Digestion and absorption of proteins

Proteins are large polymers. Unlike starch and glycogen, which are polymers of only a single type of monomer unit (glucose), proteins consist of a variety of amino acids.

There is an almost infinite variety of proteins, composed of different numbers of the different amino acids (between 50 and 1,000 amino acids in a single protein molecule), in different order. There are some 30—50,000 different proteins and polypeptides in the human body. Each protein has a specific sequence of amino acids.

Small proteins have a relative molecular mass of about 50—100 X 103, whereas some of the large complex proteins have a relative molecular mass of up to 106. In addition to proteins, smaller polymers of amino acids, containing up to about 50 amino acids, are important in the regulation of metabolism. Collectively these are known as polypeptides.

4.4.1 The amino acids

Twenty-one amino acids are involved in the synthesis of proteins, together with a number that occur in proteins as a result of chemical modification after the protein has been synthesized. In addition, a number of amino acids occur as metabolic intermediates but are not involved in proteins.

Chemically the amino acids all have the same basic structure — an amino group (—NH2) and a carboxylic acid group (-COOH) attached to the same carbon atom (the a-carbon). As shown in Figure 4.18, what differs between the amino acids is the nature of the other group that is attached to the a-carbon. In the simplest amino acid, glycine, there are two hydrogen atoms, while in all other amino acids there is one hydrogen atom and a side-chain, varying in chemical complexity from the simple methyl group (—CH3) of alanine to the aromatic ring structures of phenylalanine, tyrosine and tryptophan. Figure 4.18 does not show the structure of the 21st amino acid, the selenium analogue of cysteine, selenocysteine (section 11.15.2.5).

The amino acids can be classified according to the chemical nature of the side-chain, whether it is hydrophobic (on the left of Figure 4.18) or hydrophilic (on the right of Figure 4.18), and the nature of the group:

  • small hydrophobic amino acids: glycine, alanine, proline;
  • branched-chain amino acids: leucine, isoleucine, valine;
  • aromatic amino acids: phenylalanine, tyrosine, tryptophan;
  • sulphur-containing amino acids: cysteine, methionine;
  • neutral hydrophilic amino acids: serine and threonine;
  • acidic amino acids: glutamic and aspartic acids (the salts of these acids are glutamate and aspartate respectively);
  • amides of the acidic amino acids: glutamine and asparagine;
  • basic amino acids: lysine, arginine, histidine.

4.4.2 Protein structure and denaturation

Proteins are composed of linear chains of amino acids, joined by condensation of the

small neutral amino acids

nh3+

NH,+ 1

1 1

HCH

H3C—CH

OL

|

coo-

N COO"

COO"

H

glycine (Gly, G)

alanine (Ala, A)

proline (Pro, p)

large neutral amino acids ch, nh3+

"isoleucine (lie, I) COO" branched-chain amino acids ch, nh,

COO"

NH3+

H3C—S—CH2—CH2 CH "methionine (Met, M) COO"

aromatic amino acids

COO"

"phenylalanine (Phe, F)

COO"

"tryptophan (Trp, W)

tyrosine (Tyr, Y)

COO"

neutral hydrophilic amino acids

NH3+

OH NH3+

COO" "threonine (Thr, T)

COO cysteine (Cys, C)

acidic amino acids nh3

nh3+ 1

"OOC—CH,—CH |

"OOC—CH2—CH2—

-CH

COO-

COO"

aspartate (Asp, D)

glutamate (Glu, E)

amino acid amides

0 nh3+

II

h,n—c—ch2—ch

h2n—c—ch2—ch2—

1

asparagine (Asn, n) <-'<-)<-)

glutamine (Gin, Q)

coo"

basic amino acids

nh,+ 1

+h3n—ch2—ch2—ch2—ch2

—ch

nh3+ 1

"lysine (Lys, K)

coo"

--ch,—ch

n^^nh coo"

nh2

nh3+ 1

"histidine (His, H)

hn=c—nh—ch2—ch2—ch2

—ch

arginine (Arg, R)

coo"

Figure 4.18 The amino acids, showing their three-letter and single-letter codes. *Essential dietary amino acids that cannot be synthesized in the body.

carboxyl group of one with the amino group of another, to form a peptide bond (Figure 4.19). Chains of amino acids linked in this way are known as polypeptides.

