Questions and Answers
Classify the following molecule: ampipathic?
Classify the following molecule: hydrophilic?
Classify the following molecule: hydrophobic?
What is the pH of 1x(10^-9) M sulfuric acid (H2SO4)?
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How many carbons does this molecule contain?
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How many hydrogens are present in this molecule?
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How many of these hydrogens can engage in hydrogen bonding?
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Which of the following curve shapes corresponds most closely to performing a full titration of the amino acid isoleucine?
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What letter (A to E) represents the peptide bond that connects the two residues?
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Which bond(s) A to E do(es) not rotate freely?
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What amino acid (AA) is repeated here?
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When the pH is less than the pKa in the reaction (H+) + (A-)→HA, which statement is correct?
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When the pH is less than the pKa in the reaction (H+) + (A)→(HA+), which statement is correct?
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What is the pH of a 1 liter solution where you mixed lactic acid and NaOH so that the final concentrations are 0.35 M lactic acid and 0.15 M sodium hydroxide?
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Which atom/functional group ionizes in one of the functional groups on this molecule?
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At what approximate pH does this molecule ionize?
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Assuming that the R group does not ionize, what is the net charge on this amino acid at pH = 7?
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Which acid (and its conjugate base) would be the best buffer at pH = 3.7?
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The hydrogen bonds that cause the formation of an alpha helix occur mainly between which components?
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Identify which of these synthetic polypeptides can form an alpha helix at the given pH values.
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Which substitution would you choose for serine 146, given a goal of maintaining size/shape but changing properties?
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What type of amino acids are most likely to appear in the interior of a protein?
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A word that describes a protein that is in a dysfunctional state is?
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Which of the following is a better statement of Levinthal's paradox?
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Which types of interactions are primarily responsible for maintaining protein secondary structures?
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What does it mean for a protein to be in the 'native conformation'?
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The pH of a black coffee is ~5, while the pH of lemon juice is ~2. Lemon juice has?
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Which of the following is the most accurate and comprehensive definition of chiral isomers?
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Design a coiled-coil protein for a nanotechnological application. What amino acid will you put at position d/d'?
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What amino acid will you put at position a/a' in the coiled-coil protein design?
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What amino acid will you put at position e/e' in the coiled-coil protein design?
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What amino acid will you put at position f/f' in the coiled-coil protein design?
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How many equivalents of NaOH will it take to completely titrate phosphoric acid?
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At pH = 14, which of the molecular species above is predominant?
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At pH = 6, which of the molecular species above is predominant?
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What secondary structure primarily composes the oxygen-binding protein myoglobin?
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The impression of open space in myoglobin is likely correct.
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Which of the tri-peptides above is most likely to be found as part of a transmembrane alpha helix?
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Which of the tri-peptides above is most likely to be phosphorylated?
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For option E, what will be the total charge for the tri-peptide at pH 1?
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Study Notes
Key Terms and Definitions
- Amphipathic: Molecules that possess both hydrophobic and hydrophilic regions, influencing their behavior in solution.
- Hydrophilic: Molecules that interact favorably with water, often polar or charged.
- Hydrophobic: Molecules that repel water and do not interact well with aqueous environments.
pH and Solutions
- pH of Sulfuric Acid: 1x(10^-9) M sulfuric acid approximates a pH slightly below 7, indicating a dilute acidic solution.
- pH of Lactic Acid and NaOH Mixture: A solution containing 0.35 M lactic acid (pKa = 3.9) and 0.15 M sodium hydroxide yields a pH of approximately 3.78.
Amino Acids and Titration
- Amino acid isoleucine undergoes full titration represented by a specific curve shape, typically exhibiting sigmoidal properties.
- Peptide bonds, represented by letter C, connect amino acid residues, while certain bonds do not freely rotate.
Hydrogen Bonding and Molecular Structure
- No hydrogens from the specified molecule can engage in hydrogen bonding if it's saturated or lacks donor/acceptor sites.
- Molecular structures such as alpha helices are stabilized primarily by hydrogen bonds between backbone atoms, not R-group interactions.
Protein Structure and Properties
- Specific amino acids, like serine, arginine, and their substitutions impact protein interactions and structural integrity.
- Hydrophobic amino acids are typically found in the interior of proteins, contributing to stability.
- Denatured proteins are dysfunctional, losing their native conformation, which is their lowest energy and functional state.
Acid-Base Chemistry
- Lemon juice (pH ~2) has approximately 1000 times higher hydrogen ion concentration than black coffee (pH ~5), illustrating the logarithmic nature of pH scale.
- The net charge of amino acids at pH 7 can vary depending on their functional groups' ionization states.
Synthesis and Coiled-Coil Proteins
- Design of coiled-coil proteins requires careful selection of amino acids that fulfill specific roles while considering their properties under varying pH conditions.
- Specific positions in the coiled-coil helix (designated a/a', d/d', g/g') determine the overall structure and functionality based on chosen amino acids.
Tri-Peptides and Protein Structure
- Characteristics of tri-peptides vary based on amino acid composition, influencing their likelihood to reside in transmembrane regions or to undergo post-translational modifications like phosphorylation and disulfide bond formation.
Charge Considerations
- Charge calculations for peptides at specific pH levels are crucial for understanding their behavior in biological systems, with implications for protein interactions and stability.
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Description
Test your understanding of key concepts in biochemistry with this Exam 1 flashcard quiz. Each card challenges you to classify molecules as hydrophobic, hydrophilic, or amphipathic. Perfect for students preparing for their biochemistry exams.
