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CHAPTER 5THE STRUCTURE AND FUNCTION

OF MACROMOLECULES

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Section D: Proteins - Many Structures, Many Functions

1. A polypeptide is a polymer of amino acids connected to a specific sequence2. A protein’s function depends on its specific conformation

• Proteins are instrumental in about everything thatan organism does.• These functions include structural support, storage,

transport of other substances, intercellular signaling,movement, and defense against foreign substances.

• Proteins are the overwhelming enzymes in a cell andregulate metabolism by selectively accelerating chemicalreactions.

• Humans have tens of thousands of different proteins,each with their own structure and function.

Introduction


• Proteins are the most structurally complexmolecules known.• Each type of protein has a complex three-dimensional

shape or conformation.

• All protein polymers are constructed from the sameset of 20 monomers, called amino acids.

• Polymers of proteins are called polypeptides.

• A protein consists of one or more polypeptidesfolded and coiled into a specific conformation.


• Amino acids consist of four components attachedto a central carbon, the alpha carbon.

• These components include ahydrogen atom, a carboxylgroup, an amino group, anda variable R group(or side chain).• Differences in R groups

produce the 20 differentamino acids.

1. A polypeptide is a polymer of aminoacids connected in a specific sequence


• The twenty different R groups may be as simple asa hydrogen atom (as in the amino acid glutamine)to a carbon skeleton with various functional groupsattached.

• The physical and chemical characteristics of the Rgroup determine the unique characteristics of aparticular amino acid.



• One group of amino acids has hydrophobic Rgroups.

Fig. 5.15a


• Another group of amino acids has polar R groups,making them hydrophilic.

Fig. 5.15b

• The last group of amino acids includes those withfunctional groups that are charged (ionized) atcellular pH.• Some R groups are bases, others are acids.


Fig. 5.15c

• Amino acids are joined together when adehydration reaction removes a hydroxyl groupfrom the carboxyl end of one amino acid and ahydrogen from the amino group of another.• The resulting covalent bond is called a peptide bond.


Fig. 5.16

• Repeating the process over and over creates a longpolypeptide chain.• At one end is an amino acid with a free amino group the

(the N-terminus) and at the other is an amino acid with afree carboxyl group the (the C-terminus).

• The repeated sequence (N-C-C) is the polypeptidebackbone.

• Attached to the backbone are the various R groups.

• Polypeptides range in size from a few monomers tothousands.


• A functional proteins consists of one or morepolypeptides that have been precisely twisted, folded,and coiled into a unique shape.

• It is the order of amino acids that determines what thethree-dimensional conformation will be.

2. A protein’s function depends on itsspecific conformation


Fig. 5.17

• A protein’s specific conformation determines itsfunction.

• In almost every case, the function depends on itsability to recognize and bind to some othermolecule.• For example, antibodies bind to particular foreign

substances that fit their binding sites.

• Enzyme recognize and bind to specific substrates,facilitating a chemical reaction.

• Neurotransmitters pass signals from one cell to anotherby binding to receptor sites on proteins in the membraneof the receiving cell.


• The folding of a protein from a chain of aminoacids occurs spontaneously.

• The function of a protein is an emergent propertyresulting from its specific molecular order.

• Three levels of structure: primary, secondary, andtertiary structure, are used to organize the foldingwithin a single polypeptide.

• Quarternary structure arises when two or morepolypeptides join to form a protein.


• The primary structureof a protein is its uniquesequence of amino acids.• Lysozyme, an enzyme that

attacks bacteria, consistson a polypeptide chain of129 amino acids.

• The precise primarystructure of a protein isdetermined by inheritedgenetic information.


Fig. 5.18

• Even a slight change in primary structure can affecta protein’s conformation and ability to function.

• In individuals with sickle cell disease, abnormalhemoglobins, oxygen-carrying proteins, developbecause of a single amino acid substitution.• These abnormal hemoglobins crystallize, deforming the

red blood cells and leading to clogs in tiny blood vessels.


Fig. 5.19


• The secondary structure of a protein results fromhydrogen bonds at regular intervals along thepolypeptide backbone.• Typical shapes

that develop fromsecondary structureare coils (an alphahelix) or folds(beta pleatedsheets).


Fig. 5.20

• The structural properties of silk are due to betapleated sheets.• The presence of so many hydrogen bonds makes each

silk fiber stronger than steel.


Fig. 5.21


• Tertiary structure is determined by a variety ofinteractions among R groups and between R groupsand the polypeptide backbone.• These interactions

include hydrogenbonds among polarand/or chargedareas, ionic bondsbetween chargedR groups, andhydrophobicinteractions andvan der Waalsinteractions amonghydrophobic Rgroups. Fig. 5.22

• While these three interactions are relatively weak,disulfide bridges, strong covalent bonds that formbetween the sulfhydryl groups (SH) of cysteinemonomers, stabilize the structure.


Fig. 5.22

• Quarternary structure results from the aggregationof two or more polypeptide subunits.• Collagen is a fibrous protein of three polypeptides that

are supercoiled like a rope.

• This provides the structural strength for their role inconnective tissue.

• Hemoglobin is aglobular proteinwith two copiesof two kindsof polypeptides.


Fig. 5.23


Fig. 5.24

• A protein’s conformation can change in response tothe physical and chemical conditions.

• Alterations in pH, salt concentration, temperature, orother factors can unravel or denature a protein.• These forces disrupt the hydrogen bonds, ionic bonds,

and disulfide bridges that maintain the protein’s shape.

• Some proteins can return to their functional shapeafter denaturation, but others cannot, especially inthe crowded environment of the cell.



Fig. 5.25

• In spite of the knowledge of the three-dimensionalshapes of over 10,000 proteins, it is still difficult topredict the conformation of a protein from itsprimary structure alone.• Most proteins appear to undergo several intermediate

stages before reaching their “mature” configuration.



Fig. 5.26

• The folding of many proteins is protected bychaperonin proteins that shield out bad influences.

• A new generation of supercomputers is beingdeveloped to generate the conformation of anyprotein from its amino acid sequence or even itsgene sequence.• Part of the goal is to develop general principles that

govern protein folding.

• At present, scientists use X-ray crystallography todetermine protein conformation.• This technique requires the formation of a crystal of the

protein being studied.• The pattern of diffraction of an X-ray by the atoms of the

crystal can be used to determine the location of the atomsand to build a computer model of its structure.



Fig. 5.27

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