Protein Structure and Function
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Questions and Answers

What are proteins primarily composed of?

Amino acids

How many different amino acids are commonly found as constituents of mammalian proteins?

  • 300
  • 20 (correct)
  • 15
  • 50

    • All amino acids have a primary amino group.

    True

    What is the pH at which the carboxyl group of amino acids is typically dissociated?

    <p>Approximately 7.4</p> Signup and view all the answers

    Which of the following describes nonpolar amino acids?

    <p>They have an even distribution of electrons.</p> Signup and view all the answers

    Match the following amino acids with their classifications:

    <p>Glycine = Nonpolar Serine = Polar Aspartic Acid = Acidic Lysine = Basic</p> Signup and view all the answers

    Proline differs from other amino acids in that it has a _____ amino group.

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

    What is formed in proteins through peptide linkages?

    <p>Carboxyl and amino groups</p> Signup and view all the answers

    Where do nonpolar amino acids typically cluster in soluble proteins?

    <p>In the interior</p> Signup and view all the answers

    What amino acid is known for its unique geometry that contributes to collagen formation?

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

    Which amino acids have uncharged polar side chains?

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

    Cysteine has a hydroxyl group in its side chain.

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

    What is the term for the bond formed between the side chains of two cysteines?

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

    Which of these amino acids are proton donors at physiological pH?

    <p>Glutamic acid</p> Signup and view all the answers

    What is the characteristic feature of basic amino acids at physiologic pH?

    <p>They accept protons.</p> Signup and view all the answers

    What is the significance of the α-carbon in amino acids?

    <p>It is a chiral carbon.</p> Signup and view all the answers

    Which amino acid abbreviation represents asparagine?

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

    The pH = log 1/[H+] is used to express the concentration of protons in aqueous solution. This formula describes the ______.

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

    At what pH level are acidic amino acid side chains fully ionized?

    <p>At physiological pH.</p> Signup and view all the answers

    Which amino acid is known as a buffer due to its weakly acidic and basic properties?

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

    What are enzymes that hydrolyze peptide bonds termed?

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

    What are the two types of exopeptidases?

    <p>Aminopeptidases and Carboxypeptidases</p> Signup and view all the answers

    Endopeptidases cut at the ends of proteins.

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

    What method is used to determine the amino-terminal residue of a polypeptide?

    <p>Edman degradation</p> Signup and view all the answers

    How can the amino acid sequence of a polypeptide be determined?

    <p>By DNA sequencing</p> Signup and view all the answers

    What is one limitation of indirect protein sequencing?

    <p>It cannot predict the positions of disulfide bonds.</p> Signup and view all the answers

    The secondary structure of polypeptides includes the ___ and beta-sheet.

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

    What term is used for the general arrangements of amino acids near to one another in the linear sequence?

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

    What is the pI of glycine?

    <p>6.1</p> Signup and view all the answers

    At pH 2, to which electrode will glycine move in an electric field?

    <p>positive electrode</p> Signup and view all the answers

    Which amino acid among these has a positively charged side chain at pH 7?

    <p>Arginine (Arg)</p> Signup and view all the answers

    The peptide bond is broken by heating.

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

    In proteins, amino acids are linked by ______ bonds.

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

    What is the first step in determining the primary structure of a polypeptide?

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

    Match the following terms with their definitions:

    <p>Primary structure = Sequence of amino acids in a protein Peptide bond = Covalent bond linking amino acids Secondary structure = Repeated patterns such as α-helices and β-sheets N-terminal = Free amino end of a peptide chain</p> Signup and view all the answers

    Which of the following statements concerning the titration curve for glycine is correct?

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

    Which statement about the two cysteine residues is accurate?

    <p>They can form a disulfide bond under oxidizing conditions.</p> Signup and view all the answers

    What does the Henderson-Hasselbalch equation predict?

    <p>The ionic forms of drugs and changes in pH.</p> Signup and view all the answers

    The pH of the stomach ranges from _____ to _____ .

    <p>1.0, 1.5</p> Signup and view all the answers

    What is the typical pH of blood plasma?

    <p>7.4</p> Signup and view all the answers

    At physiological pH, the α-carboxyl group of amino acids is _____ and the α-amino group is _____.

    <p>Deprotonated; Protonated</p> Signup and view all the answers

    Match the types of side chains with their classification:

    <p>Nonpolar Side Chains = Alanine, Glycine, Isoleucine, Leucine, Methionine, Phenylalanine, Proline, Tryptophan, Valine Uncharged Polar Side Chains = Asparagine, Cysteine, Glutamine, Serine, Threonine, Tyrosine Acidic Side Chains = Aspartic Acid, Glutamic Acid Basic Side Chains = Arginine, Histidine, Lysine</p> Signup and view all the answers

    What is the maximum buffering capacity of a solution?

