Macromolecules notes

Amino Acids: Building Units of Proteins

Amino acids are organic compounds containing an amino group, -NH2, and a carboxyl group, -COOH. In alpha amino acids, both groups are attached to the same alpha carbon atom. The alpha carbon also has a hydrogen atom and a variable side chain represented by R.

There are 20 amino acids commonly found in natural proteins. The identity and properties of a protein depend on the number, type and arrangement of its amino acids. Lactic acid is not an amino acid because it does not contain an amino group.

In aqueous solution, an amino acid commonly exists as a dipolar ion, or zwitter ion. The amino group accepts a proton and becomes -NH3+, while the carboxyl group loses a proton and becomes -COO-.

points- 20 amino acids are commonly found in natural proteins.

- Alpha amino acids have the amino and carboxyl groups attached to the same carbon atom.

- A zwitter ion contains both a positive charge and a negative charge but has an overall neutral charge.

- Alanine has CH3 as its R group.

- Lactic acid is not an amino acid.

- Histidine contains an imidazole ring in its side chain.

- Ninhydrin is used for the identification of amino acids.

- All proteins contain carbon, hydrogen, oxygen and nitrogen; some also contain sulphur or other elements.

• 20 amino acids are commonly found in natural proteins.
• Alpha amino acids have the amino and carboxyl groups attached to the same carbon atom.
• A zwitter ion contains both a positive charge and a negative charge but has an overall neutral charge.
• Alanine has CH3 as its R group.
• Lactic acid is not an amino acid.
• Histidine contains an imidazole ring in its side chain.
• Ninhydrin is used for the identification of amino acids.
• All proteins contain carbon, hydrogen, oxygen and nitrogen; some also contain sulphur or other elements.

Classification of Amino Acids

Amino acids may be classified according to the nature of their side chains. Nonpolar amino acids have hydrophobic side chains. Polar amino acids have side chains that can interact with water. Acidic amino acids contain an extra carboxyl group, while basic amino acids contain an extra basic nitrogen-containing group.

The charge of an amino acid depends on the pH of the solution. Lysine is a basic amino acid. Aspartic acid and glutamic acid are acidic amino acids. Histidine is also classified among the basic amino acids because its imidazole group can accept a proton.

Another useful classification is based on whether the body can synthesise the amino acid. Essential amino acids must be obtained from the diet, while non-essential amino acids can be made by the body.

points- Nonpolar amino acids include glycine, alanine, valine, leucine, isoleucine, methionine and proline.

- Polar uncharged amino acids include serine, threonine, cysteine, asparagine, glutamine and tyrosine.

- Acidic amino acids are aspartic acid and glutamic acid.

- Basic amino acids include lysine, arginine and histidine.

- Lysine is basic in nature.

- Amino acids with hydrophobic side chains tend to occur inside globular proteins.

- The classification based on side chain is different from the classification based on nutritional requirement.

• Nonpolar amino acids include glycine, alanine, valine, leucine, isoleucine, methionine and proline.
• Polar uncharged amino acids include serine, threonine, cysteine, asparagine, glutamine and tyrosine.
• Acidic amino acids are aspartic acid and glutamic acid.
• Basic amino acids include lysine, arginine and histidine.
• Lysine is basic in nature.
• Amino acids with hydrophobic side chains tend to occur inside globular proteins.
• The classification based on side chain is different from the classification based on nutritional requirement.

Peptide Bonds and Protein Structure

A peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of another amino acid. Water is eliminated during this condensation reaction. A chain containing many amino acids joined by peptide bonds is called a polypeptide.

Proteins are polymers because they are large molecules built from repeating amino acid units. Protein structure is described at four levels: primary, secondary, tertiary and quaternary.

The primary structure is the exact sequence of amino acids. It is maintained by covalent peptide bonds, not by hydrogen bonds. Secondary structure includes alpha helices and beta-pleated sheets, mainly stabilised by hydrogen bonds. Tertiary structure is the complete three-dimensional shape of one polypeptide chain.

points- A peptide bond has the linkage -CO-NH-.

- Formation of a peptide bond is a condensation reaction that releases water.

- Primary structure means the specific amino acid sequence of a protein.

- Primary structure is due to peptide bonds, not hydrogen bonding.

- Secondary structure includes alpha helix and beta-pleated sheet.

- Hydrogen bonds help stabilise secondary structure.

- Tertiary structure is the three-dimensional folding of one polypeptide chain.

