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    Lecture # 2: Amino Acids: M123 Biochemistry, 2 SEMESTER, 2018

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    A-Naeem To'mah Al-sawaie
    The document provides an overview of amino acid structure and chemistry. It discusses the essential components of amino acids including the alpha carbon, amine, and carboxyl groups. It categorizes the different R groups found in amino acids and describes how these groups determine the amino acid properties. The document also covers ionization states, post-translational modifications, catabolism of amino acids, and peptide bond formation.

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    Lecture # 2: Amino Acids: M123 Biochemistry, 2 SEMESTER, 2018

    Uploaded by

    A-Naeem To'mah Al-sawaie
    13 views47 pages
    The document provides an overview of amino acid structure and chemistry. It discusses the essential components of amino acids including the alpha carbon, amine, and carboxyl groups. It categorizes the different R groups found in amino acids and describes how these groups determine the amino acid properties. The document also covers ionization states, post-translational modifications, catabolism of amino acids, and peptide bond formation.

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    biochemistry

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    Biochem lec3 AminoAcids

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    The document provides an overview of amino acid structure and chemistry. It discusses the essential components of amino acids including the alpha carbon, amine, and carboxyl groups. It categorizes the different R groups found in amino acids and describes how these groups determine the amino acid properties. The document also covers ionization states, post-translational modifications, catabolism of amino acids, and peptide bond formation.

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    13 views47 pages

    Lecture # 2: Amino Acids: M123 Biochemistry, 2 SEMESTER, 2018

    Uploaded by

    A-Naeem To'mah Al-sawaie
    The document provides an overview of amino acid structure and chemistry. It discusses the essential components of amino acids including the alpha carbon, amine, and carboxyl groups. It categorizes the different R groups found in amino acids and describes how these groups determine the amino acid properties. The document also covers ionization states, post-translational modifications, catabolism of amino acids, and peptide bond formation.

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    of 47

    Lecture # 2: Amino Acids

    M123 BIOCHEMISTRY,2ND SEMESTER, 2018


    outlines

    Amino Acids
    Essential / Non-essential -
    Structure
    Alpha amine
    Alpha carbon
    Alpha carboxyl
    R-group
    Stereochemistry
    D vs. L -
    R-Group Categories
    Amine – Lysine, Arginine, Histidine
    Aromatic – Tryptophan, Phenylalanine, Tyrosine
    Carboxyl – Aspartic Acid, Glutamic Acid
    Hydroxyl – Serine, Threonine, Tyrosine
    Aliphatic (non-polar) – Alanine, Glycine, Isoleucine, Leucine, Methionine, Proline, Valine
    outlines

    Other – Asparagine, Cysteine, Glutamine,


    Selenocysteine,
    Pyrrolysine
    Non-protein amino acids – Carnitine, Citrulline, Ornithine
    Ionization
    Titration & pI pH and Protein Activity -
    Post-translational Modification
    Hydroxylation / Carboxylation / Glycosylation -
    Phosphorylation -
    Catabolism
    Relation to Citric Acid Cycle -
    Glucogenic
    Ketogenic
    Peptide Bond Formation -
    Part 1 - Amino Acids
    Structure and Chemistry

    • Building Blocks of Proteins

    • Essential Amino Acids

    • Basic Structure

    • Stereochemistry

    • Side Chain Chemistry

    • Properties

    • Ionization

    • Bonding
    Amino Acids & Proteins
    • Workhorses of cell
    – Catalysis
    – Signaling
    – Structure
    – Energy/Gradient Generation
    • Proteins comprised of 20-21 amino acids
    Amino Acids
    Essential Amino Acids
    Alpha Carbon
    Basics of Structure
    Elements Alpha Carboxyl

    Alpha Amino Acids

    Differences in R Groups
    Alpha Amine
    Alpha Carbon
    Basics of Structure
    Elements Alpha Carboxyl

    Alpha Amino Acids

    Differences in R Groups
    Alpha Amine
    Examples
    Asymmetric Center

    Alpha Carbon Alpha Carboxyl

    Alpha Amine
    Alpha Carbon
    Basics of Structure
    Elements Alpha Carboxyl

    Alpha Amino Acids

    Differences in R Groups
    Alpha Amine
    Examples
    Asymmetric Center

    Alpha Carbon Alpha Carboxyl

    R
    18
    Alpha Amine
    on
    rb
    Amino Acids Ca
    Stereochemistry ri c
    et
    m
    D and L Isomers ym
    As