    <p>pH equal to pKa</p> Signup and view all the answers

    At what pH does alanine exist predominantly as a zwitterion?

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

    The net charge of alanine at pH greater than 10 is -1.

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

    Match the forms of alanine with their net charges:

    <p>Form I = +1 Form II = 0 Form III = -1</p> Signup and view all the answers

    The dissociation constant of the carboxyl group of alanine is called ___.

    <p>K1</p> Signup and view all the answers

    What happens when the pH equals pK1?

    <p>Equal amounts of Forms I and II exist</p> Signup and view all the answers

    What equation can analyze the dissociation of the carboxyl group of alanine?

    <p>Henderson-Hasselbalch equation</p> Signup and view all the answers

    Weak bases generally cross membranes more rapidly than charged molecules.

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

    What is the main factor determining the effective concentration of a permeable drug?

    <p>Relative concentrations of charged and uncharged forms</p> Signup and view all the answers

    Study Notes

    Overview of Proteins and Amino Acids

    • Proteins are abundant and functionally diverse molecules essential for life processes, including metabolism, movement, and immune response.
    • Enzymes facilitate biochemical reactions, while polypeptide hormones regulate bodily functions.
    • Collagen in bones provides a structural framework, akin to steel cables in reinforced concrete.
    • Hemoglobin transports essential molecules in the bloodstream, and immunoglobulins protect against infections.
    • Proteins are linear polymers made from amino acids, each possessing a common structural framework.

    Structure of Amino Acids

    • Over 300 amino acids exist, but only 20 are prevalent in mammalian proteins, coded by DNA.
    • Amino acids consist of:
      • A carboxyl group (-COOH)
      • A primary amino group (-NH2)
      • A distinctive side chain (R-group) attached to the α-carbon.
    • At physiological pH (around 7.4):
      • Carboxyl groups dissociate to form negatively charged carboxylate ions.
      • Amino groups tend to be positively charged.
    • Peptide linkages connect amino acids, limiting available reactive sites except for hydrogen bonding, making side chains crucial for protein function.

    Classification of Amino Acids

    • Amino acids are categorized based on side chain properties:

      • Nonpolar Side Chains:

        • Have even electron distribution; do not participate in hydrogen or ionic bonds.
        • Tend to cluster in aqueous environments, forming hydrophobic interactions.
        • Play essential roles in stabilizing protein structures by filling the protein's interior.

      • Uncharged Polar Side Chains:

        • Carry no net charge at neutral pH but can participate in hydrogen bonding.
        • Contain functional groups that can interact with water and other polar substances.

      • Acidic Side Chains:

        • Contain additional carboxyl groups that can release protons, imparting a negative charge.

      • Basic Side Chains:

        • Feature amino groups that can accept protons, giving them a positive charge.

    Specific Amino Acids

    • Proline: Unique rigid five-membered ring structure, contributes to fibrous collagen and disrupts α-helices in globular proteins.
    • Cysteine: Its sulfhydryl group (-SH) can form disulfide bridges, important for enzyme active sites and protein stabilization.
    • Sickle Cell Anemia Case: Caused by the substitution of glutamate (polar) with valine (nonpolar) in hemoglobin, affecting protein function.

    Importance of Side Chains

    • The side chains determine the amino acid's role in proteins, influencing interactions within proteins and with other molecules.
    • Hydrophobic and hydrophilic properties of side chains guide amino acid positioning in protein structures (interior vs. surface).### Disulfide Bonds in Proteins
    • Cysteines can form covalent cross-links known as disulfide bonds (–S–S–) through oxidation, resulting in cystine dimers.
    • Extracellular proteins, like albumin, utilize disulfide bonds for structural stability and transport functions.

    Amino Acid Properties

    • Amino acids with acidic side chains include aspartic acid and glutamic acid, which act as proton donors.
    • At physiological pH, aspartate and glutamate possess negatively charged carboxylate groups (–COO–).
    • Basic amino acids such as lysine and arginine accept protons and carry a positive charge at physiological pH.
    • Histidine, considered weakly basic, can exhibit either a positive charge or remain uncharged, depending on the environment.

