Protein Structure and Function Quiz
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Questions and Answers

Which of the following techniques is NOT used to determine secondary structure?

  • Nuclear Magnetic Resonance (NMR) spectroscopy (correct)
  • Fourier transform infrared spectroscopy (FTIR)
  • Circular dichroism (CD) spectroscopy
  • X-ray crystallography
  • What is a characteristic feature of the α-helix structure?

  • It allows the formation with proline residues.
  • The side chains extend into the core.
  • Each turn contains 3.6 amino acids. (correct)
  • It has left-handed coiling.
  • What amino acids make up glutathione?

  • Glutamate, lysine, leucine
  • Arginine, cysteine, phenylalanine
  • Glutamate, cysteine, glycine (correct)
  • Aspartate, cysteine, glycine
  • Which functional group is associated with glutathione?

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

    Which of the following best describes antiparallel β-sheets?

    <p>They join two or more segments running in opposite directions. (C)</p> Signup and view all the answers

    What role do β-bends play in protein structure?

    <p>They assist in forming a compact, globular shape. (D)</p> Signup and view all the answers

    What is the primary function of glutathione related to hydrogen peroxide?

    <p>It removes the toxicity of hydrogen peroxide. (B)</p> Signup and view all the answers

    What characterizes the tertiary structure of proteins?

    <p>It refers to the arrangement of domains in the polypeptide chain. (B)</p> Signup and view all the answers

    What does the primary structure of a protein refer to?

    <p>The sequence of amino acids in a protein chain (B)</p> Signup and view all the answers

    Which technique is NOT used to determine the primary structure of a protein?

    <p>NMR spectroscopy (D)</p> Signup and view all the answers

    Which bond is primarily responsible for maintaining a protein's secondary structure?

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

    Which of the following is NOT a function of glutathione?

    <p>Cleaving peptide bonds of proteins (B)</p> Signup and view all the answers

    What characterizes a protein's tertiary structure?

    <p>The overall three-dimensional shape of a single polypeptide (B)</p> Signup and view all the answers

    What color does proline produce when it reacts with ninhydrin?

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

    Which reaction is specific to phenolic amino acids?

    <p>Millon's reaction (A)</p> Signup and view all the answers

    What is the product when tyrosine reacts with mercuric salts in Millon's reaction?

    <p>Red color (D)</p> Signup and view all the answers

    Which reaction can lead to the formation of a purple ring with tryptophan?

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

    What type of peptide consists of 2 amino acids linked by one peptide bond?

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

    Which peptide contains 29 amino acids and is known for its regulatory function in glucose metabolism?

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

    What is the primary effect of the atrial natriuretic factor (ANF)?

    <p>Increases urine sodium excretion (B)</p> Signup and view all the answers

    Which of these peptides is known as an antibiotic that consists of cysteine and D-valine residues?

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

    What is the primary role of glucagon in the body during fasting?

    <p>It increases plasma glucose levels (D)</p> Signup and view all the answers

    Which hormone is secreted by parathyroid glands during hypocalcemia?

    <p>Parathyroid hormone (PTH) (A)</p> Signup and view all the answers

    How many amino acids make up the hormone calcitonin?

    <p>32 (D)</p> Signup and view all the answers

    What is the function of fibrillin in the body?

    <p>Provides a scaffold for elastin deposition (D)</p> Signup and view all the answers

    Which technique separates proteins based on their sizes and densities?

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

    Which of the following is true about the precipitation method of protein separation?

    <p>Albumin is precipitated by half saturated (NH₄)₂SO₄ (A)</p> Signup and view all the answers

    What type of protein is fibronectin?

    <p>A fibrous protein that assists in cell adhesion (D)</p> Signup and view all the answers

    What does the dialysis method separate in a mixture?

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

    What is the primary function of collagen in the body?

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

    What happens during a negative nitrogen balance?

    <p>Nitrogen intake is less than nitrogen loss (B)</p> Signup and view all the answers

    Which of the following is not a function of proteins?

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

    What type of molecule are immunoglobulins classified as?

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

    Which amino acid classification does not have a net charge at neutral pH?

    <p>Uncharged polar side chain amino acids (B)</p> Signup and view all the answers

    Which of the following amino acids has a unique imino group?

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

    Which of these proteins is known to be part of blood clotting?

