Protein Structure and Function Quiz
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Questions and Answers

What are the two main types of macromolecules that depend on protein structure and function?

Enzymes and polypeptide hormones.

What is the common structural feature shared by all proteins?

  • They are circular molecules.
  • They form rigid three-dimensional shapes.
  • They are linear polymers of amino acids. (correct)
  • They are composed entirely of lipids.

    • Proline has a primary amino group.

    False

    At physiologic pH, what is the charge of the carboxyl group of amino acids?

    <p>Negatively charged carboxylate ion (–COO–).</p> Signup and view all the answers

    Which amino acids have uncharged polar side chains?

    <p>Cysteine and tyrosine.</p> Signup and view all the answers

    The covalent cross-link formed by two cysteines is called a ______ bond.

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

    Which amino acid is unique for being weakly basic and can ionize within the physiologic pH range?

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

    What is the isoelectric point (pI) of an amino acid?

    <p>The pH at which the amino acid is electrically neutral.</p> Signup and view all the answers

    Match the following amino acids with their properties:

    <p>Alanine = Nonpolar Glutamic acid = Acidic Lysine = Basic Serine = Polar uncharged</p> Signup and view all the answers

    The Henderson-Hasselbalch equation can be used to analyze the dissociation of amino acids.

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

    Which one of the following statements concerning the titration curve for a nonpolar amino acid is correct?

    <p>Point C represents the region where the net charge on the amino acid is zero.</p> Signup and view all the answers

    Which one of the following statements concerning the peptide Val-Cys-Glu-Ser-Asp-Arg-Cys is correct?

    <p>The peptide contains a side chain that can be phosphorylated.</p> Signup and view all the answers

    If a 2-year-old child has a blood pH of 7.0 and the pKa of aspirin is 3, what is the ratio of its ionized to un-ionized forms?

    <p>10,000 to 1</p> Signup and view all the answers

    What is the sequence of amino acids in a peptide called?

    <p>primary structure</p> Signup and view all the answers

    What type of bond joins amino acids in proteins?

    <p>peptide bond</p> Signup and view all the answers

    What is the common structure of the α-helix in proteins?

    <p>A spiral structure with tightly packed coiled backbone.</p> Signup and view all the answers

    What does the term 'R group' refer to in the context of amino acids?

    <p>side chain</p> Signup and view all the answers

    The _______ of each amino acid is attached to four different chemical groups.

    <p>α-carbon</p> Signup and view all the answers

    What is the primary feature that stabilizes an α-helix?

    <p>Extensive hydrogen bonding between the peptide-bond carbonyl oxygens and amide hydrogens</p> Signup and view all the answers

    How many amino acids are present in each turn of an α-helix?

    <p>3.6 amino acids</p> Signup and view all the answers

    Which amino acid disrupts an α-helix?

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

    What is a β-sheet?

    <p>A form of secondary structure where peptide bond components are involved in hydrogen bonding, appearing pleated.</p> Signup and view all the answers

    What is the difference between parallel and antiparallel β-sheets?

    <p>Their strands are oriented differently.</p> Signup and view all the answers

    β-bends reverse the direction of a polypeptide chain.

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

    What stabilizes β-bends?

    <p>Formation of hydrogen and ionic bonds</p> Signup and view all the answers

    What is the role of molecular chaperones in protein folding?

    <p>They facilitate correct protein folding by binding to and stabilizing hydrophobic regions.</p> Signup and view all the answers

    What term refers to proteins that perform the same function but have different primary structures?

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

    What is the dominant component of the amyloid plaque in Alzheimer disease?

    <p>Amyloid beta (Aβ)</p> Signup and view all the answers

    What happens to proteins once they are denatured?

    <p>They unfold and become disorganized.</p> Signup and view all the answers

    What is the significance of the sigmoidal oxygen-dissociation curve of hemoglobin?

    <p>The sigmoidal shape allows for efficient oxygen loading and unloading in response to small changes in pO2.</p> Signup and view all the answers

    What effect does lowering pH have on the oxygen affinity of hemoglobin?

    <p>Lowering pH decreases the oxygen affinity of hemoglobin.</p> Signup and view all the answers

    What is 2,3-bisphosphoglycerate (2,3-BPG) and what role does it play in hemoglobin function?

    <p>2,3-BPG is a molecule that binds to deoxyhemoglobin and decreases its affinity for oxygen, facilitating oxygen unloading.</p> Signup and view all the answers

    The affinity of hemoglobin for carbon monoxide (CO) is less than its affinity for oxygen.

