, and if a particular protein mol-
g is shown in red and the nonpolar side
ecule is formed as a complex of more than one polypeptide chain, HOOC the complete
COOH
chains in green, while the more hydrophilic SH2 domain
structure is designated as the quaternary structure. amino (A) (B)
0.5 nm
Figureacid
3–8side
Twochains,
types shown
of sheetin gray, are
Studies of the conformation, function, and evolution of proteins have also left exposed to
structures. (A)the
An aqueous environment
antiparallel β sheet (see
(A)
revealed the central importance of(B)a unit of organization distinct from (C) these four. (Movie
Figure 3.4). (PDB
3–7C). (B) Acode: 3NMD.)
parallel β sheet. Both of
This is the protein domain, a substructure produced by any contiguous part of these structures are common in proteins.
a polypeptide chain that can fold independently of the rest of the protein into a
compact, stable structure. A domain usually contains between 40 and 350 amino
is considered to have three domains: the SH
acids, and it is the modular unit from which many larger proteins are constructed. MBoC6 m3.08/3.08 roles, while the C-terminal domain is respon
The different domains of a protein are often associated with different func-
tions. Figure 3–10 shows an example—the Src protein kinase, which functions in Later in the chapter, we shall return to this
signaling pathways inside vertebrate cells (Src is pronounced “sarc”). This protein teins can form molecular switches that trans
18
 tion in an organism.
The story we have told for the serine proteases could be repeated for hundreds
Proteins evolve and form families
of other protein families. In general, the structure of the different members of a

Figure 3–12 A com

conformations of
The backbone con
and chymotrypsin.
amino acids in the
HOOC shaded in green ar
HOOC
proteins, the two c
similar nearly every
each enzyme is cir
the peptide bonds
NH 2
NH 2 serve as substrate
by hydrolysis. The
their name from th
whose side chain i
of each enzyme an
in the cleavage rea
the right side of the
elastase chymotrypsin
mark the new ends
enzyme cuts its ow

19
 Structure
120
matters
Chapter 3: Proteins
more than sequence
120 Chapter 3: Proteins

(A) (B)
(A) helix 2 (B)
helix 2

helix 3
helix 3 helix 1
helix 1
NH2
COOH
NH2
COOH

(C)

(C)
yeast
G H R F T K E N V R I L E S W F A K N I E N P Y L D T K G L E N L MK N T S L S R I Q I K NWV S N R R R K E K T I
H2N yeast COOH
R T A F S S E O L A R L K R E F N E N - - - R Y L T E R R R QQ L S S E L G L N E AQ I K I WF QN K R A K I K K S
G H R F T K E N V R I L E S W F A K N I E N P Y L D T K G L E N L MK N T S L S R I Q I K NWV S N R R R K E K
HDrosophila
2N
R T A F S S E O L A R L K R E F N E N - - - R Y L T E R R R QQ L S S E L G L N E AQ I K I WF QN K R A K I K
Figure 3–13 A comparison of a class of DNA-binding domains, called homeodomains, in a pair of proteins from 20
Drosophila

Functional domains are shuffled: modules
demonstrated for the immunoglobulin fold, which forms the basis for antibody
molecules. Such β-sheet-based domains may have achieved their evolutionary
success because they provide a convenient framework for the generation of new
binding sites for ligands, requiring only small changes to their protruding loops
(see Figure 3–42).

121

- EGF
- H2N COOH

y CHYMOTRYPSIN
s, H2N COOH
e UROKINASE
s H2N COOH
s,
FACTOR IX
H2N COOH
y
e PLASMINOGEN
H2N COOH 1 nm
e
- immunoglobulin fibronectin kringle
Figure 3–14 Domain shuffling. An
d extensive shuffling of blocks of protein module type 3 module module
e sequence (protein domains) has occurred
y during protein evolution. Those portions
st of a protein denoted by the same shape
and color in this diagram are evolutionarily
s related. Serine proteases like chymotrypsin
are formed from two domains (brown). In 21
 each organism whose
me contains the DNA
More
otein kinasecomplex
domains, organisms have more complex proteins
120 SH2 domains. In
consist of two or more
edly in the same rela- yeast
families are common
e two-domain combi- Ep1 PHD PHD Ep2
st proteins containing
domain shuffling rel- worm