The sequence of amino acids in a protein is its primary structure. It is different for each protein, although proteins that are closely related to each other often have similar primary structures. The primary structure of a protein is determined by the gene containing the information for that protein (section 9.2).

4.4.2.1 Secondary structure of proteins

Polypeptide chains fold up in a variety of ways. Two main types of chemical interaction are responsible for this folding: hydrogen bonds between the oxygen of one peptide bond and the nitrogen of another (Figure 4.20) and interactions between the side-chains of the amino acids. Depending on the nature of the side-chains, different regions of the chain may fold into one of the following patterns:

  • a-Helix, in which the peptide backbone of the protein adopts a spiral (helix) form. The hydrogen bonds are formed between peptide bonds which are near each other in the primary sequence.
  • Pleated sheet, in which regions of the polypeptide chain lie alongside one another, forming a 'corrugated' or pleated surface. The hydrogen bonds are between peptide bonds in different parts of the primary sequence, and the regions of polypeptide chain forming a pleated sheet may run parallel or antiparallel.
Threonine H3n H3c Cooh
Figure 4.19 Condensation of amino acids to form a peptide bond.

J-j JWMWWMMV N-C-C-N-C-Oi/WVWWWUWW COOH

I Cil I li

Figure 4.20 Hydrogen bonds between peptide bonds in a peptide chain.

  • Hairpins and loops, in which small regions of the polypeptide chain form very tight bends;
  • Random coil, in which there is no recognizable organized structure. Although this appears to be random, for any one protein the shape of a random coil region will always be the same.

A protein may have several regions of a-helix, ^-pleated sheet (with the peptide chains running parallel or antiparallel), hairpins and random coil, all in the same molecule.

4.4.2.2 Tertiary and quaternary structures of proteins

Having formed regions of secondary structure, the whole protein molecule then folds up into a compact shape. This is the third (tertiary) level of structure and is largely the result of interactions between the side-chains of the amino acids, both with each other and with the environment. Proteins in an aqueous medium in the cell generally adopt a tertiary structure in which hydrophobic amino acid side-chains are inside the molecule and can interact with each other, whereas hydrophilic side-chains are exposed to interact with water. By contrast, proteins which are embedded in membranes (see Figure 4.12) have a hydrophobic region on the outside, to interact with the membrane lipids.

Two further interactions between amino acid side-chains may be involved in tertiary structure, in this case forming covalent links between regions of the peptide chain (Figure 4.21):

  • The e-amino group on the side-chain of lysine can form a peptide bond with the carboxyl group on the side-chain of aspartate or glutamate. This is nutritionally important, as the side-chain peptide bond is not hydrolysed by digestive enzymes, and the lysine, which is an essential amino acid (section 9.1.3), is not available for absorption.
  • The sulphydryl (-SH) groups of two cysteine molecules may be oxidized, to form a disulphide bridge between two parts of the protein chain.

Some proteins consist of more than one polypeptide chain; the way in which the chains interact with each other after they have separately formed their secondary and tertiary structures is the quaternary structure of the protein. Interactions between the subunits of multi-subunit proteins, involving changes in quaternary structure and the conformation of the protein, affecting activity, are important in a number of regulatory enzymes (sections 2.3.3.3 and 10.2.1).

Quaternary Structure Protein Bonds
Figure 4.2 1 Covalent links between peptide chains — on the left a side-chain peptide between the e-amino group of lysine and the Y-carboxyl group of glutamate; on the right a disulphide bridge formed by oxidation of two cysteine residues.
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