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

    What are the two types of hemoglobin found in adults?

    <p>Hemoglobin A (HbA) and Hemoglobin A2 (HbA2).</p> Signup and view all the answers

    What is the composition of fetal hemoglobin (HbF)?

    <p>HbF is composed of two alpha chains and two gamma chains (α2γ2).</p> Signup and view all the answers

    What causes sickle cell anemia?

    <p>A point mutation in the gene for β-globin</p> Signup and view all the answers

    The process that refers to the nonenzymic addition of a sugar to hemoglobin is called ___

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

    What molecule stabilizes the deoxy form of hemoglobin and decreases its affinity for oxygen?

    <p>Carbon dioxide (CO2)</p> Signup and view all the answers

    Which one of the following statements concerning protein structure is correct?

    <p>The primary driving force for protein folding is the hydrophobic effect.</p> Signup and view all the answers

    A particular point mutation results in disruption of the α-helical structure in a segment of the mutant protein. The most likely change in the primary structure of the mutant protein is:

    <p>Methionine to proline.</p> Signup and view all the answers

    In comparing the α-helix to the β-sheet, which statement is correct only for the β-sheet?

    <p>It is stabilized by interchain hydrogen bonds.</p> Signup and view all the answers

    Which one of the following best describes Alzheimer disease?

    <p>It is associated with the deposition of neurotoxic amyloid β peptide aggregates.</p> Signup and view all the answers

    What are hemeproteins?

    <p>A group of specialized proteins that contain heme as a tightly bound prosthetic group.</p> Signup and view all the answers

    What is the role of the heme group in hemoglobin?

    <p>To reversibly bind oxygen.</p> Signup and view all the answers

    What type of structure does myoglobin primarily consist of?

    <p>α-helices.</p> Signup and view all the answers

    What is unique about the oxygen-binding properties of hemoglobin compared to myoglobin?

    <p>Hemoglobin can bind four O2 molecules.</p> Signup and view all the answers

    The deoxy form of hemoglobin is called the _____ form.

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

    The _____ group of the myoglobin molecule sits in a crevice lined with nonpolar amino acids.

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

    What is the designation of the mutant β-globin chain in sickle cell anemia?

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

    What symptoms typically characterize sickle cell anemia?

    <p>Lifelong episodes of pain (crises), chronic hemolytic anemia, hyperbilirubinemia, increased susceptibility to infections, acute chest syndrome, stroke, splenic and renal dysfunction.</p> Signup and view all the answers

    Heterozygotes for the sickle cell gene usually show clinical symptoms.

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

    What causes the altered mobility of HbS during electrophoresis?

    <p>Absence of negatively charged glutamate residues</p> Signup and view all the answers

    What happens to red blood cells (RBC) in sickle cell anemia at low oxygen tension?

    <p>Deoxyhemoglobin S polymerizes inside the RBC, forming insoluble fibrous polymers resulting in sickling.</p> Signup and view all the answers

    Which of the following variables can increase sickling in sickle cell anemia?

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

    What therapy increases circulating levels of HbF in sickle cell anemia patients?

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

    HbC disease is similar to HbS but with more severe symptoms.

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

    What is the primary cause of methemoglobinemia?

    <p>Oxidation of heme iron in hemoglobin to the ferric (Fe 3+) state.</p> Signup and view all the answers

    What can lead to the accumulation of methemoglobin (HbM)?

    <p>Inherited defects</p> Signup and view all the answers

    Match the hemoglobin variant with its corresponding mutation:

    <p>HbS = Valine substitution for glutamate at position six HbC = Lysine substitution for glutamate at position six HbSC = Combination of HbS and HbC mutations</p> Signup and view all the answers

    Study Notes

    Overview of Proteins

    • Proteins are vital macromolecules involved in various life processes.
    • Functions include catalyzing metabolic reactions (enzymes), regulating metabolism (hormones), facilitating movement (contractile proteins), and supporting structural frameworks (collagen).
    • Hemoglobin and plasma albumin in blood transport essential molecules, while immunoglobulins combat infections.

    Amino Acids

    • More than 300 amino acids exist, but only 20 are encoded by DNA and found in mammalian proteins.
    • Each amino acid comprises a carboxyl group, an amino group (primary or secondary), and a unique side chain (R group).
    • At physiological pH (approximately 7.4), carboxyl groups dissociate to form negatively charged carboxylate ions, and amino groups are protonated as ammonium ions.

