Protein Structure and Function Overview
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Which one of the following statements concerning the titration curve for a nonpolar amino acid is correct?

  • Point D represents the pK of the amino acid’s carboxyl group.
  • Point C represents the region where the net charge on the amino acid is zero. (correct)
  • The amino acid could be lysine.
  • Point A represents the region where the amino acid is deprotonated.
  • Point B represents a region of minimal buffering.

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

  • The peptide contains a side chain with a secondary amino group.
  • The peptide cannot form an internal disulfide bond.
  • The peptide contains asparagine.
  • The peptide contains a side chain that can be phosphorylated. (correct)
  • The peptide would move to the cathode during electrophoresis at pH 5.

    • What is the ratio of ionized to un-ionized forms of aspirin at pH 7.0?

    10,000 to 1

    All amino acids contain a secondary amino group.

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

    What term is used for the sequence of amino acids in a protein?

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

    The ______ is the most common secondary structure of polypeptides.

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

    What determines the specific characteristics and functions of an amino acid in a protein?

    <p>R group</p> Signup and view all the answers

    What are proteins primarily composed of?

    <p>Amino acids</p> Signup and view all the answers

    Which amino acid has a secondary amino group?

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

    All amino acids are coded for by DNA.

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

    How do nonpolar amino acids behave in an aqueous environment?

    <p>They cluster together in the interior of proteins.</p> Signup and view all the answers

    The covalent bond formed between two cysteine molecules is called a ______.

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

    At physiologic pH, aspartic and glutamic acid are classified as what?

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

    What is the isoelectric point (pI) of alanine?

    <p>5.7</p> Signup and view all the answers

    Histidine can ionize within the physiologic pH range.

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

    Match the following amino acids with their characteristics:

    <p>Serine = Contains a polar hydroxyl group Cysteine = Forms disulfide bonds Aspartate = Proton donor Lysine = Basic amino acid</p> Signup and view all the answers

    What is the primary structure that determines tertiary structure in proteins?

    <p>The primary structure of a polypeptide chain.</p> Signup and view all the answers

    How many amino acids are there per turn in an α-helix?

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

    Proline can disrupt the formation of an α-helix.

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

    What stabilization forces are involved in β-bends?

    <p>Hydrogen and ionic bonds.</p> Signup and view all the answers

    A disulfide bond is formed from the sulfhydryl group (–SH) of two __________ residues.

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

    What is a common characteristic of globular proteins in terms of their structure?

    <p>They have a high density of atoms in the core.</p> Signup and view all the answers

    What is the relationship between chaperones and protein folding?

    <p>Chaperones facilitate correct protein folding.</p> Signup and view all the answers

    Protein denaturation can result in the protein resuming its original structure when conditions return to normal.

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

    What condition arises from the misfolding of amyloid proteins?

    <p>Amyloid diseases.</p> Signup and view all the answers

    The infectious form of the prion protein is designated as __________.

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

    What type of bonds primarily hold quaternary structured proteins together?

    <p>Noncovalent interactions</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

    Which symptoms are characteristic of sickle cell anemia? (Select all that apply)

    <p>Acute chest syndrome</p> Signup and view all the answers

    Individuals with sickle cell trait usually show clinical symptoms.

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

    What amino acid substitution occurs in the β-globin chains of HbS?

    <p>Glutamate is replaced with valine.</p> Signup and view all the answers

    What effect does HbS have on red blood cells at low oxygen tension? (Select all that apply)

    <p>Polymerizes inside the RBC</p> Signup and view all the answers

    What is one variable that increases the severity of sickling in sickle cell anemia?

    <p>Decreased pO2</p> Signup and view all the answers

    What effect does lowering pH have on hemoglobin's oxygen affinity?

    <p>Decreases oxygen affinity</p> Signup and view all the answers

    What is the primary function of 2,3-bisphosphoglycerate (2,3-BPG) in red blood cells?