Ep1 PHD PHD Ep2 Br

Proteins,
human

Znf Ep1 PHD PHD Ep2 Br BMB

surprising, because it
protein-coding genes.
ore complex than the Figure 3–17 Domain structure of a group
22
s of noncovalent bonds is called a binding site. A
Protein molecules comprise protein subunits
es for various large and small molecules. If a bind-
of a second protein, the tight binding of two folded
creates a larger protein molecule with a precisely
eptide chain in such a protein is called a protein
β
dentical
THE SHAPEfolded polypeptide
OF PROTEINSchains bind to each
β
AND STRUCTURE 123
angement, forming a symmetric complex of two
d together by interactions between two identical Figure 3–18 Two identical protein
subunits binding together to form
protein—a viral gene regulatory protein that binds a symmetric protein dimer. The Cro
repressor protein from bacteriophage

enes off in an infected bacterial cell—provides an lambda binds to DNA to turn off a specific
subset of viral genes. Its two identical
subunits bind head-to-head, held together
ontain many other types of symmetric protein com- by a combination of hydrophobic forces
(blue) and a set of hydrogen bonds (yellow
copies of a single polypeptide chain (for example, region). (Adapted from D.H. Ohlendorf,
D.E. Tronrud and B.W. Matthews, J. Mol.
Biol. 280:129–136, 1998. With permission
from Academic Press.)
s contain two or more types of polypeptide chains.
carries oxygen
combinations of proteinin red with
domains, blood cells,
the result contains
that there two
are nearly twice as α α
many combinations of domains found in human proteins as in a worm or a fly.
d two identical
Thus, for β-globin
example, the trypsinlike serinesubunits,
protease domainsymmetrically
is linked to at least 18
other types of protein domains in human proteins, whereas it is found covalently
multisubunit proteins
joined to only 5 different domains inare veryThiscommon
the worm. in proteins
extra variety in our cells,
MBoC6 m3.20/3.18 Figure 3–19 A protein formed as a
viegreatly
3.6). increases the range of protein–protein interactions possible (see Figure
3–79), but how it contributes to making us human is not known. symmetric assembly using two each of
23
The complexity of living organisms is staggering, and it is quite sobering to
 The observation that helices occur commonly in biological structures holds
true whether the subunits are small molecules linked together by covalent bonds
Proteins also form macrostructures
(for example, the amino acids in an α helix) or large protein molecules that are
linked by noncovalent forces (for example, the actin molecules in actin filaments).
g This
site is
can (A) A helix is an unexceptional structure, and it is generated
not surprising. actin molecule
h simply
two by placing manyfree similar subunitsassembled
next to each other, each in the same MBoC6 m3.24/3.20
minus end
o strictly
bindingrepeated relationship
subunits to the one structures
before—that is, with a fixed rotation fol-
lowed by a fixed translation along the helix axis, as in a spiral staircase.
n subunits dimer
Many Protein Molecules Have Elongated, Fibrous Shapes
binding
C, see
site proteins: even though many are large and compli-
Enzymes tend to be globular
cated, with multiple subunits, most have an overall rounded shape. In Figure 3–21,
(B)
we saw that a globular protein can also associate to form long filaments. But there
helix
are also functions that require each individual protein molecule to span a large
distance. These proteins generally have a relatively simple, elongated three-di-
mensional structure and are commonly referred to as fibrous proteins.
One large family of intracellular fibrous proteins consists of α-keratin, intro-
e (Figure
duced when we presented binding
the α helix, and its relatives. Keratin filaments are
ced from stable and are the main component in long-lived structures such as
extremely sites
tein horn, and nails. An α-keratin molecule is a dimer of two identical subunits,
hair, that
37 nm
(C) of each subunit forming a coiled-coil (see Figure 3–9). The
with the long α helices
ment sys- regions are capped at each end by globular domains containing bind-
coiled-coil
ing sites. This enables this class of protein to assemble intoring
ropelike intermediate
xfilaments—an
such a important component of the cytoskeleton that creates the cell’s
internal structural framework
binding (see Figure 16–67).
plus end

are often
Fibrous proteins sites
are especially abundant outside the cell, where they are a (A) 50 nm (B)
main component of the gel-like extracellular matrix that helps to bind collections
subunits Figure 3–21 Actin filaments. 24
Order and disorder are both essential

