Proteins serve many functions, including the following. Given are examples of each. Structure: Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails Catalysts: Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes Movement: Movement: muscles are made up of proteins called myosin and actin Transport Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes Hormones: Hormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone See p

Storage: Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron Regulation: 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 Protection: Protection: blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease globular proteins

Amino 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 zwitterion –although  -amino acids are commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt) form

Chirality of Amino Acids With the exception of glycine, all protein- derived amino acids have at least one stereocenter (the  -carbon) and are chiral –the vast majority of  -amino acids have the L- configuration at the  -carbon

Chirality of Amino Acids A comparison of the stereochemistry of L- alanine and D-glyceraldehyde

20 Protein-Derived AA Nonpolar side chains (at pH 7.0) Table 21-2 p 527

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

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

20 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 contain a second stereocenter isoleucine threonine

Electrophoresis Electrophoresis: the process of separating compounds on the basis of their electric charge –electrophoresis of amino acids can be carried out using paper, starch, agar, certain plastics, and cellulose acetate as solid supports In paper electrophoresis –a paper strip saturated with an aqueous buffer of predetermined pH serves as a bridge between two electrode vessels

Electrophoresis –a sample of amino acids is applied as a spot on the paper strip –an electric potential is applied to the electrode vessels and amino acids migrate toward the electrode with charge opposite their own –molecules with a high charge density move faster than those with low charge density –molecules at their isoelectric point remain at the origin –after separation is complete, the strip is dried and developed to make the separated amino acids visible

Isoelectric Point Isoelectric point, pI:Isoelectric point, pI: the pH at which the majority of molecules of a compound in solution have no net charge Values given in table 21-1 p527

Ionization 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 NH 3 + group to the base turning the zwitterion into a negative ion –to summarize

Ionization 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

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Cysteine SH -S-S-The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide)

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

Peptide Bond Geometry The four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120° about C and N

Fig 21.1, p.532

Peptide Bond Geometry –to account for this geometry, Linus Pauling proposed that a peptide bond is most accurately represented as a hybrid of two contributing structures –the hybrid has considerable C-N double bond character and rotation about the peptide bond is restricted

Peptides –peptide –peptide: a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain –dipeptide –dipeptide: a molecule containing two amino acids joined by a peptide bond –tripeptide –tripeptide: a molecule containing three amino acids joined by peptide bonds –polypeptide –polypeptide: a macromolecule containing many amino acids joined by peptide bonds –protein –protein: a biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds

Writing Peptides –by convention, peptides are written from the left, beginning with the free -NH 3 + 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 -NH 3 + group

Fig. 22.UN, p.530

Peptides and Proteins proteins behave as zwitterions isoelectric point, pIproteins also have an isoelectric point, pI –hemoglobin 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 their solutions

In acid solution In neutral solution In basic solution solubility of polypeptide depends on pH – least soluble at isoelectric point Fig21.2 – p 533

Levels 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 overall conformation of a polypeptide chain Quaternary structure: Quaternary structure: the arrangement of two or more polypeptide chains into a noncovalently bonded aggregation

Levels of structure Primary secondary tertiary

Primary Structure Primary structure:Primary structure: the sequence of amino acids in a polypeptide chain The number peptides derived 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 n 20 n –the number of peptides possible for a chain of n amino acids is 20 n –for a small protein of 60 amino acids, the number of proteins possible is = 10 78, which is possibly greater than the number of atoms in the universe!

Primary 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 disulfide bonds –in the table are differences between four types of insulin

Primary 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

Secondary 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

 -Helix

The h-bonding in the alpha helix is between amino and acid groups in the backbone

 -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 itall R- groups point outward from the helix

 -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.

Collagen Triple Helix

–every third position is Gly and repeating sequences are X-Pro-Gly and X-Hyp-Gly –30% of amino acids in each chain are Pro and L- hydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs –each polypeptide chain is a helix but not an  -helix –the three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine –consists of three polypeptide chains wrapped around each other in a ropelike twist to form a triple helix called tropocollagen –with age, collagen helices become cross linked by covalent bonds formed between Lys residues

Fig 21.UN, p.540

Collagen – triple helix ( 3 intertwined helices ) Each helix stabilized by steric repulsions between proline rings Structure further stabilized by H-bonding between NH of glycine & CO of amino acids on other chains and by covalent cross links formed between lysine side chains. Fig 21.9 – p 540

Tertiary Structure Tertiary structure:Tertiary structure: the overall conformation of a polypeptide chain Tertiary structure is stabilized in four ways –covalent bonds –covalent bonds, as for example the formation of disulfide bonds between cysteine side chains –hydrogen bonding –hydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine –salt bridges –salt bridges, as for example the attraction of the -NH 3 + group of lysine and the -COO - group of aspartic acid –hydrophobic interactions –hydrophobic interactions, as for example between the nonpolar side chains of phenylalanine and isoleucine

Quaternary 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

Hemoglobin

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Denaturation 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