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Questions and Answers
Classify the following molecule: ampipathic?
Classify the following molecule: ampipathic?
Classify the following molecule: hydrophilic?
Classify the following molecule: hydrophilic?
Classify the following molecule: hydrophobic?
Classify the following molecule: hydrophobic?
What is the pH of 1x(10^-9) M sulfuric acid (H2SO4)?
What is the pH of 1x(10^-9) M sulfuric acid (H2SO4)?
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How many carbons does this molecule contain?
How many carbons does this molecule contain?
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How many hydrogens are present in this molecule?
How many hydrogens are present in this molecule?
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How many of these hydrogens can engage in hydrogen bonding?
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?
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?
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?
Which bond(s) A to E do(es) not rotate freely?
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What amino acid (AA) is repeated here?
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?
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?
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?
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?
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?
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?
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?
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?
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.
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?
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?
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?
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?
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?
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'?
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?
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?
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'?
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?
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?
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?
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?
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?
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?
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?
What secondary structure primarily composes the oxygen-binding protein myoglobin?
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The impression of open space in myoglobin is likely correct.
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?
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?
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?
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.
