Amino Acid Structures - Biochemistry Notes - PDF

AMINO ACID STRUCTURES LEARNING THE BIOCHEMISTRY ALPHABET Sian Patterson, Ph.D. Associate Professor, Teaching Stream  Learning Objectives By the end of this lecture, students should be able to: Recognize the standard 20 amino acids and write their one- letter...

AMINO ACID STRUCTURES LEARNING THE BIOCHEMISTRY ALPHABET Sian Patterson, Ph.D. Associate Professor, Teaching Stream  Learning Objectives By the end of this lecture, students should be able to: Recognize the standard 20 amino acids and write their one- letter and three-letter abbreviations. Describe the organization of functional groups in an amino acid. Classify amino acids based on the chemical functional groups that are found on their side chains. Explain how disulfide bonds are formed and their importance for protein structure. Deduce the origin of an amino acid derivative. Contrast the effect of a chemical modification or post- translational modification (PTM) on an amino acid’s side chain. 2  Amino Acids in Space NASA Researchers Make First Discovery of Life's Building Block in Comet See: https://www.nasa.gov/mission_pages/stardust/news/stardust_amino_acid.html https://aip.scitation.org/doi/figure/10.1063/1.5021596 3  Amino Acids and Protein Structure The 20 amino acids have distinct side chains that contribute to a protein’s structure and function. Non-covalent and covalent interactions between the functional groups are important for holding a protein together as well as its ability to interact with other molecules. PDB# 2GHA – a sugar binding protein The interaction of hydrophilic amino acids with water help solubilize some proteins. 4  Proteins are made up of Amino Acids Proteins are polymers of amino acid residues linked in a linear chain by peptide/amide bonds → poly-peptides. Amino acids are made up an amino group, a carboxyl group and an “R” side chain. Some amino acids are essential and must be obtained from our diet. Others can be made from other molecules. 5  The 20 Standard Amino Acids at pH 7.4 Alanine Cysteine Aspartate Glutamate Phenylalanine Glycine Histidine Isoleucine Lysine Leucine (Ala, A) (Cys, C) (Asp, D) (Glu, E) (Phe, F) (Gly, G) (His, H) (Ile, I) (Lys, K) (Leu, L) Methionine Asparagine Proline Glutamine Arginine Serine Threonine Valine Tryptophan Tyrosine (Met, M) (Asn, N) (Pro, P) (Gln, Q) (Arg, R) (Ser, S) (Thr, T) (Val, V) (Trp, W) (Tyr, Y) 6 Which ONE of the following polypeptides only contains letters used to represent amino acids as 1-letter codes? A) F-L-A-M-I-N-G-O B) G-I-R-A-F-F-E C) B-A-D-G-E-R D) T-U-R-T-L-E 7 The Amino Acid Alphabet 8  Chiral Amino Acids The asymmetric alpha carbon centre results in chirality. Chiral molecules are non- https://www.nzgeo.com/stories/taking-sides/ superimposable, mirror images and Mirror Plane are called enantiomers. Isomers also exhibit optical activity. The L amino acids are the physiologically relevant structures found in plant and animal proteins. Why do we only see L amino acids in cells? 9  The Biochemistry ‘Handshake’ H NH3+ COO- R https://commons.wikimedia.org/wiki/File:Chirality_wit h_hands.svg#/media/File:Chirality_with_hands.svg Clockwise = L, the Left-hand rule 10  The 20 Standard Amino Acids at pH 7.4 Alanine Cysteine Aspartate Glutamate Phenylalanine Glycine Histidine Isoleucine Lysine Leucine (Ala, A) (Cys, C) (Asp, D) (Glu, E) (Phe, F) (Gly, G) (His, H) (Ile, I) (Lys, K) (Leu, L) Methionine Asparagine Proline Glutamine Arginine Serine Threonine Valine Tryptophan Tyrosine (Met, M) (Asn, N) (Pro, P) (Gln, Q) (Arg, R) (Ser, S) (Thr, T) (Val, V) (Trp, W) (Tyr, Y) 11 Sort the amino acids into your choice of at least 3 different categories: 12 Identifying Amino Acids based on Structures PDB# 2GHA – a sugar binding protein 13 What amino acids (represented by 1-letter codes) can you identify in the sugar binding site? 14 Amino Acids in 5HT2A Receptor – Ligand binding site 15  Non-covalent Interactions 1. Hydrogen bonds can form between hydroxyl, carboxyl, thiol, and amino groups to help with protein solubility. 