- Quaternary structure results when two or more polypeptide chains associate.

• A peptide bond has the linkage -CO-NH-.
• Formation of a peptide bond is a condensation reaction that releases water.
• Primary structure means the specific amino acid sequence of a protein.
• Primary structure is due to peptide bonds, not hydrogen bonding.
• Secondary structure includes alpha helix and beta-pleated sheet.
• Hydrogen bonds help stabilise secondary structure.
• Tertiary structure is the three-dimensional folding of one polypeptide chain.
• Quaternary structure results when two or more polypeptide chains associate.

Classification of Proteins

Proteins can be classified according to shape, composition and the products formed on hydrolysis. Fibrous proteins usually have long, thread-like structures and are generally insoluble in water. Globular proteins have compact, rounded structures and are often soluble in water.

Simple proteins yield only amino acids when completely hydrolysed. Conjugated proteins contain a protein part joined to a non-protein component. The non-protein component is called a prosthetic group. Derived proteins are formed from simple or conjugated proteins by partial hydrolysis or other chemical changes.

Examples of fibrous proteins include keratin and collagen. Examples of globular proteins include haemoglobin, enzymes and antibodies. Ceruloplasmin is a copper-containing protein present in blood plasma and helps bind and transport copper.

points- Fibrous proteins are long, thread-like and generally insoluble in water.

- Globular proteins are compact, spherical or rounded and are commonly soluble in water.

- Simple proteins yield only amino acids on complete hydrolysis.

- Conjugated proteins contain a protein part and a non-protein part.

- The non-protein part of a conjugated protein is called a prosthetic group.

- Haemoglobin is a conjugated protein containing a haem group.

- Antibodies are globular proteins with quaternary structure.

- Ceruloplasmin is a copper-containing blood plasma protein involved in copper transport.

• Fibrous proteins are long, thread-like and generally insoluble in water.
• Globular proteins are compact, spherical or rounded and are commonly soluble in water.
• Simple proteins yield only amino acids on complete hydrolysis.
• Conjugated proteins contain a protein part and a non-protein part.
• The non-protein part of a conjugated protein is called a prosthetic group.
• Haemoglobin is a conjugated protein containing a haem group.
• Antibodies are globular proteins with quaternary structure.
• Ceruloplasmin is a copper-containing blood plasma protein involved in copper transport.

Importance of Proteins

Proteins are essential components of living cells. They are required for growth, repair and maintenance of body tissues. Dietary proteins are digested into amino acids, which are then absorbed and used to form new proteins.

Proteins also perform specialised functions. Enzymes catalyse reactions, antibodies defend the body, and some hormones regulate physiological processes. Structural proteins provide strength and support, while transport proteins carry substances through blood or across cell membranes.

Proteins can also be used as a source of energy when required. However, their main dietary importance is to supply amino acids for the growth and repair of tissues.

points- Proteins are needed for growth and repair of body tissues.

- Enzymes are protein catalysts in most biological reactions.

- Antibodies help protect the body against foreign substances.

- Haemoglobin transports oxygen in blood.

- Collagen provides strength to connective tissues.

- Keratin is present in hair, nails and the outer layer of skin.

- Proteins may act as hormones, receptors and membrane transporters.

- The main dietary role of proteins is supplying amino acids, not energy.

• Proteins are needed for growth and repair of body tissues.
• Enzymes are protein catalysts in most biological reactions.
• Antibodies help protect the body against foreign substances.
• Haemoglobin transports oxygen in blood.
• Collagen provides strength to connective tissues.
• Keratin is present in hair, nails and the outer layer of skin.
• Proteins may act as hormones, receptors and membrane transporters.
• The main dietary role of proteins is supplying amino acids, not energy.

Enzymes as Biocatalysts

Enzymes are biological catalysts. Most enzymes are globular proteins, although some catalytic RNA molecules also exist. An enzyme increases the rate of a reaction without being permanently consumed.

A reacting molecule binds to a specific region of the enzyme called the active site. The enzyme and substrate form an enzyme-substrate complex. The active site places the substrate in a suitable orientation and stabilises the transition state. This lowers the activation energy of the reaction.

The lock and key model explains enzyme specificity by suggesting that the substrate fits the active site. The induced fit model states that binding causes a slight change in the shape of the active site, producing a closer fit with the substrate.

points- Enzymes are biological catalysts, also called biocatalysts.

- Enzymes lower activation energy but do not change the overall energy change of a reaction.

