L1 Protein & AAs Chemistry 2024-2025 Dentistry PDF

2024- 2025 Chapter (1): Amino acids, Protein structure and function Lecture 1 Intended Learning Outcomes By the end of these lectures , the student will be able to: Demonstrate the biological importance of amino acids and proteins. Understand the structure of amino acids. Abbreviat...

2024- 2025 Chapter (1): Amino acids, Protein structure and function Lecture 1 Intended Learning Outcomes By the end of these lectures , the student will be able to: Demonstrate the biological importance of amino acids and proteins. Understand the structure of amino acids. Abbreviate the different amino acids. Differentiate between the D and L forms of amino acids. Classify amino acids according to their side chains, metabolic fate and biologic value. Understand the meaning of peptides and proteins. Describe the orders of protein organization (folding). Explain how proteins can be denatured or misfolded. Classify proteins by different ways. Describe Fibrous proteins ; Collagen and Elastin Amino acids (A.A.) Are the fundamental structural units of proteins. Functions: Components of peptides, proteins. Precursor of glucose, nucleotides, heme and creatine and collagen. Neurotransmitters: glutamate, aspartate and glycine. Proteins L-Form Amino Acid Structure Amino Acids & Protein Chemistry  Amino Acids are the Building Blocks of Proteins In nature: > 300 different A.A. In mammalian proteins, there are 20 common A.A. Each A.A. is coded in DNA by a three-letter codon, and has at least one specific transfer RNA (tRNA). Selenocysteine is the 21st A. A. is found in many proteins, but not encoded by the three-letter codon. Central Dogma of Life Numbering of carbon atoms in Amino Acid D and L forms (mirror image, Sterioismoers enantiomers): ??? In humans amino acids are present in the L-α form , While in plants they are mostly D-form L-Form Amino Acid Structure  Classification of AAs Chemical : According to the structure of the side chain ‘R group’. Polar :According to the polarity of the side chain ‘R group’, Biological: Whether the A.A can be synthesized in the body or not. Metabolic: according to the fate of the A.A inside the body.  Classification According to the chemical structure of the side chain ‘R group’ Thiol group Branched side chains (Amides ) Indole Ring It has a rigid five - membered ring that interrupts the α- helices in globular proteins. It contributes to the fibrous structure of collagen. It is an imino rather than amino acid.  Classification according to Biological value Arginine is considered as semi-essential , as it is formed in insufficient amounts especially in growing children How the body can synthesize amino acid? Discussed later in metabolism of amino acids Essential (indispensible) Amino Acids: The 3 Branched: (Valine, Leucine and Isoleucine). The 3 Basic or positively charged: (Lysine, Arginine, and Histidine). 2 Aromatic: Phenylalanine and Tryptophan 1 OH containing and (Threonine) and 1 S containing (Methionine) N.B. It was found that Arginine can be formed in human cells yet in small amounts especially in children so it is considered a Semi- Essential amino acid Essential Amino Acids Proteins of high biological value: contain ALL 10 essential AAs e.g. animal proteins Proteins of low biological value: vegetable proteins lack one or more of essential amino acids Combinations of low biological value: corn (no lysine) + legumes (no methionine) = high biological value  Classification according to the polarity ‘hydrophilicity’ of the side chain ‘’ R’’ (1) Amino acids with non-polar side chains. They do not participate in hydrogen or ionic bonds. Include: glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline. If a non polar A.A. substitutes a polar amino acid, a pathology will result. e.g. in sickle cell disease, the non polar valine substitutes glutamate ‘polar’ in the β- chain of hemoglobin. (2) Amino acids with polar negatively charged (acidic)side chains. (3) Amino acids with polar positively charged (basic) side chains. (4) Amino acids with polar uncharged polar side chains(have zero net charge at neutral pH).????? N.B.: Location of amino acids according to their R group: Polar amino acids cluster on the surface, whereas non polar amino acids present in the interior of soluble proteins.