    <p>Regulates the binding of oxygen to hemoglobin</p> Signup and view all the answers

    Which of these treatments are used for sickle cell anemia? (Select all that apply)

    <p>Antibiotic therapy</p> Signup and view all the answers

    The Bohr effect stabilizes the T (deoxy) form of hemoglobin.

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

    What does hydroxyurea do in the treatment of sickle cell anemia?

    <p>Increases circulating levels of HbF.</p> Signup and view all the answers

    Heterozygotes for the sickle cell gene are more susceptible to severe malaria.

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

    The combination of CO2 and water forms __________ acid in the tissues.

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

    What is the composition of fetal hemoglobin (HbF)?

    <p>Two alpha chains and two gamma chains</p> Signup and view all the answers

    What is the effect of the amino acid substitution in HbC compared to HbS?

    <p>A lysine is substituted for glutamate in HbC.</p> Signup and view all the answers

    How does carbon monoxide (CO) affect hemoglobin binding?

    <p>Forms carboxyhemoglobin</p> Signup and view all the answers

    Methemoglobinemias are characterized by ______.

    <p>chocolate cyanosis</p> Signup and view all the answers

    What are hemoglobinopathies?

    <p>Genetic disorders caused by abnormal hemoglobin production</p> Signup and view all the answers

    Match the following hemoglobin types with their descriptions:

    <p>HbA = Normal adult hemoglobin HbF = Fetal hemoglobin HbA2 = Minor adult hemoglobin HbS = Sickle cell disease hemoglobin</p> Signup and view all the answers

    HbF has a lower affinity for oxygen compared to HbA.

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

    What causes sickle cell anemia?

    <p>A single nucleotide substitution in the gene for β-globin</p> Signup and view all the answers

    What happens to hemoglobin when 2,3-BPG is removed?

    <p>Increases oxygen affinity</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

    What is the most likely change in the primary structure of a mutant protein with disrupted α-helical structure?

    <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's disease?

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

    What is the main function of hemoglobin?

    <p>To transport oxygen from the lungs to the capillaries of the tissues.</p> Signup and view all the answers

    What is unique about myoglobin compared to hemoglobin?

    <p>Myoglobin can bind only one molecule of oxygen.</p> Signup and view all the answers

    Hemoglobin can carry four oxygen molecules.

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

    What type of structure does hemoglobin have?

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

    Study Notes

    Overview of Protein Structure and Function

    • Proteins are vital macromolecules, involved in nearly all life processes.
    • Functions include enzyme activity, regulation of metabolism, muscle contraction, structure in bones, transportation in blood, and immune response.
    • Proteins are linear polymers made from 20 common amino acids coded by DNA.

    Structure of Amino Acids

    • Over 300 amino acids exist, but only 20 are found in mammalian proteins.
    • Each amino acid contains a carboxyl group, an amino group, and a unique side chain (R group) attached to the α-carbon.
    • At physiological pH (~7.4), carboxyl groups dissociate (–COO–) and amino groups are protonated (–NH3+).

    Classification of Amino Acids

    • Nonpolar Amino Acids:

      • Characterized by hydrophobic side chains that do not lose or gain protons.
      • Tend to cluster in the protein's interior in polar environments; on the surface in hydrophobic environments.

    • Uncharged Polar Amino Acids:

      • Include serine, threonine, cysteine, and tyrosine, which can form hydrogen bonds.
      • Cysteine can form disulfide bonds (covalent cross-links), stabilizing protein structure.

    • Acidic Amino Acids:

      • Aspartic acid and glutamic acid act as proton donors, existing in negatively charged forms (aspartate and glutamate) at physiological pH.

    • Basic Amino Acids:

      • Lysine and arginine accept protons and are positively charged at physiological pH; histidine can be either positively charged or neutral.

    Optical Properties and Chirality

    • The α-carbon is a chiral center, leading to D and L stereoisomers.
    • Only L-amino acids are incorporated into proteins; D-amino acids are found in some antibiotics.