- An enzyme is not permanently consumed during the reaction.

- The substrate binds to the active site.

- The active site stabilises the transition state and lowers activation energy.

- Enzyme specificity results from the complementary shape and chemical properties of the active site.

- Enzyme activity is affected by temperature, pH, substrate concentration and enzyme concentration.

- Extreme temperature or pH may denature an enzyme and destroy its activity.

• Enzymes are biological catalysts, also called biocatalysts.
• Enzymes lower activation energy but do not change the overall energy change of a reaction.
• An enzyme is not permanently consumed during the reaction.
• The substrate binds to the active site.
• The active site stabilises the transition state and lowers activation energy.
• Enzyme specificity results from the complementary shape and chemical properties of the active site.
• Enzyme activity is affected by temperature, pH, substrate concentration and enzyme concentration.
• Extreme temperature or pH may denature an enzyme and destroy its activity.

Classes and Terminology of Enzymes

Enzymes are named according to the reactions they catalyse. The six major enzyme classes are oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. Dehydrogenases belong to the oxidoreductase class because they catalyse oxidation-reduction reactions involving transfer of hydrogen or electrons.

Some enzymes require a non-protein component for activity. The protein part alone is called an apoenzyme. The complete active enzyme, consisting of the apoenzyme and its required non-protein part, is called a holoenzyme. A tightly attached non-protein part is called a prosthetic group.

The study of fermentation is called zymology. Enzyme names commonly end in -ase, although some traditional names do not follow this pattern.

points- Oxidoreductases catalyse oxidation-reduction reactions; dehydrogenase is an example.

- Transferases transfer a functional group from one molecule to another.

- Hydrolases break bonds by using water.

- Lyases add or remove groups without hydrolysis or oxidation, often forming or breaking double bonds.

- Isomerases catalyse rearrangement of atoms within a molecule.

- Ligases join two molecules, usually using energy from ATP.

- Apoenzyme is the protein part of a conjugated enzyme.

- Holoenzyme is the complete active enzyme, including its required non-protein component.

• Oxidoreductases catalyse oxidation-reduction reactions; dehydrogenase is an example.
• Transferases transfer a functional group from one molecule to another.
• Hydrolases break bonds by using water.
• Lyases add or remove groups without hydrolysis or oxidation, often forming or breaking double bonds.
• Isomerases catalyse rearrangement of atoms within a molecule.
• Ligases join two molecules, usually using energy from ATP.
• Apoenzyme is the protein part of a conjugated enzyme.
• Holoenzyme is the complete active enzyme, including its required non-protein component.

Related Macromolecules: Carbohydrates, Lipids and Nucleotides

Carbohydrates, lipids and nucleic acids are also important biological macromolecules. A monosaccharide is a carbohydrate that cannot be hydrolysed into a simpler carbohydrate. Monosaccharides commonly contain 3 to 7 carbon atoms. Examples include glucose, fructose and ribose.

Fats are lipids known as glycerides. They are esters formed from glycerol, whose systematic name is propane-1,2,3-triol, and long-chain carboxylic acids called fatty acids. Nucleotides contain a nitrogenous base, a pentose sugar and phosphate group.

Thyroxine is a hormone and is not a nitrogenous base present in nucleotides. Common nitrogenous bases include adenine, guanine, cytosine, thymine and uracil.

points- A monosaccharide cannot be hydrolysed into a simpler carbohydrate.

- Monosaccharides commonly contain 3 to 7 carbon atoms.

- Glucose, fructose and ribose are monosaccharides.

- Fats are esters of glycerol and long-chain fatty acids.

- Glycerol is propane-1,2,3-triol.

- A nucleotide contains a nitrogenous base, a pentose sugar and phosphate group.

- Thyroxine is not a nucleotide base.

- DNA contains adenine, guanine, cytosine and thymine, while RNA contains uracil instead of thymine.

• A monosaccharide cannot be hydrolysed into a simpler carbohydrate.
• Monosaccharides commonly contain 3 to 7 carbon atoms.
• Glucose, fructose and ribose are monosaccharides.
• Fats are esters of glycerol and long-chain fatty acids.
• Glycerol is propane-1,2,3-triol.
• A nucleotide contains a nitrogenous base, a pentose sugar and phosphate group.
• Thyroxine is not a nucleotide base.
• DNA contains adenine, guanine, cytosine and thymine, while RNA contains uracil instead of thymine.