25
 that restrict diffusion. For example, the abundant nucleoporins that coat the inner Figure
Proteins have both structure and unstructure
surface of the nuclear pore complex form a random coil meshwork (Figure 3–24)
that is critical for selective nuclear transport (see Figure 12–8).
for intr
sequen
Slight modifications make a protein unstable
. of polyp
idemitying somethi advantageous to 60
sites fo

e
--

(
Loose close together-
binding
RICD
add/remove/cot ...

priting the same

they ar

-
medium
free-en
P -channel sion
unfolde
reversib
+
be eas
P their bi
P therefo
proces
of prote
P (C) Uns
“tethers
P
domain
P networ
a diffus
(A) BINDING (B) SIGNALING (C) TETHERING (D) DIFFUSION BARRIER for the
sometimes we need fixed
a rigid & sometimes flexibility
- -

Structur - .
unstructure

26
Sometimes non-covalent bonds are insufficient

27
 (TBSV) shown here, for example, is a
mple viruses, which takesshell
thedomain
form of a hollow sphere based on an icosahedron spherical virus about 33 nm in diameter
Figure 3–27). Capsids are often made of hundreds of identical protein subunits formed from 180 identical copies of a

Examples of macrostructures: capsid of viruses

hat enclose and protect the viral
connecting nucleic acid (Figure 3–28). The protein in such
arm
386-amino-acid capsid protein plus an
capsid must have a particularly adaptable structure: not only must it make RNA genome of 4500 nucleotides. To
construct such a large capsid, the protein
everal different kinds of contactsdomain
RNA-binding to create the sphere, it must also change this must be able to fit into three somewhat
rrangement to let the nucleic acid out to initiate viral replication once the virus THE SHAPE AND STRUCTURE OF PROTEINS
different environments. This requires three
as entered a cell. free slightly different conformations, each of
dimers which is differently colored in the virus
particle shown here. The postulated Figure 3–28 The stru
Many 128
Structures in Cells
Chapter Are Capable of Self-Assembly
3: Proteins pathway of assembly is shown; the precise
three dimers
virus. In viruses, man
three-dimensional structure has been free dimers protein subunit often
The information for forming many of the complex assemblies of macromolecules to create a spherical s
determined by x-ray diffraction. (Courtesy
n cells must be contained in the subunits themselves, because purified subunits ofSingle
Steve Harrison.) This capsid encloses
Figure 3–26 protein subunits form dimer
an spontaneously assemble into the final structure under the appropriate con- composed of either R
hexagonally protein assemblies that feature multiple
itions. The first large macromolecular aggregate shown to be capable of self-as- incomplete Figure 3–27). For geo
packed protein–protein contacts. Hexagonally particle
embly from its component parts was tobacco mosaic virus (TMV ).sheet This virus is more than 60 identica
packed globular protein subunits are
viral RNA together in a precisely
long rod in which a cylinder of protein is arranged around a helical RNA core shown here forming either flat sheets or
slight irregularities are
Figure 3–29). If the dissociated RNA and protein subunits are mixed together in tubes. Generally, such large structures are
more subunits can be
subunit not considered to be single “molecules.”
olution, they recombine to form fully active viral particles. The assembly process Instead, like the actin filament described
a larger capsid that re
unexpectedly complex and includes the formation of double rings of protein, symmetry. The tomat
previously, they are viewed as assemblies projecting domain
(TBSV) shown here, fo
hich serve as intermediates that add to the growing viral coat. formed of many different molecules.
tube shell domain spherical virus about
Another complex macromolecular aggregate that can reassemble from its formed from 180 iden
omponent parts is the bacterialcapsid ribosome.
protein This structure is composed of about intact virus
connecting arm
386-amino-acid caps
5 different protein molecules andmonomer 3 different rRNA molecules. Incubating a mix- particle RNA genome of 4500
shown as (90 dimers) construct such a larg