    Classification of Amino Acids

    • Amino acids can be categorized by their side chains: nonpolar, polar uncharged, acidic, and basic.

    Nonpolar Amino Acids

    • Nonpolar side chains promote hydrophobic interactions.
    • Tend to cluster in the interior of proteins in aqueous environments, aiding structural stability.

    Uncharged Polar Amino Acids

    • Contain hydroxyl or amide groups that can form hydrogen bonds.
    • Cysteine can form disulfide bonds, important for protein structure.
    • Polar side chains serve as attachment sites for additional compounds, such as phosphate groups.

    Acidic Amino Acids

    • Aspartic acid and glutamic acid donate protons and are negatively charged at physiological pH.

    Basic Amino Acids

    • Lysine and arginine accept protons, becoming positively charged.
    • Histidine can be protonated or neutral, playing a significant role in buffering.

    Optical Properties

    • The α-carbon of amino acids is asymmetrical, yielding two stereoisomer forms: D and L.
    • All amino acids in proteins are of the L configuration, while D-amino acids are found in some antibiotics.

    Acidic and Basic Properties

    • Amino acids act as buffers due to their ionizable groups: carboxyl (weak acid) and amino (weak base).
    • The Henderson-Hasselbalch equation relates pH to the concentration of weak acids and their conjugate bases.

    Titration and Buffering

    • Titration curves illustrate the dissociation of carboxyl and amino groups of amino acids.
    • Maximum buffering capacity occurs at pH equal to the pKa of the weak acid.
    • The isoelectric point (pI) is the pH at which an amino acid is electrically neutral, important in protein separation techniques.

    Importance of pH in Drug Absorption

    • The pH at absorption sites influences the ionic forms of drugs, affecting permeability across membranes.
    • Weak acids or bases have uncharged and charged forms; uncharged forms permeate membranes more readily.

    Application of the Henderson-Hasselbalch Equation

    • Useful in predicting pH changes in physiological systems, drug absorption, and ionic forms of drugs in varying pH environments.### Concept Maps in Biochemistry
    • Concept maps are graphical tools designed to illustrate the relationships between ideas in biochemistry.
    • They arrange information hierarchically, with general concepts at the top and specific concepts below.
    • Concept boxes represent various biochemical concepts such as free energy and oxidative phosphorylation, aiding students in organizing and assimilating new information.
    • Cross-links within concept maps allow visualization of complex relationships, promoting the integration of biochemistry concepts relevant for clinical applications and exams like the USMLE.

    Amino Acid Structure

    • Each amino acid consists of an α-carboxyl group, a primary α-amino group (except proline, which has a secondary amino group), and a distinctive side chain (R group).
    • At physiological pH, the α-carboxyl group is dissociated, while the α-amino group is protonated.
    • Amino acids can be classified as nonpolar, uncharged polar, acidic (polar negative), or basic (polar positive), with their functions determined by their side chains.
    • All amino acids, including those in peptide chains, can act as buffers.

    Henderson-Hasselbalch Equation

    • The equation describes the relationship between pH and the concentrations of a weak acid and its conjugate base.
    • Buffering capacity is maximal at pH = pKa, where the concentrations of the acid and its conjugate base are equal.

    Peptide Bonds and Protein Structure

    • Proteins are formed by amino acids linked through peptide bonds, which are resistant to denaturation, requiring extreme conditions to break.
    • Peptides have an N-terminal (free amino end) and a C-terminal (free carboxyl end), with sequences read from N- to C-terminal.
    • The peptide bond is characterized by partial double-bond character, promoting rigidity and preventing free rotation.

    Primary Structure and Disease Relevance

    • The primary structure of proteins refers to the linear sequence of amino acids, crucial for understanding genetic diseases linked to abnormal sequences.
    • Peptide bonds are cleaved under acidic conditions to identify and quantitate constituent amino acids, which can be analyzed through cation-exchange chromatography.

    Secondary Structure of Proteins

    • Secondary structure refers to the regular arrangements of amino acids forming structures like α-helices and β-sheets.
    • α-helix is a coiled structure stabilized by hydrogen bonds between peptide-bond carbonyl oxygens and amide hydrogens, containing 3.6 amino acids per turn.
    • β-sheets consist of two or more extended segments of polypeptide chains, exhibiting hydrogen bonding perpendicular to the backbone.

