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Chemistry 110. Bettelheim, Brown, Campbell & Farrell. Introduction to General, Organic and Biochemistry Chapter 22 Proteins


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Chemistry 110

Bettelheim, Brown, Campbell & Farrell

Ninth Edition

Introduction to General,

Organic and Biochemistry

Chapter 22


Step-growth polyamide (polypeptide) polymers or oligomers of L-α-aminoacids.


¾Structure:Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails.


¾Catalysts:Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes.


¾Movement:Movement: muscles are made up of proteins called myosin and actin.


¾TransportTransport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes.


¾Hormones:Hormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone.


¾Protection:Protection: the body used proteins called antibodies to fight disease; blood clotting involves the protein fibrinogen.


¾Storage:Storage: casein in milk and ovalbumin in eggs store nutrients for infants and birds; ferritin, a protein in the liver, stores iron.


¾Regulation:Regulation: specific proteins control the expression of genes, others control when gene expression takes place.

Proteins have Many Functions

Peptides & Proteins

¾Emil Fischer proposed in 1902 that proteins are long chains of amino acids joined by amide bonds. The special name given to the amide bond between the α-carboxyl group of one amino acid and the α-amino group of another is called a peptide bond. ¾A short polymer of amino acids joined by peptide bonds are classified by the number of amino acids in the chain.


¾A A dipeptidedipeptideisis a molecule containing two amino acids joined by a peptide bond.


¾A A tripeptidetripeptideisis a molecule containing three amino acids joined by two peptide bonds.


¾A polypeptide isA polypeptide is a macromolecule containing many amino acids joined by peptide bonds.


¾A protein is defined asA protein is defined as a biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds.


Proteins and Amino Acids

¾Proteins are step-growth polymers of alpha aminoacids. ¾Proteins are of two types, fibrous and globular.


¾Amino acid Amino acid are compound that contains both an amino group and a carboxyl group. In α--amino acidsamino acids the amino group is on the carbon adjacent to the carboxyl group.

¾Although α-amino acids are commonly written in the un-ionized form, they are more properly written in thezwitterionzwitterion (internal salt) form.

¾With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral. ¾Two α−aminoacids, threonine and isoleucine, have a second stereocenter.

¾The vast majority of α-amino acids have the L-configuration at the α-carbon.

Proteins - Polymers of Alpha Aminoacids


When a pure aminoacid is dissolved in water it has this form. The pH will be a value called the pI.

This is the isoelectric form. The molecule

has no net charge. A “zwitterion” or internal salt. acidic solution H OH NH3 CH COH O R pH < 2.0

In strong Acid the aminoacid will be a cation, net positive.

basic solution H OH NH2 CH CO O R pH > 10

In strong base the aminoacid will be an anion, net negative. Aminoacids are

ionic at all pH values and remain soluble in aqueous


The “Standard Set” of Amino Acids

Always shown at the isoelectric point

The "non-polar" side chain group: R =

NH3 CH CO O R H Glycine Gly G 6.06 CH3 Alanine Ala A 6.11 CH CH3 CH3 Valine Val V 6.00 CH2CH CH3 CH3 Leucine Leu L 6.04 CHCH2CH3 CH3 Isoleucine Ile I 6.04 Phe F H2C Phenylalanine 5.91 Trp W N CH2 H Tryptophan 5.88 5.74 Met M Methionine CH2CH2SCH3 Pro P Proline 6.30 N C O O H H


The “Standard Set” of Amino Acids

Always shown at the isoelectric point NH3 CH CO

O R The side chain has a polar, but neutral, group: R =

CH2OH Serine Ser S 5.68 COH CH3 H Threonine Thr T 5.64 CH2CNH2 O 5.41 Asparagine Asn N CH2CH2CNH2 O 5.65 Glutamine Gln Q

¾These groups will orient in a protein so that they project toward the aqueous layer, and will not associate with nonpolar groups. ¾They can form hydrogen bonds with water and with each other.

