Chapter 3 Amino Acids, Peptides and Proteins - Lecture Slides PDF

Chapter 3: Amino Acids, Peptides and Proteins Objectives Detail the structures and properties of the various amino acids. Construct titration curves for the amino acids. Determine the net charge of any amino acid at any pH. Calculate isoelectric points for the amino acids. Text Readings...

Chapter 3: Amino Acids, Peptides and Proteins Objectives Detail the structures and properties of the various amino acids. Construct titration curves for the amino acids. Determine the net charge of any amino acid at any pH. Calculate isoelectric points for the amino acids. Text Readings: Stryer 2nd or 3rd Editions: All of Chapter 3  Amino Acids -General- Amino acids are building blocks of proteins. Proteins are linear polymers of amino acids. All proteins are produced from 20 standard amino acids. All living organism use the same pool of amino acids to build their proteins. Twenty building blocks enables great diversity of sequences. For example: a peptide of three residues could be produced 8000 ways. a protein of 100 residues has 1.3 X 10130 possible sequences.  Amino Acids -Proteins are Polymers of Amino Acids- Proteins are linear polymers of amino acid building blocks. There are distinct advantages of creating biomolecules as polymers of smaller, simpler building blocks. 1) Simplicity of chemistry: one type of reaction for polymerization, a second type of reaction for degradation. 2) Recycling: biomolecules can be digested back to component building blocks which are reusable for production of other biomolecules. 3) Diversity: The vast number of molecules of varying lengths and sequences.  Amino Acids -General Structure- Common feature of amino acids: Side Chain Hydrogen group Central Alpha Carbon Amino Carboxyl group group The 20 amino acids differ in their side chain (R) groups. The side chains define the unique characteristics of each amino acid.  Amino Acids -Chirality- For all amino acids except glycine, the alpha carbon is bonded to four different groups, this creates a chiral center. The four different groups occupy unique spatial arrangements giving different stereoisomers labelled as the L and D isomers. Biologically proteins are made almost exclusively from L amino acids.  Amino Acids -Thoughts of Groupings- The text groups the amino acids based on the properties of their side chains. These groups include: Non-polar aliphatic Aromatic Polar, Uncharged Polar, Positively Charged Polar, Negatively Charged While this is an effective way to sub-divide the amino acids, it is important to remember that these groupings are man-made and that there are many other equally valid ways to group amino acids. It is more important to be able to compare and contrast all the amino acids rather than assign them to specific groups.  Nonpolar, Aliphatic Amino Acids polar non-polar ? or -Non-polar- charge groups (S C) > -. H-bonds > - Mainly hydrocarbon side chains. Residues with non-polar chains are often buried in the core of a protein. Proline often found at polypeptide turns, usually in combination with glycine. Glycine is the smallest amino acid and is the only one which is not chiral. Methionine is one of two amino acids with a sulfur group within its side chain. smallest KNOW : no chiral carbon > - full name > - 3 letter code > - I letter code structuredisgram > - only acid wI this structure  Amino Acids -Aromatics- rin grains Histidine can also be considered as an aromatic. Tyrosine can be post-translation modified through phosphorylation. Phosphorylation is a mechanism to regulate protein function. Other amino acids with hydroxyl groups (Serine and Threonine) also can be phosphorylated. Tryptophan, a precursor of serotonin, became a popular supplement in the 1980s A disease-outbreak among users lead to its ban by the FDA mor largest  Amino Acids -Post-translational Modification- Certain amino acids can be covalently modified after their incorporation process of making into a protein (post-translation). - aprotein. Phosphorylation is a central example of post-translational modification. Phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids (Tyr, Ser and Thr). These modifictaions are often reversible, for example, the phosphoryl group can be removed by phosphatases. structure = function phosphorylation KINASE is reversible. protein -OH protein -PO4-2 PHOSPHATASE  Amino Acids -Polar, Uncharged- Serine and Threonine can undergo phosphorylation of their hydroxyl groups. Two cysteines can form a covalent linkage called a disulfide bond. Disulfide bonds are important covalent linkages for stabilization of some protein structures. cardian - Do-  Amino Acids morebility -Disulfide Bonds- covalent Disulfide bonds form through the oxidation of the sulfhydryl groups of two cysteine residues to form a covalent linkage. Disulfides stabilize protein structures. Cysteine residues forming a disulfide bond must be in close proximity in space within the protein structure. Disulfide bonds can be inter or intra- methione cannot molecular. form sulfide-bonds. Disulfide bonds within insulin.  Amino Acids -Positively Charged- Lys and Arg always carry a +1 net charge at physiological pH. Histidine’s imidazole group has a pKa near physiological pH such that a fraction of cellular histidines will be +1 and the rest will carry a net charge of 0. In many enzymatic reactions His serves as a proton acceptor/donor. imidazole group  Amino Acids -Negatively Charged- Aspartate and Glutamate (as called aspartic acid and glutamic acid) carry a net charge of -1 at physiological pH. Glutamate is responsible for one of the five basic tastes (umami). used as a flavor enhancer (monosodium glutamate (MSG). carbo charge To  Amino Acids -Acid/Base Properties- Every amino acid has at least two groups that accept and donate protons (diprotic). All amino acids have the alpha carbon carboxyl group and amino groups. Triprotic amino acids have ionizable groups in their side chains (Lys, Arg, His, Asp, Glu, Cys and Tyr). Diprotics have two buffering regions, triprotics have three buffering regions.  Amino Acids -Acid/Base Properties- Ionizable groups in the amino acids: (1) carboxyl group (2) amino group (3) side chains of the triprotic amino acids Each ionizable group has a specific pKa. This is the pH at which that group changes its protonation state. HA A- + H+ When pH is below the pKa, the protonated form predominates (HA). When pH is above the pKa, the unprotonated form predominates (A-).  Amino Acids -Titration Curves of Carboxyl and Amino Groups- All amino acids have both carboxyl (pKa ~2.0) and an amino (pKa ~10.0) groups. At pH 7.4 these groups will be in the COO- and NH3+ forms. COOH COO- + H+ NH3+ NH2 + H+ 2 NH NH3+ = NH2 10.0 un D - pH pKa unprotonated Physiological pH 7.4 O- pH 7.4 Physiological CO pH 3+ NH protonated COOH = COO- 2.0 pKa HO protonated CO OH- Equivalents OH- Equivalents  Amino Acids -Acid/Base Properties- The dipolar ion of an amino acid is called a zwitterion. isoelectric point pl = the pka's > - average  Amino Acids -Titration of Glycine- (piprotid +1 0 -1 pKa 9.60 pKa 2.34 The isoelectric point (pI) of an amino acid -1 is the pH at which the net charge on the -1/2 molecule is equal to zero. pI is the average of the pKas on either side of where the net charge is equal to zero. 0 pI = (pKa1 + pKa2) / 2 +1/2 pI = (2.34 + 9.60) / 2 +1 pI = 5.97 Notably, all diprotics would have similar titration curves and pIs.  Amino Acids -Titration of Glutamate- pKa 2.19 +1 0 -1 -2 pKa 9.67 pKa 4.25 -2 -11/2 pI = (pKa1 + pKaR) / 2 pI = (2.19 + 4.25) / 2 -1 pI = 3.3 0 -1/2 Notably, the titration curves +1/2 +1 and pIs of aspartate and glutamate would be quite similar.  Amino Acids -Titration of Histidine- +2 +1 0 -1 pKa 1.82 pKa 9.17 pKa 6.0 -1 -1/2 0 pI = (pKaR + pKa2) / 2 pI = (6.0 + 9.17) / 2 +1/2 pI = 7.6 +1 +2 +11/2  Copyright Sourcing Images/Figures/Tables from Textbook – Permission: Courtesy of MacMillan Learning. Slide 2: Permission: Courtesy of course author Scott Napper, Saskatoon, SK: Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan. Slide 15: Source: Lehninger Principles of Biochemistry (2004) 4th Edition, page 58. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 18: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 79. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 19: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 81. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Slide 20: Source: Lehninger Principles of Biochemistry (2008) 5th Edition, page 81. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act.