Amino Acids and Their Functions
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Questions and Answers

Which amino acid is a precursor for both heme and creatine?

  • Tyrosine
  • Tryptophan
  • Histidine
  • Glycine (correct)

    • What role do tyrosine derivatives primarily play in the body?

  • They act as neurotransmitters.
  • They produce hormones and skin pigment. (correct)
  • They serve as precursors for blood clotting factors.
  • They contribute to muscle endurance.

    • Which uncommon amino acid is involved in blood clotting proteins?

  • N-methylarginine
  • γ-Carboxyglutamic acid (correct)
  • Selenocysteine
  • Desmosine

    • Which neurotransmitter is synthesized from the decarboxylation of glutamic acid?

    <p>GABA</p> Signup and view all the answers

    What function does selenocysteine primarily serve in the body?

    <p>Antioxidant activity.</p> Signup and view all the answers

    Which amino acid is specifically mentioned as being converted to histamine?

    <p>Histidine</p> Signup and view all the answers

    Which of the following amino acids is NOT typically found in proteins?

    <p>Ornithine</p> Signup and view all the answers

    What is the primary role of methylated amino acids like methylhistidine and N-methyllysine?

    <p>Functionality in muscle proteins</p> Signup and view all the answers

    Which type of protein is primarily responsible for regulating other proteins?

    <p>Regulatory Proteins</p> Signup and view all the answers

    Which of the following examples is not classified as a structural protein?

    <p>Ferritin</p> Signup and view all the answers

    Which amino acid is classified as hydrophilic and possesses a cyclic structure?

    <p>Proline</p> Signup and view all the answers

    What type of protein is responsible for the contraction of muscle tissues?

    <p>Contractile and Motile Proteins</p> Signup and view all the answers

    What is the pKa value of histidine, indicating its behavior in enzymatic reactions?

    <p>6.0</p> Signup and view all the answers

    What is the primary role of transport proteins?

    <p>Aid in the movement of substances across membranes</p> Signup and view all the answers

    Which of the following is a characteristic of cysteine?

    <p>It forms disulfide bonds.</p> Signup and view all the answers

    Which amino acid is not considered essential or indispensable for humans?

    <p>Alanine</p> Signup and view all the answers

    Which of the following is a shared characteristic of proteins with quaternary structure?

    <p>Multiple polypeptides interacting through various bond types</p> Signup and view all the answers

    Which amino acid contains two chiral carbons?

    <p>Threonine</p> Signup and view all the answers

    Which example correctly illustrates a transport protein?

    <p>Hemoglobin</p> Signup and view all the answers

    Which of the following proteins primarily serves in the storage of minerals?

    <p>Ferritin</p> Signup and view all the answers

    Which group of amino acids is classified as having acidic side chains?

    <p>Aspartate and Glutamate</p> Signup and view all the answers

    What type of bonds can tyrosine form due to its functional groups?

    <p>Hydrogen bonds</p> Signup and view all the answers

    Which of the following is not considered a functional class of proteins?

    <p>Biochemical Proteins</p> Signup and view all the answers

    Which statement about essential amino acids is true?

    <p>They include lysine and leucine.</p> Signup and view all the answers

    Which type of protein plays an active role in cell defense and protection?

    <p>Protective proteins</p> Signup and view all the answers

    What distinguishes complete proteins from incomplete proteins?

    <p>Complete proteins contain all necessary essential amino acids.</p> Signup and view all the answers

    Which of the following is an example of a conjugated protein?

    <p>Hemoglobin</p> Signup and view all the answers

    What is the primary function of lipoproteins?

    <p>Transporting lipids</p> Signup and view all the answers

    Which classification of proteins contains only amino acids?

    <p>Simple proteins</p> Signup and view all the answers

    What do metalloproteins primarily function as?

    <p>Storage proteins for metals or enzymes</p> Signup and view all the answers

    Phosphoproteins are characterized by the presence of what?

    <p>Esterified phosphates</p> Signup and view all the answers

    Which of these proteins is NOT classified as a conjugated protein?

    <p>Collagen</p> Signup and view all the answers

    Which amino acid is most frequently found in the Gly-x-y motif of collagen?

    <p>Proline</p> Signup and view all the answers

    What is the primary significance of the 40-nm gaps between adjacent collagen molecules?

    <p>They serve as attachment points for sugars to 5-hydroxylysine.</p> Signup and view all the answers

    Which type of collagen is primarily found in cartilage?

    <p>Type II</p> Signup and view all the answers

    What essential vitamin is required for the hydroxylation process of collagen synthesis?

    <p>Vitamin C</p> Signup and view all the answers

    Which of the following statements about collagen triple helices is accurate?