The “Standard Set” of Amino Acids

Always shown at the isoelectric point

NH3 CH CO O R The side chain is acidic: R =

2.98 Asp D Aspartic Acid CH2COH O 3.08 Glu E Glutamic Acid CH2CH2COH O Tyr Y H2C OH Tyrosine 5.63 5.07 Cys C Cysteine CH2SH

The side chain is basic: R = CH2CH2CH2CH2NH2 Lysine Lys K 9.47 Arginine Arg R 10.76 CH2CH2CH2NHCNH2 NH His H Histidine 7.64 N N H2C H

¾Proteins behave as zwitterions and have an isoelectricisoelectricpoint, point, pIpI,, because their side groups can be acidic and basic. HHemoglobin 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. ¾Proteins are least soluble in water at their isoelectric points and can be precipitated from their solutions.


¾The primary structure isThe primary structure is the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid.

¾The secondary structure is theecondary structure is the conformations of amino acids in localized regions of a polypeptide chain; examples are α-helix, β-pleated sheet, and random coil.


¾The tertiary structure isThe tertiary structure is the overall conformation of a polypeptide chain.

¾A quaternary structure isuaternary structure is the arrangement of two or more polypeptide chains into a non-covalently bonded aggregation.

Protein Behavior & Levels of Structure

Protein Behavior & Levels of Structure


The “Primary Structure” of Proteins

N-terminal residue C-terminal residue N CH C O R O H H H N CH C O R' O H H H N CH C O R" O H H H H2O H2O N CH C O R H H H H R' O C CH N H O R" O C CH N Peptide Bonds

¾The primary structure of proteins is the specific sequence of aminoacids in the protein chain.

¾Proteins are always written with the N-terminus on the left.

Secondary Structure of Proteins

¾Hydrogen Bonds can form between adjacent strands of polypeptide or with different portions of the same strand. ¾A stable alpha-helix has the hydrogen bonds forming between each peptide residue and the fourth peptide removed. In structural proteins a left-handed helix may form.

¾A beta-pleated sheet has the hydrogen bonds between adjacent segments. N CH C O R H H H H R' O C CH N H O R" O C CH N N CH C O R" O H N CH C O R' H H H H R O C CH N

The Alpha Helix

¾In a section of α-helix there are 3.6 amino acids per turn of the helix.

¾The six atoms of each peptide bond lie in the same plane. ¾The N-H groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix.

¾The C=O groups of peptide bonds point in the direction opposite the N-H groups, also roughly parallel to the axis of the helix.

¾The 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.

¾All the R- groups of the aminoacids point outward from the helix


The Beta Pleated Sheet

¾In a section of β-pleated sheet the six atoms of each peptide bond lie in the same plane.

¾The 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.

¾All R-groups on any one chain alternate, first above, then below the plane of the sheet, etc.

¾The distinction between secondary structure (α-helix, β-pleated sheets) and tertiary structure is that secondary structures are stabilized only by hydrogen bonds arising through the peptide units, while tertiary structure may utilize more varied elements. ¾Usually only certain portions of protein molecules, especially globular proteins, are α-helix or β-pleated sheets. The remainder is commonly random coil.

¾Some proteins, e.g. keratin, are predominately α-helix.

The Collagen Triplehelix

¾Collagen consists of three polypeptide chains wrapped around each other in a ropelike twist to form a triple helix called tropocollagen.

¾30% of amino acids in each chain are proline and L-hydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs. ¾Every third position is glycine and repeating sequences are X-Pro-Gly and X-Hyp-Gly.

¾Each polypeptide chain is a helix, called an extended helix, but not an α-helix.

¾The three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine.

¾With age, the collagen helices become cross linked by covalent bonds formed between lysine residues. This is a factor in aging, muscle stiffness, etc.


¾The tertiary structure of a protein isThe tertiary structure of a protein is the overall conformation of a polypeptide chain caused by side-group interaction. ¾The side-groups of proteins project outward from either the helices or the sheets. Side-groups in contact with the aqueous medium tend to cause folding of the helical strands or sheets.

¾Hydrophobic side-chains aggregate to minimize contact with water. They tend to tuck inside away from water.

¾Hydrophilic side-groups extend themselves in order to hydrogen-bond with the aqueous medium.


Tertiary Structure of Proteins

The tertiary structure of a protein is stabilized in four ways:


¾Covalent bonds,Covalent bonds, most commonly the formation of disulfide bonds between cysteine side chains.


¾Hydrogen bondingHydrogen bonding between polar groups of side chains, such as between the -OH groups of serine and threonine.


