Bioc 192 Lecture 4: Building Blocks of Proteins PDF

BIOC 192 Lecture 4 Building Blocks of Proteins Amino Acids, Peptides and the Peptide Bond Professor Kurt Krause Department of Biochemistry Twitter: @otagobiochemist Facebook: Biochemistry.Ot...

BIOC 192 Lecture 4 Building Blocks of Proteins Amino Acids, Peptides and the Peptide Bond Professor Kurt Krause Department of Biochemistry Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 1  The content and delivery of all resources in this course are subject to copyright and may be used only for the University’s educational purposes. Lecture slides, booklets and learning resources contain material used under copyright licenses for the purposes of teaching. You may access this material for your private study or research but may not make further copies or distribute these materials for any purpose, or in any other form, whether with or without charge. Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 2  References for Lecture 4 – Building Blocks of Proteins: Amino Acids, Peptides, and Peptide Bond are: Lecture Booklet: Part 1 – Proteins, pages 9-14 Textbook References: Chapter 4, “The structure of proteins”, pages 51-55, in your textbook OR Chapter 3, “Amino Acids and Peptides” pages 60-72, in Campbell et al. Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 3  Learning Objectives Describe the properties of amino acids and how they relate to protein structure and function Recognize the types of side chains of amino acids and understand their chemical properties Know how amino acids join to form peptides and proteins Explain the importance of the peptide bond and describe its structure and key properties Slide 4 Amino Acids and Their Properties Branden & Tooze, 1999 Slide 5 Amino Acids are Chiral Slide 6 Amino Acids in Solution as Zwitterions Slide 7  More Amino Acids Facts The twenty amino acids have a common backbone, but different side chains. Each amino acid has a full name, an abbreviated 3-letter name, and a 1-letter name. The twenty amino acids have varied chemical properties, mostly due to their side chains. In proteins, the side chains of amino acids carry out the biochemical reactions for which proteins are known. Slide 8 The 20 Standard Amino Acids in Biochemistry Amino Acid Structures - at pH 7 Amino acids chains can be classified by the chemical properties of their side chains This is only one (Uncharged) set of amino acid groupings – different Polar side Chains (Charged) groupings exist Slide 9 Glycine, G, R=H, non- Proline, R-group bonds back to chiral, flexible, almost main chain N, imino acid, rigid, in a group by itself almost in a group by itself Slide 10 Negatively charged (acidic) Positively charged (basic) Polar side chains Polar side chains Slide 11 Polar side chains, (uncharged) Slide 12  Amino Acid Names and Abbreviations One letter and three letter abbreviations exist for the names of amino acids Biochemists, clinicians often learn both Three letter abbreviations are easy to remember One letter abbreviations are very useful - sequence alignment - mutations Slide 13  One Letter Abbreviations Compact way to depict sequence Great for describing mutations in proteins Old way “there is a mutation of a glutamate to a valine at position 6 in the protein sequence” New way “E6V” - First letter – original or native amino acid - Number – location of amino acid in the protein sequence - Second letter – changed or “mutated” residue Both clinicians and biological scientists use this nomenclature Slide 14 Biomedical Use of One Letter Amino Acid Names SARS-CoV2 VOC Spike protein mutations The Wall Street Journal, 15 Jan 2022 Slide 15  Some Amino Acids have Ionisable Groups The amino and carboxyl ends of amino acids in solution are usually charged Some amino acid side chains are ionisable They contribute to the net charge of the amino acid The ionisable side chains can be classified by their pKa value Slide 16  pKa and pI Definition The pKa value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised The pI, or isoelectric point is the pH at which the net charge on an amino acid (or protein) is zero Slide 17 Some Amino Acids have Ionisable Side Chains Ca Ca Ca Ca Parrill, Mich St. U, 1997 Ca Ca Ca Ca Ca Ca Ca = alpha carbon Slide 18 Some Amino Acids have Ionisable Side Chains Ca Ca Ca Ca Ca = alpha carbon Parrill, Mich St. U, 1997 Slide 19 pKa values for Amino Acids Slide 20  Modified Amino Acids Almost all amino acids start out as one of the standard 20 They are “translated” from RNA into proteins at the ribosome Some amino acids are modified after they are added to a protein This is called “post-translational modification” Some examples are shown on the next few slides Slide 21  Cysteine can sometimes form a covalent bond with another nearby cysteine This bond is called a disulfide bond Branden & Tooze, 1999 Slide 22 Other Amino Acid Modifications 1. Phosphorylation 2. Hydroxylation 3. Carboxylation 4. Metal Binding 5. Iodination 6. Glycosylation 7. Many others Slide 23  Amino Acid Modifications – can be very important Phosphorylation – often used to control enzyme activity – like a chemical ON/OFF switch Hydroxylation – needed to prevent connective tissues diseases and scurvy, often proline & lysine involved Carboxylation – needed for blood clotting, often glutamate involved Slide 24 Phosphorylation Slide 25  Glycosylation of Threonine Asparagine often glycosylated as well as threonine Craik, DJ, U. Queensland, 2008 Slide 26 Peptide Bond, Peptides and Proteins Amino acids can be joined together with a covalent bond, called a peptide bond. Chains of amino acids can be formed. Dr. Robert Droual droualb.faculty.mjc.edu Slide 27  The Peptide Bond In the 1930s -1940s Linus Pauling and Robert Corey determined the structure of the peptide bond by X- ray crystallography. 40% double bond character, leads to planarity. Planar conformation maximizes π- bonding overlap Rotational barrier of ~80 kJ/mol Note the dipole The peptide bond is predominately trans Planar, trans, dipole Branden & Tooze,Slide 199928  Peptides and Proteins A short stretch of amino acids joined together by peptide bonds is a peptide. A longer chain of amino acids joined together, usually with a defined biological function, is a protein. When amino acids are covalently joined together in a peptide or protein, they are referred to as amino acid residues as they are no longer complete, individual, amino acids. Their location by residue number is often referred to. For example, Methionine 184, or Met 184 or M184, all refer to a methionine residue at position 184 in a protein or peptide. Slide 29 When they are linked together in a protein, amino acid side chains perform the chemistry needed to carry out the protein’s biochemical reactions. The side chains are attached to the protein main chain. Think “backbone” or “scaffolding” when thinking of the main chain. Slide 30 Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 31 Objective-based self assessment – Lecture 4 1. Draw the backbone structure of an amino acid. 2. The names of the amino acids can be abbreviated in both _____ letter and _____ letter codes. 3. What do we mean by “amino acids are chiral”? 4. What are the 4 main groups of amino acids, as discussed in the lecture? 5. What are the properties of non-polar amino acids? 6. Where in a protein would you expect to find non-polar amino acid residues? 7. What chemical groups would we expect to find in the R-group of an ionizable amino acid? 8. Where in a protein would we often find ionizable amino acid residues? 9. What is the name of the bond that links amino acids in the polypeptide chain? 10. What are the key properties of this bond (in the question above)? 11. Define pKa and pI, what can these values tell us about an amino acid side chain? 12. List some common examples of post-translational modifications. 13. What are some important functions of posttranslational modifications? Slide 32 14. Label the following amino acids according to their characteristics (e.g., polar, non-polar, charged). You do not need to identify the name of each amino acid when shown a structure alone. Slide 33