Amino Acids & Proteins PDF

**Amino Acids & Proteins** - Proteins are macromolecules made up of monomers called amino acids. Amino acids are the building block of all proteins. - An amino acid is a simple organic compound consisting of a basic group (-NH2), an acidic group (-COOH), and an organic R group that...

**Amino Acids & Proteins** - Proteins are macromolecules made up of monomers called amino acids. Amino acids are the building block of all proteins. - An amino acid is a simple organic compound consisting of a basic group (-NH2), an acidic group (-COOH), and an organic R group that is unique to each amino acid. - The term amino acid is short for alpha-amino carboxylic acid. Each molecule has a central carbon atom, called the α-carbon to which both the groups are attached. - The remaining two bonds for the central carbon are satisfied by the hydrogen atom and an organic R group. - The organic R group can be as simple as a hydrogen atom (H) or a methyl group (--- CH3) or a more sophisticated group. - Thus, the α -carbon in all the amino acids is asymmetric except in glycine where the α -carbon is symmetric with a hydrogen atom as an R group. - Amino acids are amphoteric compounds with both acidic and alkaline groups. These also always exist as ions except at the isoelectric point. - There are 20 types of amino acids which are coded by the gene of vertebrate but large numbers of modified (non-standard) amino acids are found in proteins. **Characteristics of amino acids:** ----------------------------------- - - - - - - - Classification of amino acids ----------------------------- I. Classification on the basis of R-group II\. Classification on the basis of nutrition III\. Classification on the basis of Catabolism ### I. Classification of amino acids on the basis of R-group  #### 1. Group A : Hydrophobic amino acids - - #### 2. Group B: Hydrophilic, uncharged amino acids - - #### 3. Group C: acidic amino acids - - #### 4. Group D: basic amino acids - - ### ### ### ### ### II. Classification of amino acids on the basis of Nutrition: #### 1. Essential amino acids: - - - #### 2. Non essential amino acids: - - ***3.Conditionally essential amino acids:*** Conditionally essential amino acids are usually not essential, except in times of illness and stress. ### III. Classification of amino acids on the basis of Catabolism #### 1. Glucogenic amino acids: - - #### 2. Ketogenic amino acids: - - ### 3. Both glucogenic and ketogenic amino acids: - - **Zwitterion** A zwitterion is a molecule that includes both positive and negative regions of charge. The existence of amino acids as dipolar ions in a solid state is called zwitterions. To evaluate whether a substance is zwitterionic or not, the pH range must be specified. This is because the zwitterion changes to an [anion](https://www.vedantu.com/chemistry/anion) in the presence of sufficient alkaline solution, and zwitterion changes to a cation in the presence of sufficient acid solution. **Characteristics of Zwitterion** The following are some of the characteristics of Zwitterion: - It can be formed by compounds that have both acid and base groups in their molecules such as ampholytes. - In this type of ion, the charged atoms are generally held together by one or more covalent bonds. - The atoms have stable, separated unit electrical charges in Zwitterrion Compounds. - These compounds contain quaternary ammonium cations. **Applications of Zwitterion** - Zwitterions are widely used in the process of separating protein molecules through the SDS PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis) method, which is one of the most popular techniques used in the field of molecular biology. - It has the potential to be used in a wide range of medical and biological-related fields. - Some of the most popular uses of zwitterions include medical implants, drug delivery, blood contact sensor, separation membrane, and antifouling coatings of biomedical implants (which help to prevent the build-up of microbial adhesion and biofilm formation).  **Isoelectric Point** - One of the main properties of a Zwitterion is that it has an isoelectric point, which is represented by pI, pH(I), IEP. - Generally, the pH has a great impact on the net charge on a molecule and its surrounding environment. - In this case, molecules become more charged either positively or negatively as a result of gain or loss in the number of protons. - In amino acids, the amino group is an effective proton acceptor and the carboxyl group is an effective proton donor. - The solubility of a molecule at a given pH is also impacted by the pI value. **Calculation of pH value** The pH value at the isoelectric point is calculated from the equilibrium constants such as acid and base of the Zwitterion. It is represented by the formula;  Where, pI = isoelectric point, K~a1~ = the equilibrium constant of the acid. K~a2~ = the equilibrium constant of the base. **Peptide bond:** - The bond linking two amino acids is known as a peptide bond. - A peptide bond is a special type of amide bond formed between two molecules where an α-carboxyl group of one molecule reacts with the α-amino group of another molecule releasing a water molecule. - The peptide bond is also referred to as the isopeptide bond where the amide bond forms between the carboxyl group of one amino acid and the amino group of another amino acid at other positions than the alpha. - The process of formation of the peptide bond is an example of a condensation reaction resulting in dehydration (removal of water). - Peptide bonds are covalent bonds that exist between any two amino acids resulting in a peptide chain. - A partial double bond exists between carbon and nitrogen of the amide bond which stabilizes the peptide bond. **Peptide bond formation mechanism** ------------------------------------ - - - - - - - - **Polypeptide or peptide:** A chain made up of two or more amino acids, linked by a peptide bond is known as a polypeptide or just a peptide. **Characteristics of Peptide Bonds** 1\. Peptide bonds are strong with partial double bond character: They are not broken by heating or high salt concentration. They can be broken by exposing them to strong acid or base for a long time at elevated temperature. Also by some specific enzymes (digestive enzymes). 2\. Peptide bonds are rigid and planar bonds therefore they stabilize protein structure. 3\. Peptide bond contains partial positive charge groups (polar hydrogen atoms of amino groups) and partial negative charge groups (polar oxygen atoms of carboxyl groups). **Different Forms of Peptide Bond** **Dipeptide = **contains 2 amino acid units. **Tripeptide = **contains 3 amino acid units. **Tetrapeptide =** contains 4 amino acid units. **Oligopeptide =** contains not more than 10 amino acid units. **Polypeptide = **contains more than 10 amino acid units, up to 100 residues. **Macropeptides = **made up of more than 100 amino acids. **Functions of Amino acids** 1\. In particular, 20 very important amino acids are crucial for life as they contain peptides and proteins and are known to be the building blocks for all living things. 2\. The linear sequence of amino acid residues in a polypeptide chain determines the three-dimensional configuration of a protein, and the structure of a protein determines its function. 3\. Amino acids are imperative for sustaining the health of the human body. They largely promote the: Production of hormones Structure of muscles Human nervous system's healthy functioning The health of vital organs Normal cellular structure 4\. The amino acids are used by various tissues to synthesize proteins and to produce nitrogen-containing compounds (e.g., purines, heme, creatine, epinephrine), or they are oxidized to produce energy. 5\. The breakdown of both dietary and tissue proteins yields nitrogencontaining substrates and carbon skeletons. 6\. The nitrogen-containing substrates are used in the biosynthesis of purines, pyrimidines, neurotransmitters, hormones, porphyrins, and nonessential amino acids. 7\. The carbon skeletons are used as a fuel source in the citric acid cycle, used for gluconeogenesis, or used in fatty acid synthesis. **Difference between a peptide and a protein:** A peptide is that which has less than 50 amino acids or whose molecular weight is less than 5000 Daltons. A protein is that which has more than 50 amino acids or whose molecular weight is more than 5000 Daltons. This differentiation is based upon the immunolog­ical property of the two units. Peptides are non-immunogenic, whereas proteins are immunogenic. **N-terminal and C-terminal of a protein:** The end of a protein or polypeptide where the amino group is free in known as N-terminal end and that amino acid whose amino group is free is known as N-terminal amino acid.  The end of the protein or polypeptide whose carboxylic group is free is known as C-terminal end and that amino acid whose carboxylic group is free in the protein is known as C-terminal amino acid.