Amino Acid Structure & Function PDF

## Lecture 4 ### General Structure of Amino Acid - The name "amino acid" comes from the presence of both an amine group (-NH₂) and a carboxyl group (-COOH). - The alpha carbon is the central carbon atom of the amino acid. - The alpha carbon is attached to an H atom, an amine group (-NH...

## Lecture 4 ### General Structure of Amino Acid - The name "amino acid" comes from the presence of both an amine group (-NH₂) and a carboxyl group (-COOH). - The alpha carbon is the central carbon atom of the amino acid. - The alpha carbon is attached to an H atom, an amine group (-NH₂), a carboxyl group (-COOH) and a side chain (R group). - The side chain is what differentiates amino acids from one another. ### Structure of Amino Acid - The carboxyl group (-COOH) is a proton donor and is acidic. - The amine group (-NH₂) is a proton acceptor, and is basic. - The alpha carbon is asymmetric because it is attached to four different groups. ### Note - Anything on the alpha carbon is called a "D" or "L" isomer depending on its stereochemistry. - The amino acids in our bodies are "L" isomers, while the "D" isomers can be found in bacteria. ### 20 Standard Amino Acids - There are around 300-400 types of amino acids, but only 20 are found in proteins. - These 20 are called "proteinogenic amino acids" or "standard amino acids." - Other amino acids that are not among the 20 standard amino acids can be formed through post-translational modifications (PTM). ### Classifying Amino Acids by Polarity - Amino acids are classified according to the polarity and side chain of their R group: - **Non-polar (hydrophobic)**: These amino acids have side chains that are hydrophobic and therefore do not interact well with water. - **Polar (hydrophilic)**: These amino acids have side chains that are hydrophilic and therefore interact well with water. - **Polar charged**: These amino acids have side chains that carry a positive or negative charge. - **Uncharged**: These amino acids have side chains that are polar but do not carry a net charge. ### Non-polar amino acids 1. **Glycine (Gly, G)** - The only amino acid that is optically inactive because the alpha carbon is not asymmetric. 2. **Alanine (Ala, A)** - Contains a methyl group as its side chain. 3. **Valine (Val, V)** - Contains a branched side chain. 4. **Leucine (Leu, L)** - Contains a branched side chain. 5. **Isoleucine (Ile, I)** - Contains two asymmetric carbons. 6. **Proline (Pro, P)** - The nitrogen atom in the amine group is part of a ring structure. 7. **Methionine (Met, M)** - Contains a sulfur atom. 8. **Phenylalanine (Phe, F)** - Contains a phenyl group. ### Polar uncharged amino acids 9. **Tryptophan (Trp, W)** - Contains a indole ring. 10. **Serine (Ser, S)** - Contains a hydroxyl group. 11. **Threonine (Thr, T)** - Contains a hydroxyl group. 12. **Tyrosine (Tyr, Y)** - Contains a hydroxyl group and a phenyl group. 13. **Cysteine (Cys, C)** - Contains a sulfhydryl group. 14. **Asparagine (Asn, N)** - Contains an amide group. 15. **Glutamine (Gln, Q)** - Contains an amide group. ### Polar charged amino acids 16. **Aspartic acid (Asp, D)** - Contains a carboxyl group - Acidic 17. **Glutamic acid (Glu, E)** - Contains a carboxyl group. - Acidic 18. **Lysine (Lys, K)** - Contains an amino group - Basic 19. **Arginine (Arg, R)** - Contains a guanidino group - Basic ### Histidine (His, H) - Contains an imidazole ring. - Can be both acidic and basic based on the pH. ### Selenocysteine (Sec, U) - Contains a selenocysteine and is found in humans. - Encoded by UGA (normally a stop codon). ### Pyrrolysine (Pyl, O) - Only found in bacteria. - Encoded by UAG (normally a stop codon). ### Basic vs. Acidic Amino Acids - Amino acids are classified as either basic or acidic due to their role in protein function. - **Basic amino acids:** Have a net positive charge in solution. - **Acidic amino acids:** Have a net negative charge in solution. ### Example of Basic Amino Acid Function: Histones - Histones are proteins that bind to DNA and help to package it into chromosomes. - The basic amino acids in histones positively interact with the negatively charged phosphate groups in DNA, which facilitates the binding process. ### Example of Acidic Amino Acid Function: Hemoglobin - Hemoglobin is a protein that carries oxygen in the blood. - Hemoglobin has a hydrophobic pocket that binds to oxygen. This pocket is largely made up of non-polar amino acids. - However, the outer surface of hemoglobin is composed of polar amino acids. - This allows hemoglobin to interact with the surrounding water molecules and transport oxygen to different parts of the body. ### Essential vs. Non-Essential Amino Acids - **Essential amino acids:** Cannot be synthesized by the human body and must be obtained through the diet. - **Non-essential amino acids:** Can be synthesized by the human body. - **Semi-essential amino acids:** Can be synthesized by the body, but not at sufficient levels, so they must be obtained from the diet. ### Biological Value of Protein - The biological value of protein refers to its digestibility and its content of essential amino acids. - **High biological value (HBV) proteins:** Highly digestible and contain all essential amino acids in the correct proportions. These proteins are usually found in animal sources, such as meat, poultry, fish, and eggs. - **Low biological value (LBV) proteins:** Less digestible and may lack one or more essential amino acids. These proteins are typically found in plant-based sources such as beans, lentils, and nuts. ### Conclusion The properties of amino acids, including their polarity, charge, and essentiality, determine their roles in protein structure and function. An understanding of essential amino acids is important for diet and supplementation.