    <p>They measure approximately 300 nm in length.</p> Signup and view all the answers

    Which structural feature distinguishes fibrous proteins from globular proteins?

    <p>Fibrous proteins are usually insoluble in water, unlike globular proteins.</p> Signup and view all the answers

    What is the primary function of collagen in the body?

    <p>Providing structural support to connective tissues.</p> Signup and view all the answers

    How does the structure of alpha-keratin contribute to its function in hair and nails?

    <p>It is organized in a superhelix, increasing tensile strength.</p> Signup and view all the answers

    Which statement accurately describes membrane proteins?

    <p>They have hydrophobic side chains oriented outward for membrane interaction.</p> Signup and view all the answers

    What characteristic of collagen gives it high tensile strength?

    <p>The arrangement of molecules in a triple helix.</p> Signup and view all the answers

    Which of the following proteins is a major component of skin and connective tissues?

    <p>Collagen</p> Signup and view all the answers

    Which of the following best describes fibrous proteins?

    <p>They have a regular linear structure and serve as structural elements.</p> Signup and view all the answers

    What type of bonding stabilizes the alpha-helix structure in alpha-keratin?

    <p>Hydrogen bonds between amide and carbonyl groups.</p> Signup and view all the answers

    Study Notes

    Chemistry of Amino Acids and Proteins - I

    • The topic will cover general structure of amino acids, classification of amino acids, function of amino acids, acid-base properties of amino acids, peptide bond structure and functional peptides, protein structure, biological functions of proteins, and protein classification.

    Objectives

    • Students will be able to describe the general structure of amino acids.
    • Students will be able to list the biochemical functions of amino acids.
    • Students will be able to categorize amino acids by different classification bases.
    • Students will be able to explain the acid-base properties of amino acids.
    • Students will be able to explain the peptide bond and its characteristics.
    • Students will be able to mention functional peptides.
    • Students will be able to detail protein structure.
    • Students will be able to explain the biological functions of proteins.
    • Students will be able to classify proteins.

    What are Proteins?

    • Unbranched polymers of amino acids, linked head-to-tail.
    • Major constituents of most cells.
    • Form multi-molecular complexes.
    • Folded into specific conformations.
    • Conformation and functional-group chemistry control function.
    • Responsible for most of an organism's phenotype (defining what it looks like, how it behaves, etc.).
    • Made from almost 20 different types of standard amino acids.
    • Selenocysteine is incorporated during co-translation in humans.

    Amino Acids

    • Structure:
      • Central carbon.
      • Amino group.
      • Carboxyl group.
      • Side chain (R group) - a variable group. The R group confers unique chemical functionality.
    • Chiral/Optically Active:
    • Acid-base properties.
    • Capacity to polymerize.

    Classification of Amino Acids

    • Based on:
      • Side chain character (e.g., nonpolar, aliphatic, aromatic).
      • Nutritional value (essential, non-essential, conditionally essential).
      • Metabolic fate (ketogenic, glucogenic, mixed).
      • Presence/absence in proteins.

    Amino Acid Classification by Side Chain Character

    • Hydrophobic side chain: stabilize protein structure by hydrophobic interactions.
    • Tyrosine can form hydrogen bonds.

    Classification...

    • Polar, uncharged R groups: Includes Serine, Threonine, Cysteine, Asparagine, and Glutamine.
    • Reversible formation of a disulfide bond by the oxidation of two molecules of Cysteine.

    Classification...

    • Acidic side chain: H+ (proton) donor.
      • Examples: Aspartate, Glutamate.

    Classification...

    • Amino Acids with Basic Side Chains:
    • Basic side chains: serve as H+ acceptors.
      • Examples: Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).
    • Histidine side chain: pKa=6.0, 10% protonated at pH=7. Serving as a proton donor/acceptor in many enzymatic reactions.
    • Identification of carbon atoms in amino acids: a, b, y, d etc

    Names and Codes of Amino Acids

    • Provides a list of amino acids, their single-letter and three-letter codes, and their R-group properties (e.g., hydrophobic, hydrophilic, reactive).

    Amino Acid Classification Based on Nutritional Value

    • Essential amino acids: Nine amino acids not synthesizable in the body in adequate amounts (Val, Ile, Thr, Trp, Leu, Lys, Met, Phe, and His).
    • Dispensable/non-essential amino acids: Can be synthesized in the body from essential ones.
    • Conditionally essential amino acids: Required during illness or stress. (Tyrosine, cysteine, arginine, glutamine, glycine, proline, and serine).

