Macromolecules - Proteins Overview
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Questions and Answers

What structure is 1 and 2 similar to?

  • RNA (1) and protein (2)
  • RNA (1) and DNA (2)
  • Protein (1) and RNA (2)
  • DNA (1) and RNA (2) (correct)

    • Identify the building units of Macromolecules.

  • Monomer (correct)
  • Protein
  • DNA
  • Peptide

    • Which of the non-polar amino acids is the only amino acid that does not have separate L and D isomers?

  • Valine
  • Tryptophan
  • Proline
  • Glycine (correct)
  • Phenylalanine

    • Protein structures rely on all types of chemical bonds or interactions. Covalent bonds link amino acids together to form protein primary structure, while secondary, tertiary, and quaternary structures are maintained solely by non-covalent bonds.

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

    Which of these represents an important distinction between a polypeptide and a protein?

    <p>&quot;Protein&quot; implies function, while &quot;polypeptide&quot; is a structural term. (A)</p> Signup and view all the answers

    Proline is referred to as the "helix breaker " because...

    <p>its only found in the L form, which is incompatible with helical protein structure. (A), it lacks the hydrogen atom needed for hydrogen bonding. (E)</p> Signup and view all the answers

    What makes the difference between a reaction that can take place and one that will take place?

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

    What are called ribozymes?

    <p>RNA molecules that have catalytic activity (A)</p> Signup and view all the answers

    Which of the following is NOT a major class of enzymes?

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

    Every enzyme contains a characteristic cluster of amino acids that forms the ______

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

    Coenzymes are derivatives of vitamins.

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

    Because of the shape and chemistry of the active site, enzymes have a very high ______

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

    Most enzymes are globular proteins.

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

    What is the induced conformational change?

    <p>a change in the shape of the enzyme that allows it to bind to the substrate (C)</p> Signup and view all the answers

    The induced conformational change brings needed amino acid side chains into the active site, even those that are not nearby. What is the significant effect of this action?

    <p>It positions the substrate optimally for catalysis. (C)</p> Signup and view all the answers

    What are the three common mechanisms of substrate activation?

    <p>Bond distortion, proton transfer, electron transfer (A)</p> Signup and view all the answers

    Irreversible inhibitors bind the enzyme covalently and cause permanent loss of catalytic activity.

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

    What are the two forms of reversible inhibitors?

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

    Noncompetitive inhibitors bind to the active site of an enzyme.

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

    What is substrate-level regulation?

    <p>Regulation that depends on interactions of substrates and products (D)</p> Signup and view all the answers

    Allosteric regulation is the single most important control mechanism whereby the rates of enzymatic reactions are adjusted to meet the cell's needs.

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

    Allosteric enzymes have two conformations, one in which it has affinity for the substrate and one in which it does not.

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

    Active and allosteric sites are on different subunits, the catalytic and regulatory subunits, respectively.

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

    The final product of an enzyme pathway negatively regulates an earlier step in the pathway.

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

    Many enzymes are subject to covalent modification.

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

    Zymogens are activated by themselves or other proteolytic enzymes.

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

    Flashcards

    Amino Acids

    The building blocks of proteins, consisting of a central carbon atom bonded to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a side chain (R group).

    Peptide Bond

    The covalent bond that links amino acids together in a polypeptide chain. Formed by a dehydration reaction, releasing a water molecule.

    Polypeptide

    A linear chain of amino acids linked by peptide bonds.

    Primary Structure

    The unique sequence of amino acids in a polypeptide chain. It dictates the protein's structure and function.

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    Secondary Structure

    Local, recurring patterns of protein structure, arising from hydrogen bonding between the backbone atoms of the polypeptide chain.

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    Alpha Helix

    A coiled structure formed by hydrogen bonds between backbone atoms in a polypeptide chain. R groups point outwards.

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    Beta Sheet

    A folded, sheet-like structure formed by hydrogen bonds between backbone atoms in polypeptide chains. R groups point alternately above and below the sheet.

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    Tertiary Structure

    The overall three-dimensional shape of a protein, resulting from interactions between side chains (R groups). It determines the protein's function.

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    Quaternary Structure

    The arrangement of multiple polypeptide chains (subunits) in a protein complex. Only applies to proteins with more than one subunit.

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    Monomeric Protein

    Proteins that are composed of a single polypeptide chain.

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    Multimeric Protein

    Proteins that are composed of two or more polypeptide chains (subunits).

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    Activation Energy

    The minimum amount of energy required by reactants to reach the transition state and undergo a chemical reaction.

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    Catalyst

    A substance that speeds up a chemical reaction without being consumed in the process.

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    Enzymes

    Biological catalysts that are usually proteins. They accelerate and regulate biochemical reactions in living organisms.

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    Active Site

    The region on an enzyme's surface where a substrate binds and where catalysis occurs.

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    Cofactors

    Non-protein molecules that assist enzymes in their catalytic activity. Often metal ions or organic molecules.

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    Coenzymes

    Organic molecules that act as cofactors.

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    Specificity

    The ability of an enzyme to bind and catalyze reactions with specific molecules, due to the shape and chemical properties of its active site.

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    Competitive Inhibition

    The non-covalent binding of a molecule to an enzyme's active site that prevents substrate binding and catalytic activity.

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    Noncompetitive Inhibition

    The non-covalent binding of a molecule to an enzyme at a site other than the active site, resulting in changes to the enzyme's activity.

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    Feedback Inhibition

    A type of enzyme regulation where the product of a metabolic pathway inhibits an earlier step in the pathway.

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    Phosphorylation

    The process of adding or removing phosphate groups to an enzyme, which can affect its activity. This is a common mechanism of reversible enzyme regulation.