    Disruption of Secondary Structures

    • Proline disrupts α-helical formation due to its unique structure, and charged amino acids can cause repulsion, preventing smooth helical structures.
    • β-bends reverse the direction of polypeptide chains, aiding in forming compact protein shapes and are commonly found on protein surfaces.

    Key Takeaways

    • Concept maps are essential for visualizing and integrating biochemistry knowledge.
    • Understanding amino acid properties and their roles as buffers is crucial for grasping protein functionality.
    • The structure of proteins hinges on peptide bonds, with significant implications for health and disease.
    • Secondary structures like α-helices and β-sheets are integral to proteins' three-dimensional shapes and functionalities.### β-Bends and Secondary Structures
    • β-Bends typically connect strands of antiparallel β-sheets and consist of four amino acids, often including proline and glycine, which help introduce kinks in the polypeptide chain.
    • Stabilization of β-bends occurs through hydrogen bonds and ionic interactions.
    • Approximately half of globular proteins are composed of repetitive structures (α-helices and β-sheets) while the other half features loops or coils, which are ordered but less regular.

    Supersecondary Structures (Motifs)

    • Supersecondary structures, or motifs, combine α-helices, β-sheets, and coils to form specific patterns in the protein's core.
    • Motifs play a crucial role in the protein's function and can be linked to DNA binding activities, like the helix-loop-helix motif in transcription factors.

    Tertiary Structure of Globular Proteins

    • Tertiary structure refers to the overall 3D arrangement of protein domains, influenced by the primary structure (amino acid sequence).
    • The compact structure of globular proteins in aqueous solutions features hydrophobic side chains buried internally while hydrophilic groups reside on the surface.

    Domains

    • Domains are functional units within polypeptides and are crucial for structure, often containing supersecondary structural elements.
    • Longer polypeptide chains (over 200 amino acids) typically contain multiple domains that fold independently.

    Interactions Stabilizing Tertiary Structure

    • Disulfide bonds form between cysteine residues to stabilize protein structure and prevent denaturation in extracellular environments.
    • Hydrophobic interactions: Nonpolar amino acids cluster in the interior, while polar/charged residues appear on the surface.
    • Hydrogen bonds enhance solubility by forming between polar side chains and the aqueous environment.
    • Ionic interactions involve attraction between negatively charged and positively charged side chains.

    Protein Folding

    • Folding occurs via ordered pathways within the cell, driven by hydrophobic effects.
    • As proteins fold, secondary structures form first, followed by tertiary structures, leading to a stable, functional conformation known as the native state.

    Denaturation of Proteins

    • Denaturation disrupts secondary and tertiary structures without breaking peptide bonds, caused by heat, solvents, acids, bases, and metals.
    • Denaturation can be reversible or irreversible, impacting protein solubility and leading to aggregation.

    Role of Chaperones in Protein Folding

    • Molecular chaperones are essential for the proper folding of many proteins, preventing premature folding and misfolding during synthesis.
    • Chaperonins, a class of chaperones, form cage-like structures that facilitate correct folding in a protected environment.

    Quaternary Structure of Proteins

    • Quaternary structure involves the assembly of multiple polypeptide chains, stabilized by noncovalent interactions.
    • Isoforms perform identical functions but have different primary structures, while isozymes are enzyme-specific isoforms.

    Protein Misfolding

    • Misfolded proteins can lead to aggregation, associated with various diseases and may result from spontaneous mutation or abnormal processing.
    • Amyloid diseases involve the accumulation of misfolded proteins, with amyloid β (Aβ) implicated in Alzheimer’s disease as a neurotoxic aggregate.

    Prion Diseases

    • Prion diseases are caused by conformational changes in prion proteins (PrP), leading to transmissible spongiform encephalopathies (TSEs) like Creutzfeldt-Jakob disease, without detectable nucleic acids.
    • Normal PrPC can convert to the infectious PrPSc form through changes in conformation, characterized by an increase in β-sheets.

    Summary of Key Concepts

    • Native conformation denotes the functional state of proteins, determined by amino acid sequences and interactions.
    • Protein structure coherence is maintained through secondary, tertiary, and quaternary structures, essential for the protein's biological function.
    • Correct folding depends on chaperones, while dysfunctions in folding lead to denaturation and potential diseases, emphasizing the importance of proper protein structure in health.

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