    Classification Based on Metabolic Fate

    • Ketogenic: Catabolically yield intermediates convertible to Acetyl-CoA or Acetoacetyl-CoA. (e.g., Leucine, Lysine, Isoleucine, Phenylalanine , Tyrosine, Tryptophan, etc.)
    • Glucogenic: Yield intermediates of glycolysis or Kreb's cycle. (e.g., Alanine, Arginine, Asparagine, Aspartate, Glutamate, Glutamine, Glycine, Histidine, Methionine, Proline, Serine, Threonine, Valine, etc).
    • Mixed Ketogenic/Glucogenic: Yield both intermediates for glycolysis or Kreb's cycle and those convertible to Acetyl-CoA. (e.g., Phenylalanine, Tyrosine, Tryptophan, etc).

    Some Common Biological Functions of Amino Acids

    • Formation of peptides and proteins.
    • Stabilizing the 3D structure of proteins.
    • Vital for enzyme catalysis at active sites.
    • Source of glucose.
    • Sources of sulfur (S) for Fe-S center formation (Cysteine & Methionine).
    • For nucleic acid synthesis.
    • Roles in detoxification mechanisms (e.g., Glycine & Methionine).
    • Methyl group donors in methylation reactions (e.g., Methionine).

    Amino Acids as Precursors of Biologically Important Derivatives

    • Glycine: Precursor for heme and creatine.
    • Tyrosine: Precursor for hormones (thyroxine, triiodothyronine, epinephrine, norepinephrine), and skin pigment melanin.
    • Tryptophan: Precursor of niacin and serotonin.
    • Histidine: Precursor to histamine.

    Uncommon Amino Acids – Found in proteins

    • Hydroxylysine and hydroxyproline (mainly in collagen).
    • Tyrosine and Triiodothyronine (hormones).
    • N-methylarginine and N-acetyllysine (in histone proteins).
    • Methylhistidine, -N-methyllysine and N,N,N-trimethyllysine (methylated amino acids in myosin).
    • Y-Carboxyglutamic acid(for blood clotting proteins & Ca2+ containing proteins).
    • Desmosine (in fibrous protein elastin).
    • Selenocysteine (derived from serine, introduced during protein synthesis, key role in antioxidant activity e.g. Glutathione peroxidase active site).

    Amino Acids not found in proteins

    • GABA (a potent neurotransmitter).
    • Histamine (smooth muscle contraction).
    • Serotonin (neurotransmitter).
    • ß-Alanine.
    • Epinephrine (adrenaline).
    • Ornithine & Citrulline (in urea cycle).
    • Dopa (precursor of melanin).
    • S-adenosylmethionine (SAM) (methyl donor in transmethylation reactions).

    Acid-Base Properties of Amino Acids

    • At low pH, the amino acid exists as the ammonium form.
    • At neutral pH, the amino acid exists as a zwitterion (dipolar ion).
    • At high pH, the amino acid exists as the carboxylate form.
    • The pI is the average of pKa1 and pKa2, representing the specific pH at which the molecule is electrically neutral.

    pI of Neutral Amino Acids

    • Calculating the pI: the average of pKa1 (ionization of carboxyl group) and pKa2 (ionization of amine group).

    pI of Amino Acids

    • The pI of alanine.

    Amino Acids with Ionizable Side Chains.

    • pI of Lysine (shows the process).

    pI of Amino Acids

    • Show pIs for acidic, neutral and basic amino acids.

    Peptide Bond & Functional Peptides

    • Peptide bonds (amide bonds): Condensation reactions.
    • Forming dipeptides, tripeptides, etc.
    • N-terminal and C-terminal.
    • Predicting acid-base behavior (free -amino and -carboxyl groups).
    • Characteristic pI.
    • pKa value for ionizable group changes in peptides.
    • Examples: Serylglycyltyrosylalanylleucine, or Ser-Gly-Tyr-Ala-Leu.

    Planar Peptide Groups in a Polypeptide Chain

    • Amide nitrogens are non-basic.
    • Rotation around C-N bond is restricted.
    • Peptide groups are planar.

    Biologically Active Peptides

    • Glutathione: Formed from y-glutamic acid, cysteine, and glycine. Protects cell membranes. A good example.
    • Slightly larger peptides/oligopeptides:
      • Insulin (two polypeptide chains).
      • Corticotropin (hormone).

    Commercial Peptide: Example

    • Aspartame (dipeptide).

    Structure and Classification of Proteins

    • A summary of protein structure levels and types.

    Protein Structure

    • The 3-D structure depends on amino acid types, number, and sequence.
    • Folding, twisting, and coiling create a unique shape.
    • The structure determines the protein's function.
    • Native structure depends on: interactions with solvent molecules, pH and ionic composition of the solvent, sequence of amino acids.