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

    How many of the discovered amino acids are coded for by DNA in mammals?

    <p>20 (C)</p> Signup and view all the answers

    What type of proteins are characterized by their compact forms resulting from the folding of polypeptide chains?

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

    Which type of bond is NOT responsible for maintaining the tertiary structure of proteins?

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

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

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

    Which forces contribute to the stability of quaternary structure in proteins?

    <p>Hydrogen bonds and van der Waals forces (A)</p> Signup and view all the answers

    Chaperones are known for which primary function in protein folding?

    <p>Preventing faulty folding of proteins (D)</p> Signup and view all the answers

    What does salting in refer to in the context of protein solubility?

    <p>Boosting protein solubility with small amounts of salt (B)</p> Signup and view all the answers

    Which of the following proteins is known to lose function when its subunits are dissociated?

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

    Which type of proteins are typically water insoluble due to their non-polar side chains?

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

    Flashcards

    What are proteins?

    Proteins are large polymers made up of chains of amino acids. They are crucial for many functions in living organisms.

    How many standard amino acids are there?

    The 20 standard amino acids are the ones that are coded by DNA and are used in building mammalian proteins.

    What are the components of an amino acid?

    They have a carboxyl group (COOH), an amino group (NH2), a unique side chain (R), and a hydrogen atom attached to the central carbon atom.

    What are non-polar amino acids?

    Non-polar side chains: These amino acids are hydrophobic, meaning they don't like water.

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    What are uncharged polar amino acids?

    Uncharged polar side chains: These amino acids have a neutral charge at a neutral pH.

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    What are the main functions of proteins?

    Proteins provide structural support, act as enzymes to speed up reactions, function as hormones, transport molecules, help with clotting, act as receptors, fight off infections, and store molecules.

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    What is nitrogen balance?

    Nitrogen intake equals nitrogen loss, indicating a balanced state.

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    What is negative nitrogen balance?

    When nitrogen intake is less than nitrogen loss, it can occur during conditions like fasting or illness.

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    3-Decarboxylation

    The removal of a carbon dioxide molecule (CO₂) from an amino acid, resulting in the formation of a biologically active amine.

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    Ninhydrin Reaction

    A chemical reaction involving decarboxylation and deamination, producing a colored product used to detect amino acids. Most amino acids react with ninhydrin to produce a blue color, while proline reacts to form a yellow color.

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    Biuret's Reaction

    A test used to detect the presence of proteins and peptides. It involves the reaction of proteins with copper sulfate (CuSO₄) in a basic environment, resulting in the formation of a complex that produces a characteristic violet color.

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    Millon's Reaction

    A chemical test specific for phenolic amino acids, such as tyrosine. It involves the reaction of tyrosine with mercury ions (Hg²⁺), leading to the formation of a red-colored complex.

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    Xanthoproteic Reaction

    A reaction that identifies aromatic amino acids like phenylalanine and tyrosine. When treated with concentrated nitric acid (HNO₃), these amino acids produce a yellow-orange colored solution.

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    Rosenheim Test

    A test specific for the indole group, found in the amino acid tryptophan. The reaction involves the interaction of tryptophan with formaldehyde and concentrated sulfuric acid, resulting in the formation of a purple ring at the interface of the two layers.

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    Peptides

    Molecules composed of two or more amino acids linked together by peptide bonds. Peptides can be classified based on their chain length.

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    Peptide Bond

    A covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid.

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    What is glutathione (G-SH)?

    A tripeptide found in cell membranes, composed of glutamate, cysteine, and glycine.

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    What's the functional group of glutathione?

    The thiol group (-SH) of cysteine.

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    What are the forms of glutathione?

    Glutathione exists in two forms: the reduced form (G-SH) and the oxidized form (G-S-S-G).

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    What is a protein?

    A protein is a macromolecule composed of a chain of 50 or more amino acids joined by peptide bonds.

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    What is the conformation of a protein?

    The protein's 3-dimensional structure, essential for its function.

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    What is the primary structure of a protein?

    The sequence of amino acids in a protein chain.

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    What bond is responsible for the primary structure of a protein?

    A bond between the carboxyl group of one amino acid and the amino group of the next.

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    What is the secondary structure of a protein?