    Acidic and Basic Properties

    • Amino acids possess weakly acidic α-carboxyl groups and weakly basic α-amino groups.
    • The Henderson-Hasselbalch equation relates pH, the concentration of acid, and its conjugate base, forming a buffer system.

    Buffers and Titration of Amino Acids

    • Buffers resist pH change; can be created from weak acids and their conjugate bases.
    • Titration demonstrates the release of proton from amino acids, with specific pKa values for titratable groups.
    • For alanine, pK1 (~2.3) corresponds to the carboxyl group, and pK2 (~9.1) to the amino group.

    Isoelectric Point (pI)

    • The pI is the pH where an amino acid has a net charge of zero, averaged between pK1 and pK2.
    • Separation of proteins by charge occurs at pH above pI, showing proteomic variations related to diseases.

    Applications of Henderson-Hasselbalch Equation

    • Useful for studying how pH affects the concentration of ionic drug forms across different environments, influencing absorption and permeability through cell membranes.
    • Understanding drug behavior in physiologic systems is critical for pharmacology and medicine.### Concept Maps in Biochemistry
    • Concept maps visually illustrate relationships between biochemical concepts, aiding students in understanding how topics connect.
    • They are structured hierarchically, displaying general concepts at the top and specific concepts below.
    • Concept maps serve as templates to efficiently organize and integrate new information with existing knowledge.
    • Cross-links in concept maps allow for visualization of complex interconnections between different ideas.

    Amino Acids Structure and Classification

    • Each amino acid features an α-carboxyl group and an α-amino group (except proline, which has a secondary amino group).
    • At physiological pH, the α-carboxyl group dissociates into a negatively charged carboxylate ion, while the α-amino group becomes protonated.
    • Amino acids possess unique side chains (R groups) determining their classification: nonpolar, uncharged polar, acidic (polar negative), or basic (polar positive).
    • All free amino acids and charged residues can function as buffers in biological systems.

    Henderson-Hasselbalch Equation

    • The equation relates pH, pKa, and the ratio of ionized ([A–]) to un-ionized ([HA]) forms, particularly for weak acids.
    • Buffering is effective within ±1 pH unit of the pKa, peaking at pH = pKa when [A–] = [HA].

    Protein Structure Levels

    • Four organizational levels: primary, secondary, tertiary, and quaternary structures characterize proteins.
    • Primary structure is defined by the unique sequence of amino acids linked by peptide bonds, crucial for protein function.

    Peptide Bonds

    • Peptide bonds form between the α-carboxyl group of one amino acid and the α-amino group of another, resulting in stable, covalent connections.
    • These bonds exhibit partial double-bond character, contributing to the rigidity of the polypeptide chain.

    Amino Acid Composition Determination

    • Polypeptides are hydrolyzed using strong acid, separating individual amino acids for analysis through cation-exchange chromatography.
    • Separated amino acids are quantified spectrophotometrically by their reaction with ninhydrin.

    Protein Sequencing Techniques

    • Edman degradation identifies amino acids from the N-terminal end of a polypeptide by labeling and hydrolyzing the first residue repeatedly.
    • Cleavage methods using multiple agents generate overlapping fragments for complex polypeptide sequencing.

    Secondary Structure of Proteins

    • Secondary structure emerges from regular arrangements of amino acids, forming α-helices and β-sheets.
    • α-Helices are stabilized by hydrogen bonds between peptide-bond carbonyl oxygens and amide hydrogens, with 3.6 amino acids per turn.
    • Proline and bulky side chains disrupt α-helices due to steric hindrance.

    β-Sheets Structure

    • β-sheets consist of multiple peptide chains (β-strands) that hydrogen bond, resulting in a pleated surface.
    • β-sheets can be organized in parallel or antiparallel arrangements, contributing to protein stability.

    β-Bends (β-Turns)

    • β-bends reverse the direction of polypeptide chains, helping achieve compact, globular protein shapes.
    • Commonly located on protein surfaces, these bends often include charged amino acid residues.### β-Bends
    • Connect successive strands of antiparallel β-sheets; composed generally of four amino acids.
    • Often includes proline, causing bends, and glycine, with the smallest R group.
    • Stabilized by hydrogen and ionic bonds.