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    Dephosphorylation

    The process of removing a phosphate group from an enzyme.

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    Proteolytic Cleavage

    The process of converting an inactive enzyme precursor (zymogen) into an active enzyme. This involves irreversible cleavage of the polypeptide chain.

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    Zymogens

    Inactive precursor forms of enzymes that are activated by proteolytic cleavage, often found in the pancreas, coagulation cascade, and complement cascade.

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    Protein Folding

    The folding of a protein into a specific three-dimensional structure, driven by interactions between amino acid side chains and the surrounding environment.

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    Proteome

    The collection of all proteins produced by an organism.

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    Nucleic Acids

    A type of biological molecule that consists of a long chain of nucleotides joined together. There are two main types: DNA and RNA.

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    DNA

    A complex structure containing genetic information organized into units called genes. DNA is the genetic code for all living organisms.

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    RNA

    A molecule involved in protein synthesis. RNA translates the genetic code from DNA into proteins.

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    Messenger RNA (mRNA)

    A type of RNA that carries genetic information from DNA to ribosomes, where proteins are synthesized.

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    Transfer RNA (tRNA)

    A type of RNA that acts as an adapter molecule, bringing specific amino acids to the ribosome during protein synthesis.

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    Ribosomal RNA (rRNA)

    A type of RNA that is part of the ribosome, the site of protein synthesis. rRNA plays a structural and catalytic role.

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    Study Notes

    Macromolecules - Proteins

    • Proteins perform many functions in cells, including:
      • Catalyzing reactions (enzymes)
      • Providing support and shape (structural proteins)
      • Facilitating movement (motility proteins)
      • Controlling and coordinating cell function (regulatory proteins)
      • Transporting substances (transport proteins)
      • Communicating between cells (signaling proteins)
      • Responding to chemical stimuli from the environment (receptor proteins)
      • Protecting against disease (defensive proteins)
      • Serving as reservoirs of amino acids (storage proteins)

    Monomers of Proteins

    • The monomers of proteins are amino acids.
    • Only 20 kinds of amino acids are used in protein synthesis.
    • Every amino acid has the same basic structure.
    • All amino acids in human body are L-amino acids.

    Protein Structure Levels

    • Primary Structure: The linear sequence of amino acids in a polypeptide chain.
    • Secondary Structure: The local folding of the polypeptide chain, often into a-helices or β-sheets, stabilized by hydrogen bonds.
    • Tertiary Structure: The overall three-dimensional shape of the polypeptide chain, stabilized by various interactions involving R-groups, including: hydrogen bonds, disulfide bonds, ionic bonds, Van der Waals forces, and hydrophobic interactions.
    • Quaternary Structure: The arrangement of multiple polypeptide chains in a protein, stabilized by the same forces involved in tertiary structure.

    Protein Sizes

    • Proteins vary greatly in size.
    • The largest protein is titin (34,350 amino acids).
    • The smallest protein is insulin (51 amino acids).
    • The average protein size is around 300 amino acids.
    • Estimates exist of the number of different proteins of 100 amino acids that can be made with 20 amino acids.
    • Data from various organisms are provided via plots to show protein size distributions.

    Protein Folding

    • The polypeptide chain folds into a specific 3-D shape due to the interactions of amino acid side chains (R groups).
    • Covalent (peptide bonds and disulfide bonds) and non-covalent (hydrogen bonds, ionic bonds, Van der Waals forces, hydrophobic interactions) bonds are involved.
    • The interactions between the amino acid side chains contribute to the specific 3-dimensional structure (folding) of the protein.

    Protein Domains

    • Proteins with similar functions often share common domains.
    • Proteins with multiple functions may have separate domains for each function.

    Protein Structure Prediction

    • Primary structure determines the final folded shape of a protein.
    • Tools like AlphaFold and AlphaFold2 create accurate 3D protein structure predictions.
    • A database of predicted structures is available for research.

    Quaternary Structure

    • Quaternary structure describes how multiple polypeptide chains associate to form a multimeric protein.
    • The type of interactions that hold the chains together are the same as those involved in maintaining tertiary structure.

    Disease Prion Protein

    • The disease prion protein PrPsc is characterized by its multimeric amyloid fibril, parallel in-register architecture, and high β sheet content.
    • A comparative comparison with its healthy form PrPc is presented in terms of structure, including the primary and secondary forms.

    Enzyme Characteristics and Regulation

    • All enzymes have a specific active site with a particular shape for interactions with substrates.
    • The active site interacts in specific ways with substrates, changing the substrate shape or causing temporary covalent bonds, leading to bond distortion, proton transfer, and electron transfer.
    • Some enzymes require cofactors, like prosthetic groups (metal ions) or coenzymes (vitamin derivatives), to function.
    • Enzymes are very specific to the substrate that they interact with.
    • Enzyme function is highly sensitive to temperature changes, optimal activity occurring at a specific temperature.
    • Enzyme function is also highly pH dependent, with activity varying greatly depending on pH.
    • Enzyme activity can be regulated in numerous ways, including covalent modification, feedback inhibition, allosteric regulation, product inhibition, and proteolytic activation by reversible and irreversible inhibitors.
    • Enzymes can be regulated by the addition or removal of chemical groups such as phosphorylation, dephosphorylation, methylation, demethylation, acetylation and deacetylation.

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    Description

    This quiz covers the essential roles and structures of proteins, including their various functions in cells. Discover the significance of amino acids as the building blocks of proteins, and learn about the different levels of protein structure. Test your knowledge on the types and roles of proteins in biological systems.

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