    Almost all biological amino acids


    are in the L-configuration
    Categorizing Amino Acids

    Non-Polar Carboxyl Amine Aromatic Hydroxyl Other

    Alanine Aspartic Acid Arginine Phenylalanine Serine Asparagine

    Glycine Glutamic Acid Histidine Tryptophan Threonine Cysteine

    Isoleucine Lysine Tyrosine Tyrosine Glutamine

    Leucine Selenocysteine

    Methionine Pyrrolysine

    Proline

    Valine
    Ionizable R-groups
    Name Charged R-group Approximate R-group pKa

    Aspartic Acid -COO- 4.1


    Glutamic Acid -COO- 4.1

    Lysine -NH3+ 10.5


    Arginine =NH2+ 12.5
    Histidine =-NH+ 6.0
    Cysteine -S- 8.2

    Tyrosine -O- 10.5


    Amino Acids
    Aromatic R-Groups

    Alpha Carbon
    Tryptophan

    Alpha Amine
    Alpha Carboxyl
    Tyrosine Phenylalanine
    Amino Acids R
    Aromatic R-Groups

    Tryptophan
    R R

    Tyrosine Phenylalanine
    Amino Acids R
    Aromatic R-Groups
    Charges at Physiological pH

    Tryptophan
    R R

    Ionizes at high pH Tyrosine Phenylalanine


    Amino Acids
    Aliphatic R-Groups

    Alanine Glycine Proline Isoleucine

    Leucine Valine Methionine


    Amino Acids
    Aliphatic R-Groups

    Alanine Glycine Proline Isoleucine

    Leucine Valine Methionine


    Amino Acids
    Aliphatic R-Groups
    Charges at Physiological pH
    Amino Acids
    R-Group Carboxyls

    Aspartic Acid Glutamic Acid


    Amino Acids
    R-Group Carboxyls

    R
    R

    Aspartic Acid Glutamic Acid


    Amino Acids
    R-Group Carboxyls
    Charges at physiological pH

    R
    R

    Aspartic Acid Glutamic Acid


    Amino Acids
    Hydroxyl R-Groups

    Serine

    Threonine

    Tyrosine
    Amino Acids
    Hydroxyl R-Groups

    Serine

    Threonine

    Tyrosine
    Amino Acids
    Hydroxyl R-Groups
    Charges at Physiological pH

    Serine

    Threonine

    Ionizes at high pH

    Tyrosine
    Amino Acids
    Sulfhydryl R-Group

    Cysteine
    Amino Acids
    Sulfhydryl R-Group

    Ionizes at about pH = 8

    +
    Cysteine
    Amino Acids
    Carboxamide R-Groups

    Asparagine Glutamine
    Amino Acids
    Carboxamide R-Groups

    Asparagine Glutamine
    Amino Acids
    Carboxamide R-Groups

    Asparagine Glutamine
    Amino Acids
    Ionizable Amine R-Groups

    Arginine

    Lysine

    Histidine
    Amino Acids
    Ionizable Amine R-Groups

    Arginine

    Lysine

    Histidine
    Amino Acids
    Ionizable Amine R-Groups
    Charges at Physiological pH

    Arginine

    Lysine

    Histidine
    Rare Amino Acids
    Non-Protein Amino Acids

    Carnitine

    Also - Citrulline, Ornithine, others


    Amino Acids
    Ionization
    Amino Acids
    Ionization -by pKa Values
    Amino Acids
    Ionization -by pKa Values
    Amino Acids
    Ionization -by pKa Values
    Amino Acids
    Ion Locations in Titration

    Charge = -1
    Amino Acids
    Ionization -by pKa Values

    Charge = 0
    Amino Acids
    Ionization -by pKa Values

    Charge = -1
    Amino Acids
    Ionization -by pKa Values

    Charge = -2
    Ionization Changes Charges Within Proteins

    Changes in Charge Change Activities


    Post-translational Modifications
    Phosphorylated Amino Acids
    Breakdown of Amino Acids
    Peptide Bond Formation

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