Amino Acids & Proteins: Fundamentals
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Questions and Answers

What primarily determines the degree of rotation in a peptide bond?

  • The temperature of the environment
  • The length of the polypeptide chain
  • The size of the R groups of the amino acids (correct)
  • The presence of amino acid sequences

    • Which type of interaction occurs specifically between hydrophobic side chains?

  • Hydrophobic interactions (correct)
  • Electrostatic interactions
  • Van der Waals interactions
  • Hydrogen bond

    • What is the term used for proteins that consist of two or more polypeptide chains?

  • Monomeric proteins
  • Tetrameric proteins
  • Oligomeric proteins (correct)
  • Dimeric proteins

    • What type of bond is formed between cysteine residues in proteins?

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

    How are the subunits of a protein classified when they are not identical?

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

    What type of amino acids are characterized by their non-polar nature and hydrophobic properties?

    <p>Hydrophobic and non-polar (B)</p> Signup and view all the answers

    Which of the following amino acids can be classified as basic?

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

    What is a primary characteristic of aromatic amino acids?

    <p>They absorb UV light. (C)</p> Signup and view all the answers

    Which of the following describes the primary structure of a protein?

    <p>The linear sequence of amino acids (C)</p> Signup and view all the answers

    Which type of solvents can aliphatic amino acids dissolve more easily in?

    <p>Non-polar solvents like oils (D)</p> Signup and view all the answers

    What contributes to the overall charge of a protein?

    <p>The properties of the amino acids that make it up (B)</p> Signup and view all the answers

    Which amino acid is known for having a cyclic R group?

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

    What type of proteins have a non-protein moiety attached?

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

    What primarily determines the formation of secondary structures in proteins?

    <p>Regular folding of backbone atoms (A)</p> Signup and view all the answers

    Which type of secondary structure is characterized by right-handed helices?

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

    In which type of β-structure do chains run in opposite directions?

    <p>Anti-parallel β-structure (B)</p> Signup and view all the answers

    What percentage of the structure of globular proteins is typically in alpha helices?

    <p>27% (D)</p> Signup and view all the answers

    Which amino acids are most commonly found in the interior of globular proteins?

    <p>Hydrophobic amino acids like Val and Leu (A)</p> Signup and view all the answers

    What defines the tertiary structure of a protein?

    <p>Interactions between amino acids far apart in the primary sequence (C)</p> Signup and view all the answers

    What is true about the geometry of a peptide bond?

    <p>C=O and C-N atoms are planar. (B)</p> Signup and view all the answers

    In what type of protein are mostly beta structures expected to be found?

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

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    Flashcards

    Amino Acid

    The basic unit of a protein.

    R Group Classification

    Amino acids are classified based on their R group's chemical properties.

    Types of Amino Acids

    Amino acids can be aliphatic, aromatic, acidic, basic, etc.

    Zwitterions

    Amino acids that can have both positive and negative charges.

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    Solubility of Amino Acids

    Generally soluble in polar solvents like water and insoluble in organic solvents.

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    Primary Structure of Proteins

    The linear sequence of amino acids in a protein chain.

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    Protein Size Variation

    Proteins can range from 51 to 2000 amino acids in length.

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    Globular vs Fibrous Proteins

    Proteins are categorized as globular (functional) or fibrous (structural).

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    Peptide bond rotation

    The degree of rotation in peptide bonds is limited by the size of R groups and the bond's double bond characteristics.

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    Hydrophobic interactions

    Forces that occur between hydrophobic side chains, avoiding water and stabilizing protein structure, typically found in the core of globular proteins.

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    Electrostatic interactions

    Attractions between charged side chains, such as COO- and NH+, contributing to protein stability.

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    Disulfide bond

    A strong bond formed between cysteine side chains, linking polypeptide chains together, important for stability.

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    Quaternary structure

    The arrangement of multiple polypeptide chains (subunits) in a protein, categorized as oligomeric with terms like dimer and trimer.

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    Secondary Structure

    Local conformations of the polypeptide chain due to backbone folding without side chains.

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    Super Secondary Structures

    Arrangement of secondary structures in a specific manner or pattern.

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    Tertiary Structure

    3D structure of a protein due to interactions between distant amino acids.

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    Alpha Helix

    A right-handed coil with hydrogen bonds between neighboring peptide bonds.

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    Beta Structure

    Hydrogen-bonded arrangement of peptide chains, forming pleated sheets.

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    Hydrophobic Amino Acids

    Amino acids that are typically found inside proteins away from water.

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    Peptide Bond Geometry

    The planar structure formed by the C=O and C-N atoms in peptide bonds.

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    Study Notes

    Amino Acids & Proteins

    • Amino acids are the basic building blocks of proteins.
    • Each amino acid has a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R-group).
    • The R-group distinguishes one amino acid from another, determining its chemical properties.
    • Amino acids exist as L-stereoisomers in most proteins.
    • Amino acids are classified based on the chemical properties of their side chains (e.g., hydrophobic, polar, acidic, basic).
    • Examples include aliphatic amino acids (Leu, Ile, Ala, Val), aromatic amino acids (Phe, Trp, Tyr), amino acids containing sulfur (Cys, Met), amino acids with hydroxyl groups (Thr, Ser), acidic amino acids (Asp, Glu), basic amino acids (Lys, Arg, His), imino acids (Pro), and amides (Gln, Asn).
    • Proteins vary greatly in size, ranging from small proteins with fewer than 100 amino acids to large proteins with thousands.
    • Examples of proteins with varying sizes include insulin and collagen.
    • Myoglobin, a protein, has 153 amino acids, while hemoglobin has ~574 amino acids.
    • Proteins are categorized as globular or fibrous proteins, performing diverse functions such as enzymes, structural components, and transport.
    • Proteins can be conjugated containing a non-protein moiety such as heme.

    Protein Structure

    • Proteins are biopolymers composed of amino acids linked by peptide bonds.

    • The linear sequence of amino acids in a protein is called the primary structure.

    • The polypeptide chain folds into local conformations (secondary structures) stabilized by hydrogen bonds between backbone atoms.

    • Common secondary structures include alpha-helices (a lot of hydrogen bonding between C=O and N-H groups of neighboring peptide bonds) and beta-sheets (hydrogen bonds between neighboring peptide bonds of the same or different chains).

    • Local conformations of the polypeptide chain formed as a result of the regular folding of backbone atoms or common patterns within protein structures

    • These patterns result from hydrogen bonds between neighboring peptide bonds

    • Secondary structure gives rise to Super secondary structure(conformations of particular group of secondary structures)

    • The 3-dimensional arrangement of the polypeptide chain is called the tertiary structure. This is a result of interactions between amino acids that are far apart in the primary sequence of the protein.

    • The association of multiple polypeptide chains forms the quaternary structure of certain proteins, as seen in oligomeric proteins.

    • Large proteins may contain multiple subunits.

    • The arrangement of polypeptide chains (subunits) results in the quaternary structure in oligomeric proteins.

    Forces Influencing Protein Structure

    • The peptide bond has a planar structure. The degree of rotation depends upon the sizes of the R groups
    • Hydrogen bonds form between the N-H and C=O groups of peptide bonds.
    • Hydrophobic interactions occur between non-polar amino acid side chains, driving them to cluster together in the protein interior.
    • Electrostatic interactions occur between charged amino acid side chains.
    • Van der Waals interactions are weak attractions between atoms.
    • Disulfide bonds (covalent bonds between cysteine residues) contribute to protein stability, particularly in certain proteins.

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