¾Salt bridgesSalt bridges, formation of ionic bonds, most commonly the attraction of the side group ammonium ions of one of the basic aminoacids, (lysine, arginine) and the -COO-in the side-group of one of the acidic aminoacids (aspartic acid, glutamic acid). ¾Hydrophobic interactionsydrophobic interactions, such as between the nonpolar side chains of phenylalanine, leucine, isoleucine.


Quaternary Structures of Proteins


¾The quaternary structure is the arrangement of polypeptide The quaternary structure is chains into a noncovalently bonded aggregation.

¾The individual chains are held in together by hydrogen bonds, salt bridges, and hydrophobic interactions.

¾Prosthetic Groups often get incorporated.

1) In one case, collagen, three helical coils form a triple helix, like a steel cable. Although the lysine side chain residues are linked together by covalent bonds, the triple strands of tropocollagen eventually overlap lengthwise to form fibrils or micro-fibres.

2) In another case, adult hemoglobin,adult hemoglobin, two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each combine with each chain surrounding an iron-containing heme prosthetic group unit. Fetal etal hemoglobin is slightly different.

hemoglobin is slightly different.


¾A glycoprotein isA glycoprotein is a protein to which one or more carbohydrate units are bonded. There are two common types:


¾OxygenOxygen--linked linked saccharidessaccharidesin whichin which a glycosidic bond between the anomeric carbon of a saccharide and the OH group of serine, threonine, or hydroxylysine has been formed. Example: the mucins which coat and protect mucous membranes.



C C O NH H CH2 O O CH3 C HO HO HN H2COH O β-N-Acetyl-D-glucosyl-serine ¾

¾NitrogenNitrogen--linked linked saccharidessaccharidesin which an N-glycosidic bond in which between the anomeric carbon of N-acetyl-D-glucosamine and the nitrogen of the side chain amide group of asparagine has been formed. Examples are the proteoglycans.

β-N-Acetyl-D-glucosyl-asparagine C C O NH H CH2 C O N H O CH3 C HO HO HN H2COH O



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

Methods involve both physical and chemical means. Few methods change the primary structure of proteins.

Physical denaturing agents include:


¾Heat can disrupt hydrogen bonding; in globular proteins Heat unfolding of the polypeptide chains may occur resulting in coagulation and precipitation.

¾Sonic disruption or whipping can disrupt tertiary and quaternary structure.

¾Dehydration – removal of water, drying-out can change tertiary and quaternary structure.



Chemical denaturing agents include:


¾6 M aqueous urea will disrupt hydrogen bonding.6 M aqueous urea will


¾Surface-Surface-active agents such as active agents such as detergents disrupt hydrogen bonding.


¾Reducing agents commonly 2-mercaptoethanol Reducing agents commonly (HOCH2CH2SH) cleaves disulfide bonds by reducing -S-S-groups to -SH -S-S-groups. Permanent wave processes do this.


¾Heavy metal ions such as: PbHeavy metal ions such as 2+, Hg2+, and Cd2+form water-insoluble salts with -SH groups on cysteine. Hg2+for example forms -S-Hg-S-.


¾Alcohols affect the water content and hydrophobic/hydrophilic Alcohols affect the water content and hydrophobic/hydrophilic relationships.

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



Digestion of Proteins

Hydrolysis (breakdown) Recovers Constituent Amino Acids.

N CH C O R H H H H R' O C CH N H O R" O C CH N Peptide Bonds H2O + H2O + N CH C O R O H H H N CH C O R' O H H H N CH C O R" O H H H

Essential aminoacids, ones our bodies cannot make, are obtained this way from our diet. All the others can be obtained too.


Common Properties of Proteins

¾Protein shape is essential to its function. Sometimes changing its shape can be lethal – Prions – Proteinaceous Infectuous Particles – are altered proteins that can cause natural proteins to change shape – Mad Cow disease or Bovine Spongiform Encephalopathy, Scrapie, Kuru, Creutzfeldt-Jacob disease. ¾Sometimes a single aminoacid substitution can cause a protein to have the wrong shape. Sickle cell anemia is an example. ¾Proteins have isoelectric points just like amino acids. At the isoelectric points proteins are uncharged (net neutral, dipolar) and clump together (precipitate, denature). Away from the isoelectric point they have a like charge, either positive or negative and repel each other thus remaining in solution. ¾At the isoelectric point neither proteins nor amino acids will drift toward either electrode (anode or cathode) in an electric field.


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