    The spatial arrangement of adjacent amino acid residues in a protein chain, stabilized by hydrogen bonds.

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    Globular proteins

    Globular proteins, like myoglobin and albumin, are compactly folded polypeptide chains, creating a spherical shape.

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    Fibrous proteins

    Fibrous proteins, like keratin and collagen, are extended polypeptide chains, forming a long, fiber-like structure.

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    Tertiary structure bonds

    Hydrogen bonds, hydrophobic interactions, disulfide bonds, and ionic interactions stabilize a protein's tertiary structure.

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    Quaternary structure

    The quaternary structure of a protein is formed when multiple polypeptide chains (subunits) come together.

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    Bonds in quaternary structure

    The forces that hold subunit chains together in a quaternary structure include hydrogen bonds, electrostatic bonds, hydrophobic bonds and van der Waals forces.

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    Chaperones

    Chaperones are proteins that assist in the proper folding of other proteins.

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    Water-soluble proteins

    Proteins with polar side chains exposed on their surface are water-soluble, like albumin.

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    Water-insoluble proteins

    Proteins with non-polar side chains exposed on their surface are water-insoluble, like keratin and collagen.

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    Circular Dichroism (CD) spectroscopy

    A method using circularly polarized light to study the secondary structure of proteins. It measures the difference in absorbance of left and right circularly polarized light, revealing information about the arrangement of amino acids in the protein.

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    Fourier Transform Infrared (FTIR) Spectroscopy

    A method using infrared light to study the secondary structure of proteins. It measures the vibrations of different chemical bonds in the protein, specifically those in the peptide backbone, which are indicative of alpha-helices and beta-sheets.

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    What is an alpha-helix?

    A tightly coiled, rod-like structure found in proteins, with the peptide backbone winding around a central axis. It is typically right-handed, meaning it spirals clockwise when viewed from the N-terminus.

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    What is a beta-sheet?

    A sheet-like structure formed by two or more polypeptide chains (or segments of the same chain) held together by hydrogen bonds between the backbone atoms. Peptide chains can run parallel or antiparallel to each other.

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    What are Loop regions?

    Segments of polypeptide chains that connect secondary structural elements. They are often rich in charged amino acids, giving them flexibility and contributing to the overall shape of the protein.

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    Glucagon - What is it and what does it do?

    A polypeptide hormone released by the pancreas's alpha cells during fasting. It raises blood glucose levels by boosting glycogen breakdown into glucose in the liver.

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    Parathyroid Hormone (PTH) - What is it and what does it do?

    A polypeptide hormone secreted by parathyroid glands when blood calcium levels are low. It raises blood calcium by increasing calcium absorption in the gut and releasing it from bones.

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    Calcitonin - What is it and what does it do?

    A polypeptide hormone secreted by thyroid gland's parafollicular cells when blood calcium levels are high. It lowers blood calcium by inhibiting bone resorption.

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    Fibrillin - What is it, where is it, and what's its role?

    A fibrous protein made by fibroblasts that forms a framework for elastin deposition. It's found in structures like lens suspensory ligaments and the aorta.

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    Fibronectin - What is it and what does it do?

    A fibrous protein comprised of two identical subunits joined by disulfide bonds. It acts as a bridge between cells and the extracellular matrix.

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    Chromatography - How does it work?

    A process that separates substances based on their distribution between a stationary phase (e.g., paper or gel) and a mobile phase (e.g., liquid).

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    Electrophoresis - What is it?

    The movement of charged particles in an electric field towards oppositely charged electrodes.

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    Ultracentrifugation - How does it work?

    A method used to separate proteins based on their densities by spinning them at high speeds in a centrifuge.

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    Study Notes

    Proteins and Amino Acids

    • Proteins are large polymers of L-amino acids
    • Proteins are the most abundant and functionally important molecules in living systems.
    • Main functions of proteins include:
      • Structural functions: Collagen in bones, elastin in lungs
      • Enzymes: Pepsin, lipase, urease
      • Hormones: Growth hormone, insulin, glucagon, oxytocin
      • Transporters: Lipoproteins, hemoglobin
      • Blood clotting factors: Fibrinogen, prothrombin
      • Receptors: Insulin receptor
      • Defence molecules: Immunoglobulins (IgM, IgA, IgG, IgE, IgD)
      • Storage: Myoglobin (oxygen), ferritin (iron)
      • Contractile proteins: Actin, tubulin
    • Nitrogen balance:
      • Nitrogen intake equals nitrogen loss (balanced)
      • Nitrogen intake greater than loss (positive) e.g. growing children, pregnancy
      • Nitrogen intake less than loss (negative) e.g. fasting, starvation, disease
    • Over 300 amino acids exist in nature, but only 20 are common in mammalian proteins.
    • These 20 amino acids are coded for by DNA