    Primary Structure of Proteins

    • Describes the sequence and number of amino acids in a protein chain.
    • Determined by gene sequence.
    • Contains the information necessary to fold into its native structure.
    • Amino acid sequence example for Lysozyme.

    Does Amino Acid Sequence Determine Protein Function?

    • Example: Oxytocin (uterine contractions, milk release).
    • Example: Vasopressin (regulates water balance).
    • Change in amino acid sequence can cause problems: Hemoglobin (sickle-cell anemia).

    Secondary Structure of Proteins

    • Formed by hydrogen bonds.
    • Describes the folding pattern.
    • Common types: alpha helix, beta pleated sheet, turns/bends.
    • The development of regular hydrogen-bond patterns creates distinct folding patterns.

    Secondary Structure: Examples

    • Alpha helix: peptide carbonyl H-bonded to peptide N-H group.
    • Beta pleated sheet: each strip of paper as a single peptide strand.

    Secondary Structure: Examples

    • Three-ten helix.
    • 27 ribbon.

    Secondary Structure: Examples

    • Beta bulge.

    Super Secondary Structures

    • Helix-loop-helix.
    • Coiled coils.
    • Helix bundles.
    • Beta-alpha-beta units.
    • Hairpins.
    • Beta meander.
    • Greek key.
    • Beta-sandwich.
    • Zinc finger.
    • Leucine zipper.

    Tertiary Structure of Proteins

    • Shows the overall 3-D folding pattern of a polypeptide.
    • Determined by interactions between R groups.
    • Bonds involved in tertiary structure:
      • Hydrogen bonds.
      • Hydrophobic interactions.
      • Disulfide bridges.
      • Ionic bonds.
      • Van der Waals forces.

    Examples of Some Domains

    • β-barrel.
    • Bundle.
    • Saddle.

    Quaternary Structure of Proteins

    • Formed by more than one polypeptide chain.
    • Organized by the same types of bonds as tertiary structures.
    • Intracellular enzymes are oligomers (examples).
    • Advantages of quaternary association:
      • Stability.
      • Genetic economy and efficiency (less DNA needed for monomer).
      • Bringing catalytic sites together to regulate catalytic activity.

    Advantages of Quaternary Association

    • Stability
    • Genetic economy and efficiency
    • Bringing catalytic sites together

    Examples of Proteins with Quaternary Structure

    • Listing specific examples of proteins and their subunit numbers.

    Protein Classification Based on Nutritional Value

    • Complete or high-quality proteins
    • Incomplete or low-quality proteins

    Protein Classification Based on Composition

    • Simple proteins
    • Conjugated proteins

    Types of Conjugated Proteins

    • Glycoproteins
    • Lipoproteins
    • Nucleoproteins
    • Phosphoproteins
    • Metalloproteins
    • Hemoproteins
    • Flavoproteins

    Protein Classification Based on Shape (Architecture)

    • Fibrous proteins: long and thin, insoluble
      • Examples: Collagen (triple helix), α-keratin.
    • Globular proteins: roughly spherical, soluble
      • Examples: Insulin, Hemoglobin, Enzymes

    Membrane Proteins

    • Hydrophobic side chains for membrane interaction.
    • Insoluble in aqueous but soluble in detergents.
    • Have fewer hydrophilic amino acids compared to cytosolic proteins.

    Common Fibrous and Globular Proteins: Occurrence & Use

    • Tabular presentation of fibrous and globular proteins, their occurrence, and use.

    Example of Fibrous Proteins: α-Keratin

    • Major components of hair and nails.
    • α-helix strands wound into "superhelix" structure.
    • Stabilized by H-bonds.

    Your Hair

    • Image of a cross-section of hair showing the different components.

    Examples of Fibrous Proteins: Collagen

    • Constituent of connective tissues.
    • Triple helix structure.
    • Rigid, high tensile strength.
    • Important for running, jumping.
    • Types of collagen: I, II, III.

    Examples of Fibrous Proteins: Collagen

    • Tropocollagen (basic structural unit of collagen).
    • Composed of three polypeptide chains, each longer than 1000 amino acids.
    • Sequence repeats (Gly-x-y motif): x and y are often proline or hydroxyproline.
    • Crucial role in intermolecular and intramolecular cross-links.
    • Hydroxylation requires ascorbic acid (vitamin C).

    Examples of Fibrous Proteins: Collagen

    • Collagen triple helices are 300 nm long, with 40-nm gaps between adjacent collagen molecules in a row.
    • Pattern repeats every five rows (5 x 68 nm = 340 nm).
    • The hole regions are for sugar attachment, organizing fibril assembly, and bone formation.

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