22 22-1 © 2006 Thomson Learning, Inc. All rights reserved General, Organic, and Biochemistry, 8e Bettelheim, Brown CAmpbell, and Farrell

2222

22-1© 2006 Thomson Learning, Inc.All rights reserved

General, Organic, General, Organic, and Biochemistry, 8eand Biochemistry, 8e

Bettelheim, BrownBettelheim, Brown

CAmpbell, and FarrellCAmpbell, and Farrell

2222


Chapter 22Chapter 22

ProteinsProteins

2222


ProteinsProteins• Proteins serve many functions, including the following. Given are examples of each.• 1.Structure:1.Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails.

• 2. Catalysts:2. Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes.

• 3. Movement:3. Movement: muscles are made up of proteins called myosin and actin.

• 4. Transport4. Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes.

• 5. Hormones:5. Hormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone.

2222


ProteinsProteins• 6. Protection:6. Protection: blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease.

• 7. Storage:7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron.

• 8. Regulation:8. Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place.

• Proteins are divided into two types:• fibrous proteins• globular proteins

2222


Amino AcidsAmino Acids• Amino acid: Amino acid: a compound that contains both an amino group and a carboxyl group.• -Amino acid-Amino acid:: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group.

• Although -amino acids are commonly written in the un-ionized form, they are more properly written in the zwitterion zwitterion (internal salt) form.

R-CH-COH

NH2

OR-CH-CO-

NH3+

O

Un-ionizedform

Zwitterion

2222


Chirality of Amino Chirality of Amino AcidsAcids• With the exception of glycine, all

protein-derived amino acids have at least one stereocenter (the -carbon) and are chiral.• The vast majority of protein-derived -amino acids have the L-configuration at the -carbon.

H NH3+

COO-

CH3

+H3N H

COO-

CH3

D-Alanine L-Alanine

(Fischer projections)

2222


Chirality of Amino Chirality of Amino AcidsAcids• A comparison of the stereochemistry of

L-alanine and D-glyceraldehyde (as Fischer projections):

H NH3+

COO-

CH3

+H3N H

COO-

CH3

H OH

CHO

CH2OH

HO H

CHO

CH2OH

D-Alanine L-Alanine

D-Glyceraldehyde L-Glyceraldehyde

the naturally occurring form

the naturally occurring form

2222


20 Protein-Derived AA20 Protein-Derived AA• Nonpolar side chains (at pH 7.0)

NH3+

COO-

NH3+

COO-

NH3+

COO-

NH3+

COO-

NH3+

COO-S

NH3+

COO-

NH H

COO-

NH3+

COO-

NH

COO-

NH3+

Alanine (Ala, A)

Glycine (Gly, G)

Isoleucine (Ile, I)

Leucine (Leu, L)

Methionine (Met, M)

Phenylalanine (Phe, F)

Proline (Pro, P)

Tryptophan (Trp, W)

Valine (Val, V)

2222


20 Protein-Derived AA20 Protein-Derived AA• Polar side chains (at pH 7.0)

NH3+

COO-

HS

NH3+

COO-

HO

Cysteine (Cys, C)

Tyrosine (Tyr, Y)

NH3+

COO-H2N

O

NH3+

COO-

H2N

O

NH3+

COO-

HO

NH3+

COO-OH

Asparagine (Asn, N)

Glutamine (Gln, Q)

Serine (Ser, S)

Threonine (Thr, T)

2222


20 Protein-Derived AA20 Protein-Derived AA• Acidic and basic side chains (at pH 7.0)

NH3+

COO--O

O

NH3+

COO--O

O NH3+

COO-

NH

H2N

NH2+

NH3+

COO-

N

NH

NH3+

COO-H3N

Glutamic acid (Glu, E)

Aspartic acid (Asp, D)

Histidine (His, H)

Lysine (Lys, K)

Arginine (Arg, R)

+

2222


20 Protein-Derived AA20 Protein-Derived AA 1. All 20 are -amino acids.

2. For 19 of the 20, the -amino group is primary; for proline, it is secondary.

3. With the exception of glycine, the -carbon of each is a stereocenter.

4. Isoleucine and threonine each contain a second stereocenter.

2222


Ionization vs pHIonization vs pH• The net charge on an amino acid depends on the pH of the solution in which it is dissolved.• If we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion.

• If we now add a strong acid such as HCl to bring the pH of the solution to 2.0 or lower, the strong acid donates a proton to the -COO- of the amino acid turning the zwitterion into a positive ion.

+

RH3N-CH-C-O

-O

+ H3O+ +

RH3N-CH-C-OH

O+H2O

2222


Ionization vs pHIonization vs pH• If we add a strong base such as NaOH to the solution and bring its pH to 10.0 or higher, a proton is transferred from the NH3

+ group to the base turning the zwitterion into a negative ion.