ure of the individual components ribbon under appropriate conditions in a test tube RNA-binding domain
must be able to fit into
auses them to spontaneously re-form modelthe original structure. Most importantly, different environments
uch reconstituted ribosomes are able to catalyze protein synthesis. As might be 10 nm free slightly different confo
20 nm
xpected, Some protein subunits
the reassembly of ribosomesassemble intoa flat
follows sheets
specific in which
pathway: thecertain
after subunits are dimers which is differently co
roteins arranged in hexagonal
have bound to the RNA,patterns. Specialized
this complex membrane
is then recognized proteins
by otherare pro-
sometimes Figure 3–27 The protein capsid of a particle shown here. T
eins, andarranged thissimplest
so on,the
until way in case,
lipid abilayers.
the structure is With
complete.
long core a slight
protein change
or other in the geometry
macromolecule of the
provides virus. The structure of the simian virus
a scaffold pathway of assembly
SV40 three-dimensional stru
It isindividual subunits,
still notthat
clear a hexagonal
how some
determines the sheet
of extent
the more can be converted
elaborate
of the final into
Thisaistube
self-assembly
assembly. (Figure 3–26)
processes
the mechanism thatcapsid
deter-has been determined by x-ray determined by x-ray d
crystallography and, as
MBoC6 for the capsids of
m3.30/3.26
or, withMany
re regulated. more changes,
minesstructures
the lengthinto
in ofa hollow
the cell,
the TMV sphere.
for Protein
example,
particle, seem
where tubes
to and
RNAaspheres
thehave precisely
chain that bind
provides manytheother
core.
viruses, it is known in atomic of Steve Harrison.)
efinedspecific RNA
length that isand
many
Similarly, DNA coremolecules
a times protein in their
than thatinterior
greaterinteracting of form the
theirm3.31/3.27
with
MBoC6
component
actin coats
is thought oftoviruses.
macromol-
determinedetail.
the length
(Courtesy of Robert Grant, Stephan
cules. How The formation
such
of length
the thin offilaments
closed structures,
determination such is
is achieved
in muscle. asinrings,
manytubes,
casesor spheres, In
a mystery. provides
Crainic, and James M. Hogle.)
additional stability because it increases the number of bonds between the protein
MBoC6 m3.29/3.25
subunits. Moreover, because such a structure is created by mutually dependent,
cooperative interactions between subunits, a relatively small change that affects
each subunit individually can cause the structure to assemble or disassemble.
These principles are dramatically illustrated in the protein coat or capsid of many
simple viruses, which takes the form of a hollow sphere based on an icosahedron
(Figure 3–27). Capsids are often made of hundreds of identical protein subunits
that enclose and protect the viral nucleic acid (Figure 3–28). The protein in such capsid protein intact virus
monomer particle
a capsid must have a particularly adaptable structure: not only must it make shown as (90 dimers)
(A) (B)
several different kinds of contacts to create the sphere, it must also change this50 nm ribbon
arrangement to let the nucleic acid out to initiate viral replication once the virus model

has entered a cell.
Many Structures in
Figure 3–29 The structure of tobacco mosaic virus (TMV). (A) An electron micrograph of the viral particle, which consists of 10 nm
a single long RNA molecule enclosed in a cylindrical protein coat composed of identical protein subunits. (B) A model showing
part of the structure of TMV. A single-stranded RNA molecule of 6395 nucleotides is packaged in a helical coat constructed 28
Cells Arecopies
from 2130 Capable ofprotein
of a coat Self-Assembly
158 amino acids long. Fully infective viral particles can self-assemble in a test tube from
Overview for today
MAIN OBJECTIVE
Get familiar with the basic shape and structure of proteins

1.What are proteins made of?

2.What is primary structure?
3.What is secondary structure?
4.What is tertiary structure?
5.What is quaternary structure?
6.Why and how do proteins fold?
7.Why are domains/modules beneficial?
8.What is the connection between sequence and form?
29