2. Hydrogen bonds can also form between amino acid side chains within a protein’s structure. 3. Hydrophobic interactions can occur between aliphatic and hydrophobic side chains. 4. Ionic interactions are important for ligand, cofactor and/or substrate binding in enzymes. 5. Salt bridges can form between positively and negatively charged amino acids. 16 Timberlake – General Organic and Biological Chemistry 17  Disulfide Bonds Disulfide bonds covalently cross-link two cysteines together. Disulfide bridges can be intrachain or between different polypeptide chains. These linkages can stabilize structures. Protein Disulfide Isomerase (PDI) enzymes help catalyze this oxidation reaction. 18  Secreted vs. Cytosolic Proteins Disulfide bond formation is a post- translational modification (PTM) that occurs in some secreted proteins as they pass through the Endoplasmic Reticulum (ER). Cytosolic proteins usually contain cysteines due to the reducing nature of the cytosol. Disulfide bonds can be broken by reducing agents in the cytosol or in Insulin contains 3 disulfide bonds – the lab (eg. β-mercaptoethanol). 2 interchain and 1 intrachain. 19  Perms and Disulfide Bonds Alpha keratin is a protein with a high content of Cysteines and Cystines. Hydrogen bonding between keratin fibres also contributes to curly or wavy hair. Perms involve redcing the crosslinks chemically along with heat to break non-covalent interactions, then adding an oxidizing agent to make new crosslinks in the desired structure. 20  Hydrophobic Amino Acids For soluble proteins, hydrophobic (non-polar) amino acids can be found on the interior of proteins, maximizing the number of hydrophilic interactions with water. Hydrophobic amino acids may still be found on the surface to allow for non- covalent interactions. White - Hydrophilic Red - Hydrophobic 21  Post-Translational Modifications Addition or removal of functional groups can change the structure of a protein and affect its function and/or degradation. Disulfide bond formation is a type of post-translational modification. Important covalent modifications include: Phosphorylation Ubiquitination Glycosylation Acetyl, methyl, hydroxyl, carboxyl Cofactor/ligand binding is also important for structure/function. 22 Amino acid modifications 23  Amino Acid Metabolism In addition to being found in polypeptide proteins, amino acids can be metabolized to form other important molecules including: Hormones Neurotransmitters Nitrogenous bases (DNA/RNA) Energy-producing intermediates Taurine – found in Red Bull 24  Amino Acid ‘Derivatives’ Serotonin Mono-Sodium Glutamate (MSG) Cadaverine Epinephrine 25 Why do you think N and Q are non-essential amino acids? 26  Amino Acid Mutations The amino acid sequence determines the 3D structure of proteins and can reveal important information about a protein’s evolutionary history. It can be used to elucidate a protein’s function using homology searches. Mutations in the primary sequence can lead to a change in structure, function or disease. 27 ATG AUG Met Silent: Non-conservative: Conservative: You are studying a structural protein that contains a Cysteine that may be important for its structure. Design an experiment to create a new protein to test this hypothesis. 29  Key Messages There are 20 standard amino acids found in plants and mammals that can be represented by a 1-letter and 3-letter code. All amino acids have an alpha carbon bound to an amino group, a carboxyl group, a hydrogen and a distinct side chain. Interactions between functional groups on the amino acids are important for a protein’s structure and/or function. Amino acids may be covalently modified or metabolized to other molecules with different cellular functions. Changing an amino acid’s side chain can drastically alter the properties or have more subtle effects. 30