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Questions and Answers
Which amino acid is characterized by a cyclic structure that reduces structural flexibility in polypeptides?
Which amino acid is characterized by a cyclic structure that reduces structural flexibility in polypeptides?
- Alanine
- Proline (correct)
- Isoleucine
- Methionine
What effect do the side chains of alanine, valine, leucine, and isoleucine mainly contribute to within proteins?
What effect do the side chains of alanine, valine, leucine, and isoleucine mainly contribute to within proteins?
- Hydrophilic interactions
- Electrostatic interactions
- Disulfide bond formation
- Hydrophobic effect (correct)
Which amino acid is considered to have the simplest structure among the nonpolar aliphatic R groups?
Which amino acid is considered to have the simplest structure among the nonpolar aliphatic R groups?
- Isoleucine
- Glycine (correct)
- Phenylalanine
- Methionine
Which of the following amino acids has a nonpolar thioether group in its side chain?
Which of the following amino acids has a nonpolar thioether group in its side chain?
Which aromatic amino acid is significantly more polar due to the presence of a hydroxyl group?
Which aromatic amino acid is significantly more polar due to the presence of a hydroxyl group?
What occurs during the formation of a peptide bond?
What occurs during the formation of a peptide bond?
Among the aromatic amino acids, which one absorbs ultraviolet light the most strongly?
Among the aromatic amino acids, which one absorbs ultraviolet light the most strongly?
What structural characteristic primarily differentiates tryptophan from the other aromatic amino acids?
What structural characteristic primarily differentiates tryptophan from the other aromatic amino acids?
Which reaction is primarily favored under standard biochemical conditions involving dipeptides?
Which reaction is primarily favored under standard biochemical conditions involving dipeptides?
What is the primary contribution of phenylalanine to the spectroscopic properties of proteins?
What is the primary contribution of phenylalanine to the spectroscopic properties of proteins?
What term is used for a molecule consisting of two amino acids linked by one peptide bond?
What term is used for a molecule consisting of two amino acids linked by one peptide bond?
What is the role of the α-amino group in peptide bond formation?
What is the role of the α-amino group in peptide bond formation?
What type of reaction is peptide bond formation categorized under?
What type of reaction is peptide bond formation categorized under?
How many amino acids are required to form a tripeptide?
How many amino acids are required to form a tripeptide?
What defines a polypeptide in contrast to a protein?
What defines a polypeptide in contrast to a protein?
What process occurs when peptide bonds are broken involving water?
What process occurs when peptide bonds are broken involving water?
What is primarily assessed to monitor the purification of a protein?
What is primarily assessed to monitor the purification of a protein?
Which level of protein structure describes the sequence of amino acid residues?
Which level of protein structure describes the sequence of amino acid residues?
What do we refer to when discussing the three-dimensional folding of a polypeptide?
What do we refer to when discussing the three-dimensional folding of a polypeptide?
Which term describes stable arrangements of amino acid residues leading to recurring patterns?
Which term describes stable arrangements of amino acid residues leading to recurring patterns?
What type of structure involves proteins that consist of multiple polypeptide subunits?
What type of structure involves proteins that consist of multiple polypeptide subunits?
Why is the sequence of amino acid residues significant in proteins?
Why is the sequence of amino acid residues significant in proteins?
In which structure do covalent bonds, such as peptide and disulfide bonds, play a critical role?
In which structure do covalent bonds, such as peptide and disulfide bonds, play a critical role?
What is a significant characteristic of tertiary structure?
What is a significant characteristic of tertiary structure?
Which amino acids are classified as polar, uncharged R groups?
Which amino acids are classified as polar, uncharged R groups?
What contributes to the polarity of serine and threonine?
What contributes to the polarity of serine and threonine?
Cysteine can form which type of bond when oxidized?
Cysteine can form which type of bond when oxidized?
Which amino acid has a pK near neutrality and can exist in both positively charged and uncharged forms at pH 7.0?
Which amino acid has a pK near neutrality and can exist in both positively charged and uncharged forms at pH 7.0?
What is the isoelectric point (pI) of glycine?
What is the isoelectric point (pI) of glycine?
What is a key role of disulfide bonds in proteins?
