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Transcript of CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINSlightcat-files.s3. CH. 26 - AMINO ACIDS, PEPTIDES, AND...

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    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

  • 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.

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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  • ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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  • CONCEPT: THE 20 AMINO ACIDS: BLANK WORKSHEET

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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.

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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?

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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?

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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)

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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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

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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  • CONCEPT: ISOELECTRIC POINT PRACTICE 1: Calculate the isoelectric point of tyrosine (Y)

    PRACTICE 2: Calculate the isoelectric point of glutamic acid (E)

    ORGANIC - CLUTCH

    CH. 26 - AMINO ACIDS, PEPTIDES, AND PROTEINS

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