    Amino Acid Abbreviations

    • Each amino acid has a three-letter abbreviation and a one-letter symbol (e.g., Glycine = Gly = G).
    • Unique first letters are used for symbols if only one amino acid corresponds to that letter (e.g., Isoleucine = I).
    • Common amino acids are prioritized for letter assignments to prevent duplication (e.g., Glycine = G, Glutamate = E).

    Optical Isomerism in Amino Acids

    • Amino acids are chiral, except glycine, which has two identical hydrogen atoms on its α-carbon, rendering it optically inactive.
    • Amino acids exist in D (dextrorotatory) and L (levorotatory) forms, with L-designated forms being predominant in proteins.

    Acidic and Basic Properties

    • Amino acids possess weakly acidic α-carboxyl and basic α-amino groups, contributing to their buffering ability in solutions.
    • The Henderson-Hasselbalch equation relates pH, pKa, and the concentrations of a weak acid and its conjugate base, helping describe buffer systems.

    Buffering Capacity

    • Buffers resist pH changes by balancing weak acids with their conjugate bases (e.g., acetic acid and acetate).
    • Maximum buffering occurs at pH equal to pKa, facilitating stability within ±1 pH unit.

    Titration of Amino Acids

    • During titration, amino acids like alanine exhibit different ionic forms: protonated in acidic solutions, zwitterionic (net charge of zero) at isoelectric point, and negatively charged in basic solutions.
    • The carboxyl group of amino acids can dissociate to form negatively charged carboxylate ions, displaying variations in net charge based on solution pH.### Henderson-Hasselbalch Equation and Amino Acids
    • Dissociation Constant (K1): Refers to the carboxyl group of amino acids, denoted as K1 due to a second titratable group being present.
    • Henderson-Hasselbalch Equation: Used to analyze dissociation for alanine, represented as:
      • [ \text{pH} = \text{pK1} + \log\left(\frac{[\text{II}]}{[\text{I}]}\right) ]
    • Forms of Alanine:
      • Form I: Fully protonated form
      • Form II: Isoelectric form
      • Form III: Fully deprotonated form

    Dissociation of Functional Groups

    • Amino Group (K2): The amino group (–NH3+) is a weaker acid than the carboxyl group (–COOH) and has a larger pKa.
    • pKa Values:
      • pK1 for –COOH: 2.3 (most acidic)
      • pK2 for –NH3+: 9.1 (less acidic)
    • Titration Curve: Illustrates the stepwise deprotonation of alanine's groups, indicating critical pH values where buffering occurs.

    Buffering Regions and Isoelectric Point (pI)

    • Buffer Pairs:
      • –COOH/–COO– effective around pK1.
      • –NH3+/–NH2 effective around pK2.
    • Isoelectric Point (pI):
      • At neutral pH (5.7), alanine exists as a dipolar form (Form II) with a net charge of zero.
      • pI calculated as average of pK1 and pK2:
      • [ \text{pI} = \frac{2.3 + 9.1}{2} = 5.7 ]

    Separation of Plasma Proteins

    • Charge-Based Separation: Proteins migrate toward the positive electrode at pH above the pI, indicating a negative charge.

    Amphoteric Nature of Amino Acids

    • Ampholytes: Substances like amino acids can act as both acids and bases, displaying amphoteric properties.

    Applications of Henderson-Hasselbalch Equation

    • pH Calculation: Predicts how pH of solutions is influenced by concentrations of weak acids/salts, such as in the bicarbonate buffer system ([ \text{HCO}_3^- ]).
    • Drug Absorption:
      • Weak acids (e.g., aspirin, pK = 3.5) are more protonated in low pH environments, enhancing membrane permeability.
      • Uncharged drug forms (HA for weak acids and B for weak bases) cross membranes more easily than charged forms.
    • Ionization of Drugs: Ratio of charged to uncharged forms is determined by local pH and the drug's pK value, impacting absorption efficiency.

    Concept Maps for Biochemistry

    • Visualization Tool: Concept maps organize biochemical ideas hierarchically, helping students link concepts together logically.
    • Construction: Consists of concept boxes connected by lines that represent the relationships between ideas, facilitating comprehension.

    Overall Summary

    • The Henderson-Hasselbalch equation is critical for understanding the behavior of amino acids and drug absorption related to pH changes and dissociation constants. The charge properties at specific pH values elucidate the functional dynamics of molecular interactions in biological systems.

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    Ch 1-2 Amino acid and Structure of Protein PDF

    Description

    This quiz covers the fundamental concepts of protein structure and function, focusing on amino acids and their properties. Understand the significance of various amino acids and their roles in protein synthesis and structure. Perfect for students studying biochemistry or molecular biology.

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