• to summarize:

+

RH3N-CH-C-O

-O

+ OH-

RH2N-CH-C-O

-O

+H2O

pH 2.0 pH 5.0 - 6.0 pH 10.0Net charge +1 Net charge 0 Net charge -1

+

RH3N-CH-C-O

-O+

RH3N-CH-C-OH

O

RH2N-CH-C-O

-OOH-

H3O+

OH-

H3O+

2222


Isoelectric PointIsoelectric Point• Isoelectric Isoelectric point, pI:point, pI:The pH at which the majority of molecules of a compound in solution have no net charge.

6.015.41

5.655.976.026.025.745.486.485.685.87

5.895.97

pI

valinetryptophan

threonineserineprolinephenylalaninemethionineleucineisoleucineglycineglutamine

asparaginealanine

Nonpolar &polar side chains

10.76

2.77

5.073.22

7.599.74

5.66

pI

tyrosine

lysinehistidine

glutamic acidcysteine

aspartic acid

arginine

AcidicSide Chains

BasicSide Chains pI

2222


CysteineCysteine• The -SHSH (sulfhydryl) group of cysteine is easily oxidized to an -S-S--S-S- (disulfide).

+

CH2

H3N-CH-COO-

SH

oxidation

reduction

+

CH2

H3N-CH-COO-

S

+H3N-CH-COO

-CH2

S

CysteineCystine

2

a disulfidebond

2222


Other Amino AcidsOther Amino Acids• Hydroxylation (oxidation) of proline, lysine, and tyrosine, and iodination for tyrosine, give these nonstandard amino acids.

NH H

COO-

HO

Hydroxyproline

NH3+

COO-H3N+ OH

Hydroxylysine

C

C-O-

O

HH3N

OII

I IOH

Thyroxine

2222


PeptidesPeptides• In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds.• peptide bondpeptide bond:: The special name given to the amide bond between the -carboxyl group of one amino acid and the -amino group of another.

O

O-H3N

CH3H3N O-

CH2OH

O

H3NN

CH3

O CH2OH

O

O-

H

H2O+

Alanine (Ala) Serine (Ser)

++

+

peptide bond

Alanylserine (Ala-Ser)

+

2222


PeptidesPeptides• PeptidePeptide: A short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain.

• DipeptideDipeptide: A molecule containing two amino acids joined by a peptide bond.

• TripeptideTripeptide: A molecule containing three amino acids joined by peptide bonds.

• PolypeptidePolypeptide: A macromolecule containing many amino acids joined by peptide bonds.

• ProteinProtein: A biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds.

2222


Writing PeptidesWriting Peptides• By convention, peptides are written from the left, beginning with the free -NH3

+ group and ending with the free -COO- group on the right.

• C-terminal amino acid:C-terminal amino acid: the amino acid at the end of the chain having the free -COO- group.

• N-terminal amino acid:N-terminal amino acid: the amino acid at the end of the chain having the free -NH3

+ group.

H3N

OH

NH O

HN

COO-

O-

OC6H5O

+

C-terminalamino acid

N-terminalamino acid

Ser-Phe-Asp

2222


Peptides and ProteinsPeptides and Proteins• Proteins behave as zwitterions.• Proteins also have an isoelectric point, isoelectric point, pIpI.• At its isoelectric point, the protein has no net charge.

• At any pH above (more basic than) its pI, it has a net negative charge.

• At any pH below (more acidic than) its pI, it has a net positive charge.

• Hemoglobin, for example, has an almost equal number of acidic and basic side chains; its pI is 6.8.

• Serum albumin has more acidic side chains; its pI is 4.9.

• Proteins are least soluble in water at their isoelectric points and can be precipitated from solution at this pH.

2222


Levels of StructureLevels of Structure• Primary structure:Primary structure: the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid.

• Secondary structure:Secondary structure: conformations of amino acids in localized regions of a polypeptide chain; examples are -helix, -pleated sheet, and random coil.

• Tertiary structure:Tertiary structure: the complete three-dimensional arrangement of atoms of a polypeptide chain.

• Quaternary structure:Quaternary structure: the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.

2222


Primary StructurePrimary Structure• Primary structure:Primary structure: the sequence of amino acids in a polypeptide chain.

• The number peptides possible from the 20 protein-derived amino acids is enormous.• there are 20 x 20 = 400 dipeptides possible.• there are 20 x 20 x 20 = 8000 tripeptides possible.

• the number of peptides possible for a chain of nn amino acids is 2020nn.

• for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078, which is possibly greater than the number of atoms in the universe!

2222


Primary StructurePrimary Structure• Figure 22.6 The hormone insulin consists of two polypeptide chains held together by two interchain disulfide bonds.

2222


Primary StructurePrimary Structure• Just how important is the exact amino acid sequence?• Human insulin consists of two polypeptide chains having a total of 51 amino acids; the two chains are connected by two interchain disulfide bonds.

• In the table are differences between four types of insulin.A Chain

positions 8-9-10B Chain

position 30

HumanCow

Hog

Sheep

-Thr-Ser-Ile--Ala-Ser-Val-

-Thr-Ser-Ile-

-Ala-Gly-Val-

-Thr-Ala

-Ala

-Ala

2222


Primary StructurePrimary Structure• Vasopressin and oxytocin are both nonapeptides but have quite different biological functions.

