Questions and Answers
What is the role of the α carbon in amino acids?
Which of the following amino acid classes contains the most members?
Which amino acid is unique for having a second hydrogen atom instead of an R group?
How many enantiomers can amino acids have?
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The R group in amino acids is significant because it determines what?
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Which of the following statements about L stereoisomers is true?
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What are the four substituents attached to the α carbon in amino acids?
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Which class of amino acids is likely to be negatively charged at physiological pH?
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How many amino acids belong to the aromatic class?
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What is the primary structure of proteins characterized by?
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Which method uses cross-linked polyacrylamide gels to visualize proteins?
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Which technique is NOT typically used for studying protein structure at atomic resolution?
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Which of the following describes the secondary structure of proteins?
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What can mass spectrometry NOT determine about proteins?
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What does the purification factor in chromatography represent?
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What is the defining feature of oligomeric proteins?
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Which amino acid contributes the highest percentage in bovine cytochrome c?
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What is the primary purpose of 'salting out' in protein purification?
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Which protein class contains a non-amino acid component known as a prosthetic group?
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How is the number of amino acid residues in a protein estimated?
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Which of the following is a characteristic of metalloproteins?
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What is the first step in the process of purifying proteins?
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In column chromatography, what factor affects the migration rates of proteins through the solid phase?
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What is the average molecular weight of an amino acid used for residue estimation?
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What defines a multisubunit protein?
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What is the isoelectric point (pI) formula for amino acids without ionizable side chains?
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Which R group type contributes to the hydrophobic effect in protein structures?
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Cysteine can participate in the formation of which type of bonds?
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At a pH greater than the isoelectric point (pI), how does the amino acid’s net charge behave?
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Which of the following describes the process of forming a peptide bond?
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How many peptide bonds are found in a tripeptide?
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Which of the following amino acid groups does NOT form hydrogen bonds?
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At what pH does a zwitterion of an amino acid occur?
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Which of the following is true about protein molecular weight?
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Which notation indicates the sequence of amino acids in a peptide using one-letter codes?
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What principle does ion-exchange chromatography rely on for protein separation?
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Which type of chromatography would be most effective for separating proteins based on their size?
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In ion-exchange chromatography, which factor can influence protein affinity?
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Which type of chromatography utilizes cation and anion exchangers?
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What will elute first from a gel filtration column?
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What can be used to elute proteins from affinity chromatography?
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Considering a crude cellular extract with a total protein of 10,000 mg, which procedure would significantly reduce protein concentration?
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What is the total activity after the precipitation with ammonium sulfate in the purification table?
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In the purification steps, what happens to specific activity as the sample size decreases?
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What is the function of the bound charged groups in ion-exchange chromatography?
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Study Notes
Amino Acids
- Amino acids consist of an α carbon bonded to four substituents: a carboxyl group, an amino group, a hydrogen atom, and a unique R group (side chain).
- Glycine is unique with a second hydrogen atom in place of an R group.
- Amino acid residues in proteins are L stereoisomers, making them optically active.
- Amino acids are classified into five main groups based on their R groups: nonpolar aliphatic, aromatic, polar uncharged, positively charged, and negatively charged.
pKa Values
- Cysteine features three pKa values:
- pK1 for the carboxyl group: 1.96
- pK2 for the amino group: 10.28
- pK3 for its side chain: 8.18
Types of R Groups
- Nonpolar, Aliphatic R Groups: Contribute to protein structure stability via the hydrophobic effect.
- Aromatic R Groups: Absorb UV light at 270-280 nm and can enhance hydrophobic effects.
- Polar, Uncharged R Groups: Capable of forming hydrogen bonds and disulfide bonds (e.g., cysteine).
- Positively Charged R Groups: Display significant positive charge at physiological pH (7.0).
- Negatively Charged R Groups: Carry a net negative charge at physiological pH (7.0).
Protonation States and Isoelectric Point (pI)
- Amino acids can act as weak acids or bases; zwitterions dominate at neutral pH.
- Titration reveals cation, zwitterion, and anion forms, with pK1 and pK2 defining acidic and basic characteristics, respectively.
- For amino acids without ionizable side chains, pI is calculated as (pK1 + pK2) / 2.
Peptides
- Peptides are chains of amino acids linked by covalent peptide bonds formed via condensation and cleaved by hydrolysis.
- Types of peptides vary by the number of amino acids: dipeptide (2), tripeptide (3), oligopeptide (a few), polypeptide (many, <10 kDa), protein (thousands, >10 kDa).
- Peptides are named from the amino-terminal (N-terminal) to the carboxyl-terminal (C-terminal) residue.
Peptide Composition and Subunits
- Peptides can be multisubunit, formed from multiple polypeptides noncovalently, or oligomeric with identical subunits (protomers).
Protein Composition
- Proteins have highly variable amino acid composition, exemplified by differences in bovine cytochrome c and chymotrypsinogen.
Estimation of Amino Acid Residues
- The number of amino acid residues can be estimated as molecular weight/110, factoring out the water molecule lost during peptide bond formation.
Conjugated Proteins
- Conjugated proteins contain non-amino acid components known as prosthetic groups, including lipids, carbohydrates, phosphate groups, heme, and specific metals.
Protein Separation and Purification
- Proteins can be separated based on size, charge, binding properties, and solubility. Common methods include salt precipitation, fractionation, dialysis, and chromatography.
Column Chromatography
- Protein migration utilizes a buffered solution through a solid phase, with the rate affected by protein properties.
Electrophoresis
- Utilized to visualize and analyze purified proteins based on charge-to-mass ratios. Involves polyacrylamide gels and staining methods for visualization.
Protein Structure Levels
- Four structural levels:
- Primary: Linear sequence and covalent bonds of amino acids.
- Secondary: Patterns like alpha-helices and beta-sheets.
- Tertiary: 3D folding configuration.
- Quaternary: Assembly of multiple polypeptide chains.
Protein Structural Analysis Techniques
- Traditional protein sequencing methods involve protein labeling and protease digestion.
- Advanced techniques include X-ray crystallography, NMR spectroscopy, and Cryo-EM for atomic resolution structure.
- Mass spectrometry offers insights into molecular mass, amino acid sequences, and proteomes.
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Description
This quiz covers the structural features of amino acids, including the α carbon and its four substituents. Dive into the unique characteristics of various amino acids and their role in forming peptides and proteins. Ideal for students studying biochemistry or molecular biology.