Download 18,5 Primory structure of proteins 18.6 Secondory stractare of proteins

I8.6 Secondary
Structureof Proteins
565
Fouow-upro rHECnsrln Polnr: Runner'shish
Karla sometimes experiences runner's high during
her runs. \Alhat is causing this effect? Many sports
physiologists believe that runner's high comes from
increases in the levels of enkephalins in the brain.
These increases, which
remarkabie feel"* "urrr"
ings of well-belng, appear
to be stimulated by
endurance exercises such as distance running. The
effects of enkephalins appear to last beyond the
period of exercise to increase all-around mental alertness and a sense of comfort. Exercise is a good thiag,
but like most good things, it can be overdone, since
the body may suffer from exhaustion and other
breakdornmswhen overtaxed without sufficient time
to recover. Enkephalins may be responsrble in part
for the potentially harmful addiction of some people
IO eXCeSStVe
exerclse_
18,5Primorystructureof proteins
AIM: To chorocterizethe primory structureof o protein
Focus
The primary structure is the
first level of organization of a
protein.
Protein
proteios(Greek): offirst
importance
INhen the number of amino acid residuesbecomesgreater than about 40, a
naturally occurringpeptide is called aprotein. On average,a peptide molecule containing 100amino acid residueshas a molar mass of about 10,000
g. Proteins are so vitai to living organisms that many of the remaining topics in this book concernthem. The structuresof proteins areusuallystudied
at four levels of organization: primary structlffe, secondarystructure, tertiary structure, and quaternary structure. The prirnary structure of a peptide or protein is the order in which the amino acid residuesof a peptide or
protein molecule are linked by peptide bonds. The primary structure of a
protein molecule alsoincludesany disulfidebridgesthat the molecule contains.Iust aswe sawfor peptidesin the precedingsection,differencesin the
chemicaland biologicalpropertiesof proteins result from differencesin the
order of amino acidsin the polypeptide chain (primary structure).The secondary tertiary and quaternary structuresof proteins are discussedin the
following three sections.
18.6Secondory
stractareof proteins
AIMS: To describethe bonding ond structurein the following
secondarystructuresof proteins: alpho helix, beto-pleoted
sheet,ond collogenhelix. Todistinguishomong the
following fibrous proteins: olpho keratin, beto kerotin,
ond collagen.
The alpha heli5 beta-pleated
sheet, and collagen helix are
three types of secondary structures found in proteins.
The polypeptide chains of many proteins contain specific,repeating patterns of folding of the peptide backbone. Thesespecific,repeating patterns
of folding of the peptide backboneconstitute the protein'ssecondary structure. Three commonly found patterns are the alpha helix, t]r.ebeta-pleated
sheet,andthe collagen helix.
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l8 Amino Acids,Peptides,and Proteins
CHAPTER
Alpha helix
In someproteins, regionsof the backboneof the peptide chain are coiled into
a spiral shape called an alplaalnelix, similar to a corkscrew.As Figure lB.3
shows, a corkscrew must be turned in a right-handed, or clockwise, direction to penetrate a cork. The alpha helixes of proteins are always righthanded. The helixes are held together by hydrogen bonds, shornmin Figure
18.4,formed between the hydrogen of an N-H of a peptide bond and the
carbonyl oxygen of another peptide bond group four residues away in the
samepeptidechain.
The tightnessof coiling is such that 3.6 amino acid residuesof the peptide backbone make each ftrll turn of the alpha helix. There are no amino
acid residue side chains inside the alpha helix; they are located on the outside. The cyclic amino acid proline does not fit well into the peptide backbone of alpha helixes. Alpha helixes in long protein chains often end at a
place where proline residues occur in the primary structure. Proline is
Figute18.5
A corkscrewmust be turned in a
right-handed,or clockwise,direction to penetratea cork.
t
To N-terminal
I
Figute18.4
A peptide chain twisted into a
right-handedalpha helix constitutes
a protein'ssecondarystructure.The
N-terminalto C-terminaldirection
is from top to bottom. The dotted
lines show the hydrogenbonds
betweenthe carbonylorygen of
one amino acid residueand the
N-H hydrogenof another,four
amino acid residuesfurther down
the chain.
t;
18.6Secondary
Structure
of Proteins
(a) Helical peptide
chain
(b) Alpha keratin
Figure18.5
Threehelicalpeptidechains,like
the one shown in (a), are twisted
or supercoiled
to form a rope in
alpha keratin(b).