    Nonrepetitive Secondary Structure

    • About half of globular proteins feature repetitive structures such as α-helices and β-sheets.
    • The rest comprises loops or coils, which have less regular structures.
    • "Random coil" describes disordered structures from denatured proteins.

    Supersecondary Structures (Motifs)

    • Combinations of secondary structural elements create specific geometric motifs in globular proteins.
    • Motifs form the core of the protein and are linked by loop regions like β-bends.
    • Specific motifs, including helix-loop-helix, are associated with particular functions.

    Tertiary Structure of Globular Proteins

    • Tertiary structure arises from primary structure; involves folding of domains.
    • Compact structure in aqueous solutions; hydrophobic side chains are buried, while hydrophilic groups are on the surface.

    Domains

    • Fundamental units of structure and function in polypeptides, often with more than 200 amino acids.
    • Combinations of supersecondary structures create domain cores; can fold independently.

    Interactions Stabilizing Tertiary Structure

    • Disulfide Bonds: Covalent links formed by cysteine residues, enhancing protein stability and preventing denaturation.
    • Hydrophobic Interactions: Nonpolar side chains aggregate in the interior, while polar side chains remain on the surface in contact with water.
    • Hydrogen Bonds: Occur between polar side chains and solvent, enhancing protein solubility.
    • Ionic Interactions: Occur between charged groups in side chains, contributing to overall stability.

    Protein Folding

    • Determines the three-dimensional shape of functional proteins; occurs rapidly within the cell.
    • Involves ordered pathways driven by the hydrophobic effect and leads to a low-energy state.

    Denaturation of Proteins

    • Refers to the unfolding and disorganization of protein structures without breaking peptide bonds.
    • Caused by heat, organic solvents, strong acids/bases, detergents, and heavy metal ions.
    • Can be reversible or irreversible; denatured proteins are often insoluble.

    Role of Chaperones in Protein Folding

    • Chaperones, or heat shock proteins, assist in protein folding by stabilizing hydrophobic regions of nascent polypeptides.
    • Include Hsp70, which keeps proteins unfolded during synthesis, and Hsp60, which forms cage-like structures for proper folding.

    Quaternary Structure of Proteins

    • Composed of two or more polypeptide chains, which may be identical or unrelated.
    • Stabilized by noncovalent interactions; subunits may function independently or cooperatively, as seen in hemoglobin.

    Protein Misfolding

    • Can lead to aggregates of misfolded proteins, often associated with aging and diseases.
    • Amyloid Diseases: Misfolding can be caused by mutations or abnormal cleavages, leading to neurotoxic aggregates implicated in conditions like Alzheimer’s, Huntington's, and Parkinson's diseases.

    Alzheimer Disease

    • Characterized by the accumulation of neurotoxic amyloid β peptides, derived from amyloid precursor protein.
    • Involves β-pleated sheet fibrils that are neurotoxic and contribute to cognitive decline.

    Prion Diseases

    • Caused by prion protein (PrP) alterations, leading to transmissible spongiform encephalopathies.
    • Infectious agent, PrPSc, differs from the normal PrPC form based on its three-dimensional structure; infectious prions resist degradation and induce structural changes in healthy proteins.

    Summary

    • Native conformation defines the functional state of a protein.
    • Primary structure determines folding, secondary and tertiary structures stabilize it.
    • Chaperones facilitate folding; denaturation alters structures without breaking peptide bonds.
    • Misfolding and aggregation lead to diseases, highlighting the importance of correct protein conformation for health.

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    Description

    This quiz covers the fundamental aspects of protein structure and function, focusing on amino acids and their roles in biological processes. Learn how proteins serve vital functions in the body, from enzymes to contractile fibers. Test your knowledge on the diverse roles of proteins in living systems.

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