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 (B)</p> Signup and view all the answers

    What function does selenocysteine primarily serve in the body?

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

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

    <p>Histidine (C)</p> Signup and view all the answers

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

    <p>Ornithine (B)</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 (B)</p> Signup and view all the answers

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

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

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

    <p>Ferritin (A)</p> Signup and view all the answers

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

    <p>Proline (C)</p> Signup and view all the answers

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

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

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

    <p>6.0 (B)</p> Signup and view all the answers

    What is the primary role of transport proteins?

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

    Which of the following is a characteristic of cysteine?

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

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

    <p>Alanine (A)</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 (D)</p> Signup and view all the answers

    Which amino acid contains two chiral carbons?

    <p>Threonine (A)</p> Signup and view all the answers

    Which example correctly illustrates a transport protein?

    <p>Hemoglobin (C)</p> Signup and view all the answers

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

    <p>Ferritin (C)</p> Signup and view all the answers

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

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

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

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

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

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

    Which statement about essential amino acids is true?

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

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

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

    What distinguishes complete proteins from incomplete proteins?

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

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

    <p>Hemoglobin (A)</p> Signup and view all the answers

    What is the primary function of lipoproteins?

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

    Which classification of proteins contains only amino acids?

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

    What do metalloproteins primarily function as?

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

    Phosphoproteins are characterized by the presence of what?

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

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

    <p>Collagen (B)</p> Signup and view all the answers

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

    <p>Proline (C)</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. (C)</p> Signup and view all the answers

    Which type of collagen is primarily found in cartilage?

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

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

    <p>Vitamin C (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. (B)</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. (A)</p> Signup and view all the answers

    What is the primary function of collagen in the body?

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

    Which statement accurately describes membrane proteins?

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

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

    <p>Collagen (A)</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. (B)</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. (A)</p> Signup and view all the answers

    Flashcards

    Insulin's Function

    Insulin regulates blood glucose levels.

    Protein Structure Levels

    Protein structure progresses from amino acid sequence (primary) to interactions among different parts of the protein (quarternary).

    Protein Function: Enzymes

    Enzymes speed up biochemical reactions in the body.

    Transport Proteins

    Transport proteins move substances throughout the body.

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    Storage Proteins

    Storage proteins store nutrients for later use by the body.

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    Amino Acid Classification: pKa of Histidine

    The histidine side chain has a pKa of 6.0. This means at a pH of 7, 10% of histidine molecules are protonated. This property makes them proton donors and acceptors.

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    Essential Amino Acids

    Essential amino acids are nine amino acids that the human body can't create in sufficient amounts on its own, so they must be acquired from food.

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    Contractile Proteins

    Contractile proteins enable movement and muscle contraction.

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    Tyrosine and its Properties

    Tyrosine is an amino acid that can form hydrogen bonds. It is less hydrophobic than phenylalanine, but still bulky.

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    Structural Proteins

    Structural proteins support cells and tissues by providing strength and protection.

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    Disulfide Bond Formation

    A disulfide bond is formed by oxidizing two cysteine molecules. This is a reversible process.

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    Protein Classification

    Proteins are categorized based on their function in the body.

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    Acidic Side Chains

    Acidic amino acid side chains donate protons (H+).

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    Basic Side Chains

    Basic amino acid side chains accept protons (H+).

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    Amino Acid Classification by Nutritional Value

    Categorization of amino acids based on whether they are synthesized in the human body.

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    Hydrophobic Amino Acids (List)

    Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Cysteine, Methionine are hydrophobic amino acids.

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    Amino acid precursors for heme

    Glycine is a precursor for heme synthesis.

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    Amino acid precursors for hormones

    Tyrosine is a precursor for thyroxine, triiodothyronine, epinephrine, norepinephrine, and melanin.

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    Tryptophan's derivatives

    Tryptophan can be converted to niacin and serotonin.

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    Histidine's conversion

    Histidine can be converted to histamine.

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    Hydroxylysine and hydroxyproline function

    Present mostly in collagen and connective tissues.

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    Selenocysteine role

    A rare amino acid important in antioxidant activity, especially in enzymes like glutathione peroxidase.

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    Amino acids not in proteins

    GABA (from glutamic acid), histamine (from histidine), serotonin (from tryptophan), beta-alanine,epinephrine/adrenaline are important neurotransmitters and other molecules.

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    Ornithine and Citrulline's role

    Crucial in the urea cycle and arginine synthesis.

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    Complete Proteins

    Contain all essential amino acids crucial for body function, promoting muscle growth and repair.

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    Incomplete Proteins

    Lack one or more essential amino acids.

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    Simple Proteins

    Made only of amino acids.

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    Conjugated Proteins

    Proteins made of amino acids plus other components.

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    Glycoproteins

    Conjugated proteins with carbohydrates.

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    Lipoproteins

    Conjugated proteins involved in lipid transport.

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    Nucleoproteins

    Conjugated proteins associated with nucleic acids.

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    Protective Proteins

    Proteins that play roles in the immune system and defending the body.

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    Collagen Types

    There are several types of collagen, each with specific functions. Type I is found in bones, tendons, and skin, Type II is prevalent in cartilage, and Type III is found in blood vessels.

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    Tropocollagen: Structure

    Tropocollagen is the basic structural unit of collagen. It consists of three intertwined polypeptide chains, each over 1000 amino acids long, mainly composed of glycine and proline.

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    Glycine's Role in Collagen

    Glycine is abundant in collagen, occurring every third amino acid. This allows for tight packing of the three polypeptide chains, forming a strong triple helix.

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    Hydroxylation in Collagen

    Hydroxylation, the addition of hydroxyl groups to proline and lysine, is crucial for collagen stability. It requires ascorbic acid (Vitamin C).

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    Collagen Fibril Gaps

    Collagen fibrils have 40-nm gaps between adjacent molecules. These gaps are essential for sugar attachment and play a role in bone formation.

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    Fibrous Proteins

    Long, thin proteins with a simple, regular linear structure. They are insoluble in water and play a structural role in cells, forming large cables and threads.

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    Globular Proteins

    Spherical proteins with a compactly folded structure. They are soluble in water and perform diverse functions in cells.

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    Membrane Proteins

    Proteins embedded in cell membranes, with hydrophobic regions interacting with the membrane's lipid environment.

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    -Keratin

    A fibrous structural protein found in hair and nails. It forms a right-handed helix and is stabilized by hydrogen bonds.

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    Collagen's Structure

    Collagen is a fibrous protein composed of three intertwined helices, giving it high tensile strength.

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    Collagen: Function

    Collagen provides structural support in connective tissues, such as tendons, cartilage, and skin.

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    Collagen: Benefits

    Collagen's tensile strength enables your body to withstand stresses during activities like running and jumping.

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    Protein Classification: Shape

    Proteins are classified based on their shape into fibrous (long and thin) and globular (spherical) categories.

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    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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    Chemistry of Amino Acids and Proteins - I AAU 2024 PDF

    Description

    This quiz explores various amino acids, their roles, and functions in the human body. Questions cover topics such as precursors for important compounds, neurotransmitter synthesis, and types of proteins. Test your knowledge of biochemical principles related to amino acids!

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