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sometimes called an alpha helix disrupter for this reason. The inability of
proline to fit into the alpha helix is one of many piecesof euidencethai the
secondarystructure of a protein is determined by its primary structure.
Much of what is knolrrn about protein alpha helixes comes from studies
of fibrous proteins. Fibrous proteins tend to be long, rod-shapedmolecules
with great mechanical strength. Such proteins are usually insoluble in
water, dilute salt solutions, and other solvents. The polypeptide chains of a
class of fibrous proteins called alpha keratins consist mainly of alpha
helixes.Alpha keratins form the hard tissue of hooves, horns, outer skin
layer (epidermis), hair, wool, and nails of mammals. We see in Figure lB.5
complexprotein molecules consisting of long alpha helixes that are twisted
together-supercoiled-in
ropes of three or seven strands. It takes many
supercoiled ropes to make a strong but elastic wool fiber. If you have ever
washed a wool sweater, you know that warm, wet wool fibers can be
stretched,but they eventually return to their original length. This is because
the alphahelixes of the damp fibers are easilypulled into an extended form.
The extended form is less stable than the alpha helix. It will, in time, return
to the original alpha helix. Disulfide bridges (seeSec.lB.1) between alpha
helixes help to make alpha keratins rigid; the alpha keratins of a hard hoof
have more disulfide linkages than relatively elastic epidermis.
Beta-pleated
sheet
Figure l8.6 showsthe beta-pleatedsheet,another kind of secondarystructure commonly found in proteins. Thebeta-pleated sheet consistsof peptide chains arranged side by side toform a structure that resemblesa pieceof
paper folded into many pleats. The carbonyl groups of one zigzagpeptide
backbone are hydrogen bonded to peptide N-H hydrogens of adjacent
peptide chains that run in opposite directions in the N-terminal to C-ter-
Figure18.6
A beta-pleated
sheetis another
kindof secondary
structure.
Hydrogenbonds(shownasdottedlines)
holdadjacentstrandsof the sheet
together.
C-terminal
t-=
N-terminal
':a:--
-a.
@ carbon
@ o*yg"n
@ uirrog".r $
;g Hydrogen
sidectrain I Hydrogenbond
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l8 Amino Acids,Peptides,and Proteins
CHAPTER
Figure18.8
Silkfibroinconsistsof
stackedbeta-pleated
sheets.The smallR
groupsof glycyland
alanylresidues
permit the stacking
to occur.
Figure18.7
Spiderwebs are made of fibroin,a
protein that existsmainly as betapleatedsheets.
. ; .Jl'_'
:::
minal sense.Beta-pleatedsheetsare formed by separatestrandsof protein
or by a single chain looping back on itself.
Beta keratin s are a classof fibrous proteins that consist mainly of betapleated sheets.The long, thin fibers secretedby silkworms and spiders (Fig'
18.7)are composedof fibroin, a well-studied beta keratin. Fibroin consists
mainly of layersof beta-pleatedsheets,as shornrnin Figure lB.B.Again, the
primary structure of a protein determinesits secondarystructure.Fibroin
peptide chains are particularly rich in glycyl and alanyl residues.The small
side chains of these residuesare important to the organization of fibroin,
since larger side chains would interfere with the packing of the sheetsin
layers.
Collagen
helix
Collagenis yet another kind of fibrous protein. Collagen is the most abundant protein in human beingsand many otheranimals with spinal columns
(uertebrates).
About one-third of the protein in the human body is present
as the collagenof bones,teeth, inner skin layer (dermis),tendons,and cartilage.The inner material of the eye lens is almost pure collagen.Collagen
occurs in all organs,where it imparts strength and stiffness.
Collagenis formed from three peptide chains,each a helix, wound into
a rope.Thereare important differencesbetweenalpha helixesand collagen
helixes,however.Collagenis rich in proline (40To),which does not fit into
regular alpha helixes, and collagen helixes are not as tightly coiled as alpha
helixes. Unlike alpha helixes, which are right-handed, collagen helixes are
left-handed. Collagen contains large quantities of glycine (35%) and the
unusual amino acids4-hydroxlproline (5%)and S-hydroxylysine(1%).
OH
I
H9-9u,
tt
cHr.
.cH-co2H
N
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H2N-CH2-CH-CH2 -C"r-f
I
-n
co2H
H
4-Hydroxyproline
T"'
5-Hydroxylysine