ORGANIC - BROWN 8E CH AMINO ACIDS AND PROTEINS.

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2 CONCEPT: INTRODUCTION TO PROTEINS Proteins are polypeptides that have some biological function. Peptides are composed of polymers of monomeric units called α-amino acids The 20 most common α-amino acids found in proteins differ only in the identity of the the group sidechain Amino acids form peptide polymers via bonds. This polymer is also called primary structure Dipeptide = -amino acid polymer Tripeptide = -amino acid polymer Oligopeptide = to -amino acid polymer Polypeptide = to -amino acid polymer - Each dehydrated amino acid is called a Standard Amino Acids: Over 700 amino acids occur naturally, however the 20 most common amino acids all share the following traits: a. They are α-amino acids b. They have an L-(S)-configuration at the chiral carbon EXAMPLE: Circle the amino acids you believe to be standard. Place a box around non-standard (rare) amino acids. Page 2

3 CONCEPT: AMINO ACID CONFIGURATION All of the chiral amino acids derived from proteins have an L-(S)-configuration at the α-carbon The L-configuration is commonly represented in the following ways: EXAMPLE: Convert the amino acid Histadine (H) into a Fischer Projection. Indicate if the chiral center is R or S. PRACTICE: Provide the Fischer Projection representation of D-Aspartic Acid. Indicate if the chiral center is R or S. PRACTICE: Convert the following Fischer Projection of L-Proline into a bondline structure Page 3

4 CONCEPT: AMINO ACID CLASSIFICATION You will likely need to memorize the 20 standard amino acids that are derived from proteins. You may be responsible to know: Names, structures, 3-letter abbreviations, 1-letter symbols, structural categories, functional categories, pkas We will be using the Clutch Prep Amino Acid Breakdown (next page) to organize all this information Categorization of Amino Acids: There is no universally agreed upon method of categorization. The two most common methods are and 1. Structural Categorization: Based on molecular/structural similarities/differences between amino acids. Common categories include aliphatic, aromatic, sulfur-containing, etc. - Problematic because some amino acids fit into 1 category EXAMPLE: Propose structural categories for the following amino acids. 2. Functional Categorization Based on the functional similarities/differences between amino acids reacting in an aqueous environment Common categories include nonpolar, polar, neutral, acidic, basic, hydrophobic, hydrophilic, etc - Problematic because different sources categorize differently Page 4

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6 CONCEPT: THE 20 AMINO ACIDS: BLANK WORKSHEET Page 6

7 CONCEPT: THE 20 AMINO ACIDS: NON-POLAR SIDECHAINS PRACTICE 1: Non-Polar Sidechains - Fill in the missing sidechains on the following target tripeptide. PRACTICE 2: Non-Polar Sidechains - Fill in the missing sidechains on the following target tripeptide. PRACTICE 3: Non-Polar Sidechains - Provide the complete structure of the tripeptide P-F-W Page 7

8 CONCEPT: THE 20 AMINO ACIDS: POLAR SIDECHAINS PRACTICE 1: Polar Sidechains - Provide the Fischer Projection of Glutamine (Q) PRACTICE 2: Polar Sidechains - Provide the complete structure of the dipeptide Asn-Cys PRACTICE 3: Polar Sidechains - Fill in the missing sidechains on the following target oligopeptide. Page 8

9 CONCEPT: THE 20 AMINO ACIDS: ACIDIC/BASIC SIDECHAINS PRACTICE 1: Acidic/Basic Sidechains - Provide the Fischer Projection of Amino Acid (H) PRACTICE 2: Acidic/Basic Sidechains - Fill in the missing sidechains on the following target oligopeptide. PRACTICE 3: Acidic/Basic Sidechains - Provide the complete structure of the oligopeptide V-I-D-Y. Based on your knowledge of hydrophobicity, which side of the peptide is more likely bury itself within the protein? Page 9

10 CONCEPT: ACID-BASE PROPERTIES OF AMINO ACIDS Up to this point we have represented amino acids as neutral structures. However, at physiological ph (7.4), amino acids exist as zwitterions (net neutral molecule with of charges) In Determining Acid-Base Equilibrium, we learned that the side of the reaction with the pka is favored - From now on, we ll be representing amino acids/peptides in their zwitterionic form: Determining the Predominant Forms of Amino Acids: Amino acids are amphoteric, meaning that they can react either as an or as a. We will be using pka values to determine the ionized forms at any ph (see Amino Acid Breakdown for values) Remember, according to H/H equation, when ph = pka, exactly half of the functional group is ionized When ph < pka, protonated form predominates. When ph > pka, deprotonated form predominates EXAMPLE: Ionized forms of phenylalanine (F) at various ph Additionally, 7 of 20 amino acids have ionizable sidechains. You may need to memorize these 7 pkas. When predicting the ionization of these, we must take into account the pka of the sidechain as well EXAMPLE: Predict the predominant form of lysine (K) at ph 8.5. What is the net charge? Page 10

11 PRACTICE 1: Predict the predominant form and net charge of tyrosine (Y) at ph 10. What is the net charge? PRACTICE 2: Determine the net charge of the dipeptide R-C at ph 4.3. (Hint: Peptide bonds do not count) Page 11

12 CONCEPT: ISOELECTRIC POINT The isoelectric point (pi) is the ph at which an amino acid has net charge (max zwitterion concentration). For a generic amino acid, the pi is calculated by taking the of the two functional groups EXAMPLE: Propose an approximate isoelectric point for the following generic amino acid based on approximate pka values Isoelectric Point of Non Acidic/Basic Amino Acids: Calculate as a generic amino acid. Look up exact pka values and average. Isoelectric Point of Acidic/Basic Amino Acids: Now there are three ionizable groups. Average the pkas that correspond with the two similar groups. Isoelectric Point of Cysteine: An exception: Non-acidic/basic, however you average S/-O Page 12

13 CONCEPT: ISOELECTRIC POINT PRACTICE 1: Calculate the isoelectric point of tyrosine (Y) PRACTICE 2: Calculate the isoelectric point of glutamic acid (E) Page 13