    Structure of Amino Acids

    • Each amino acid has a central carbon atom (α-carbon) bonded to:
      • A carboxyl group (COOH)
      • An amino group (NH2)
      • A hydrogen atom
      • A variable side chain (R group)
    • Proline has a secondary amino group (imino group)

    Classification of Amino Acids

    • Amino acids are classified based on chemical structure, nutritional importance, and metabolic fate.

      1. Amino acids with non-polar side chains (hydrophobic): Glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, proline
      1. Amino acids with uncharged polar side chains: These have zero net charge at a neutral pH. Serine, threonine, tyrosine, asparagine, glutamine, cysteine
      1. Amino acids with charged polar side chains, which are either acidic or basic: These amino acids are either negatively (acidic) or positively (basic) charged. Aspartic acid, glutamic acid, lysine, arginine, histidine

    Summary of Chemical Classification of Amino Acids (Table)

    • Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, and Proline: Non-polar amino acids
    • Serine, Threonine, Tyrosine, Cysteine, Asparagine, and Glutamine: Polar neutral amino acids
    • Aspartic acid, Glutamic acid, Lysine, Arginine, and Histidine: Polar charged amino acids
    • Phenylalanine, Tryptophan, Tyrosine: Aromatic amino acids
    • Serine, Threonine, Tyrosine, Cysteine, Asparagine, and Glutamine: Alcohlic OH amino acids
    • Other amino acids: based on their characteristics.

    1- Essential Amino Acids (8)

    • Cannot be synthesized in the body
    • Need to be obtained from diet, these include: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine

    2- Semi-Essential Amino Acids (2)

    • Synthesized in the body, but not in enough amounts for growing children. These include: Arginine, Histidine

    3- Non-Essential Amino Acids (10)

    • Synthesized in the body in sufficient quantities, these include: Alanine, Asparagine, Aspartic acid, cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, Tyrosine

    Metabolic Classification of Amino Acids

    • Ketogenic: Leucine (only pure ketogenic amino acid), can be used for energy, forming ketone bodies(only one)
    • Ketogenic and Glucogenic (glycogenic): phenylalanine, tyrosine, tryptophan, lysine, threonine, can be used for both energy and glucose production
    • Glucogenic (glycogenic): All others used for energy and glucose production.

    Protein Reactions, classification of proteins

    • Protein denaturation, breaking down of peptide structures, primarily proteins

    • Important features about denaturation of proteins

    • Chemical changes like H-bonds, S-S bonds, and ionic interactions are broken.

    • All protein levels (except primary) are lost.

    • Biological activity is lost.

    • Denatured protein is insoluble.

    • Denaturation can be reversible or irreversible.

    Protein Structures

    • Primary: Sequence of amino acids
    • Secondary: Formation of alpha-helices and beta-sheets; hydrogen bond formation
    • Tertiary: Three-dimensional structure of a polypeptide chain; formation of bonds within or between segments
    • Quaternary: Structure of a multi-subunit protein; multiple tertiary protein assemblies

    Fibrous Proteins

    • Extended form proteins: e.g., Keratin, Collagen, Myosin
    • Bonds in fibrous structures: hydrogen bonds, hydrophobic interactions, disulfide bonds, ionic interactions,
    • Characteristics: Structural role, water insoluble, strong, and fibrous.

    Globular Proteins

    • Spherical shape;
    • Examples: (albumins, globulins, protamines, histones, etc.)

    Conjugated Proteins

    • Composed of protein and non-protein components: eg. Nucleoproteins, lipoprotein, glycoproteins, phosphoproteins, metalloproteins.
    • These components provide various functional roles.

    Methods of Protein Separation

    • Chromatography
    • Electrophoresis
    • Precipitation
    • Ultracentrifugation
    • Dialysis

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