• Vasopressin is an antidiuretic hormone.• Oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk.Cys S S Cys Pro Gly NH2

Tyr AsnPhe Gln

Cys S S Cys Pro Leu NH2

Tyr AsnIle Gln

Vasopressin Oxytocin

2222


Secondary StructureSecondary Structure• Secondary structure:Secondary structure: conformations of amino acids in localized regions of a polypeptide chain.• The most common types of secondary structure are -helix and -pleated sheet.

• -Helix:-Helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral.

• -Pleated sheet:-Pleated sheet: a type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel.

2222


-Helix-Helix• Figure 22.8(a) The -helix structure.

2222


-Helix-Helix• In a section of -helix;

• There are 3.6 amino acids per turn of the helix.• The six atoms of each peptide bond lie in the same plane.

• N-H groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix.

• C=O groups of peptide bonds point in the opposite direction, also roughly parallel to the axis of the helix.

• The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it.

• All R- groups point outward from the helix.

2222


-Pleated Sheet-Pleated Sheet• Figure 22.8(b). The -pleated sheet structure.

2222


-Pleated Sheet-Pleated Sheet• In a section of -pleated sheet;

• The six atoms of each peptide bond lie in the same plane.

• The C=O and N-H groups of peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them.

• All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.

2222


Collagen Triple HelixCollagen Triple Helix• Figure 22.11 The collagen triple helix.

2222


Collagen Triple HelixCollagen Triple Helix• Consists of three polypeptide chains wrapped around each other in a ropelike twist to form a triple helix called tropocollagen.

• 30% of amino acids in each chain are Pro and L-hydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs.

• Every third position is Gly and repeating sequences are X-Pro-Gly and X-Hyp-Gly.

• Each polypeptide chain is a helix but not an -helix.

• The three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine.

• With age, collagen helices become cross linked by covalent bonds formed between side chains of Lys residues.

2222


Tertiary StructureTertiary Structure• Tertiary structure:Tertiary structure: the overall conformation of an entire polypeptide chain.

• Tertiary structure is stabilized in four ways:• Covalent bondsCovalent bonds, as for example, the formation of disulfide bonds between cysteine side chains.

• Hydrogen bondingHydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine.

• Salt bridgesSalt bridges, as for example, the attraction of the -NH3

+ group of lysine and the -COO- group of aspartic acid.

• Hydrophobic interactionsHydrophobic interactions, as for example, between the nonpolar side chains of phenylalanine and isoleucine.

2222


Tertiary StructureTertiary Structure• Figure 22.13 Forces that stabilize 3° structure of proteins

2222


Quaternary StructureQuaternary Structure• Quaternary structure:Quaternary structure: the arrangement of polypeptide chains into a noncovalently bonded aggregation.• The individual chains are held in together by hydrogen bonds, salt bridges, and hydrophobic interactions.

• Hemoglobin• Adult hemoglobin:Adult hemoglobin: two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each.

• Each chain surrounds an iron-containing heme unit.

• Fetal hemoglobin:Fetal hemoglobin: two alpha chains and two gamma chains; fetal hemoglobin has a greater affinity for oxygen than does adult hemoglobin.

2222


HemoglobinHemoglobin• Figure 22.15 The 4° structure of hemoglobin.

2222


HemoglobinHemoglobin• Figure 22.16 The structure of heme.

2222


Quaternary StructureQuaternary Structure• Figure 22.17 Integral membrane protein of rhodopsin made of -helices.

2222


Quaternary StructureQuaternary Structure• Figure 22.18 The -barrel of an integral membrane protein of the outer membrane of a mitochondrion is made of eight -pleated sheets.

2222


DenaturationDenaturation• DenaturationDenaturation: the process of destroying the native conformation of a protein by chemical or physical means.• Some denaturations are reversible, while others permanently damage the protein.

• Denaturing agents include:• Heat:Heat: heat can disrupt hydrogen bonding; in globular proteins, it can cause unfolding of polypeptide chains with the result that coagulation and precipitation may take place.

2222


DenaturationDenaturation• 6 M aqueous urea:6 M aqueous urea: disrupts hydrogen bonding.• Surface-active agents: Surface-active agents: detergents such as sodium dodecylbenzenesulfate (SDS) disrupt hydrogen bonding.

• Reducing agents:Reducing agents: 2-mercaptoethanol (HOCH2CH2SH) cleaves disulfide bonds by reducing -S-S- groups to -SH groups.

• Heavy metal ions:Heavy metal ions: transition metal ions such as Pb2+, Hg2+, and Cd2+ form water-insoluble salts with -SH groups; Hg2+ for example forms -S-Hg-S-.

• Alcohols:Alcohols: 70% ethanol, for example, which denatures proteins, is used to sterilize skin before injections.

2222


End End Chapter 22Chapter 22

ProteinsProteins

Documents

22 22-1 © 2006 Thomson Learning, Inc. All rights reserved General, Organic, and Biochemistry, 8e Bettelheim, Brown CAmpbell, and Farrell