What is a key role of disulfide bonds in proteins?
At which pH does glycine exhibit a net negative charge?
At which pH does glycine exhibit a net negative charge?
Which of the following amino acids is considered positively charged at pH 7.0?
Which of the following amino acids is considered positively charged at pH 7.0?
What type of amino acids have the most hydrophilic R groups?
What type of amino acids have the most hydrophilic R groups?
What type of form does glycine predominantly take at its isoelectric point?
What type of form does glycine predominantly take at its isoelectric point?
What happens when asparagine and glutamine undergo hydrolysis?
What happens when asparagine and glutamine undergo hydrolysis?
What happens to glycine at pH 1.0?
What happens to glycine at pH 1.0?
Which statement is true about the pK values of amino acids resembling glycine?
Which statement is true about the pK values of amino acids resembling glycine?
What causes glycine molecules to have greater net electric charge as the pH deviates from its isoelectric point?
What causes glycine molecules to have greater net electric charge as the pH deviates from its isoelectric point?
What charge does glycine have at pH 2.34?
What charge does glycine have at pH 2.34?
Which of the following is not true about the general properties of amino acids with similar structures to glycine?
Which of the following is not true about the general properties of amino acids with similar structures to glycine?
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Study Notes
Nonpolar, Aliphatic R Groups
- Amino acids with nonpolar and hydrophobic R groups include alanine, valine, leucine, isoleucine, and proline.
- These side chains cluster together, stabilizing protein structures through the hydrophobic effect.
- Glycine has the simplest structure; its small side chain weakly contributes to the hydrophobic effect.
- Methionine contains a slightly nonpolar thioether group in its side chain.
- Proline has a cyclic structure and a secondary amino group, granting it rigidity and reducing the flexibility of polypeptide regions.
Aromatic R Groups
- Phenylalanine, tyrosine, and tryptophan possess aromatic side chains that are primarily hydrophobic.
- Tyrosine can form hydrogen bonds due to its hydroxyl group and is significant in enzyme function.
- Tryptophan and tyrosine absorb ultraviolet light around 280 nm; phenylalanine absorbs less, influencing protein characterization.
- Absorbance spectra show that tryptophan absorbs UV light significantly more than tyrosine.
Polar, Uncharged R Groups
- This group includes serine, threonine, cysteine, asparagine, and glutamine, which are hydrophilic because they can form hydrogen bonds with water.
- Serine and threonine have polar hydroxyl groups; asparagine and glutamine have polar amide groups.
- Cysteine has a modestly polar sulfhydryl group, capable of weak hydrogen bonding and oxidative dimerization to form cystine via disulfide bonds.
- Disulfide bonds can stabilize the structure of proteins by linking polypeptide chains or regions.
Positively Charged (Basic) R Groups
- Positively charged amino acids include lysine (with a primary amino group), arginine (with a guanidinium group), and histidine (with an imidazole group).
- Histidine can be positively charged or neutral at pH 7.0, functioning as a proton donor/acceptor in enzyme activity.
- Glycine can’t ionize at its side chain; its isoelectric point (pI) is the average of its carboxyl and amino group pK values, calculated at 5.97.
- Glycine will migrate toward positive or negative electrodes depending on pH relative to its pI.
Amino Acids and Acid-Base Properties
- Amino acids with a single α-amino group and α-carboxyl group exhibit titration curves similar to glycine.
- Common pK values: carboxyl group's pK between 1.8 to 2.4 and amino group's pK between 8.8 to 11.0.
- Peptide bonds form through a condensation reaction, linking amino acids and releasing water; its reverse is hydrolysis.
- Oligopeptides consist of a few amino acids, while polypeptides contain many, with proteins often formed from thousands of residues.
Protein Structure
- The primary structure consists of the sequence of amino acid residues linked by peptide and disulfide bonds.
- Secondary structure refers to stable arrangements within a polypeptide, like α-helices or β-sheets.
- Tertiary structure pertains to the overall 3D folding of a single polypeptide chain.
- Quaternary structure describes the spatial arrangement of multiple polypeptide subunits in a protein complex.
- Primary structure's significance links amino acid sequences closely to protein function, influencing biochemical analysis and functional studies.
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