Post on 10-Jan-2020
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 □ Oligopeptide = ____ to ____-amino acid polymer
□ Tripeptide = ____-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.
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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
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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
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CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS
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CONCEPT: THE 20 AMINO ACIDS: BLANK WORKSHEET
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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
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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.
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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?
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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?
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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)
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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
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