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Questions and Answers
What happens to glutamate side chain at a lower pH compared to a higher pH?
What happens to glutamate side chain at a lower pH compared to a higher pH?
- Deprotonates at lower pH, remains protonated at higher pH
- Protonates at all pH levels
- Remains neutral at all pH levels
- Remains protonated at lower pH, deprotonates at higher pH (correct)
What happens to arginine side chain at a higher pH compared to a lower pH?
What happens to arginine side chain at a higher pH compared to a lower pH?
- Protonates at higher pH, deprotonates at lower pH
- Deprotonates at higher pH, remains protonated at lower pH (correct)
- Deprotonates at all pH levels
- Remains protonated at all pH levels
Which type of group is present in the side chain of arginine amino acid?
Which type of group is present in the side chain of arginine amino acid?
- Guanidinium group (correct)
- Amide group
- Carboxylic acid group
- Carbonyl group
In basic conditions, what happens to negatively charged side chains?
In basic conditions, what happens to negatively charged side chains?
At what pH does the carboxylic acid group in glutamate start to deprotonate?
At what pH does the carboxylic acid group in glutamate start to deprotonate?
What is the role of hydrogen ions in the side chains' ionization process?
What is the role of hydrogen ions in the side chains' ionization process?
Which aromatic amino acid has the strongest absorbance peak around 280 nm?
Which aromatic amino acid has the strongest absorbance peak around 280 nm?
What does the height of the peak or the intensity of absorbance correlate with in a protein sample?
What does the height of the peak or the intensity of absorbance correlate with in a protein sample?
Which of the following amino acids is not typically found in the interior of proteins, away from water-exposed surfaces?
Which of the following amino acids is not typically found in the interior of proteins, away from water-exposed surfaces?
What is the significance of the specific wavelengths at which proteins absorb UV light most strongly?
What is the significance of the specific wavelengths at which proteins absorb UV light most strongly?
What technique is used to analyze the concentration and purity of proteins in a sample?
What technique is used to analyze the concentration and purity of proteins in a sample?
Which of the following amino acids has side chains containing alcohol (-OH) groups?
Which of the following amino acids has side chains containing alcohol (-OH) groups?
Which amino acid contains a pyrroline ring as part of its side chain?
Which amino acid contains a pyrroline ring as part of its side chain?
Which amino acid derivative is used as the initial amino acid in the synthesis of proteins in prokaryotes and in mitochondria of eukaryotes?
Which amino acid derivative is used as the initial amino acid in the synthesis of proteins in prokaryotes and in mitochondria of eukaryotes?
Which amino acid analogue has a selenium atom (-SeH) replacing the sulfur atom in cysteine?
Which amino acid analogue has a selenium atom (-SeH) replacing the sulfur atom in cysteine?
What is the approximate pKa value of the amino group (NH2) in amino acids?
What is the approximate pKa value of the amino group (NH2) in amino acids?
What is the pKa value of the carboxyl group (COOH) in amino acids?
What is the pKa value of the carboxyl group (COOH) in amino acids?
At physiological pH (around 7.4), most amino acids have a net charge close to which of the following?
At physiological pH (around 7.4), most amino acids have a net charge close to which of the following?
What is the formula for calculating the isoelectric point (pI) of an amino acid?
What is the formula for calculating the isoelectric point (pI) of an amino acid?
Which amino acids may have a third pKa value associated with their side chain ionization in pI calculations?
Which amino acids may have a third pKa value associated with their side chain ionization in pI calculations?
In the Henderson-Hasselbalch equation, what does [A-] represent?
In the Henderson-Hasselbalch equation, what does [A-] represent?
What mainly contributes to the charges in a polypeptide chain after polymerization?
What mainly contributes to the charges in a polypeptide chain after polymerization?
'Chains of linked amino acids' is known as what in the context of polypeptides?
'Chains of linked amino acids' is known as what in the context of polypeptides?
How are individual residues in a polypeptide chain identified?
How are individual residues in a polypeptide chain identified?
What is the main property that Hydrophobic Interaction Chromatography (HIC) utilizes for molecule separation?
What is the main property that Hydrophobic Interaction Chromatography (HIC) utilizes for molecule separation?
In Size Exclusion Chromatography (SEC), which molecules elute first?
In Size Exclusion Chromatography (SEC), which molecules elute first?
What is a major advantage of Affinity Chromatography over other chromatography techniques?
What is a major advantage of Affinity Chromatography over other chromatography techniques?
What type of molecules get trapped in the porous beads in Size Exclusion Chromatography?
What type of molecules get trapped in the porous beads in Size Exclusion Chromatography?
Which chromatography technique uses gradient elution to change the composition of the mobile phase over time?
Which chromatography technique uses gradient elution to change the composition of the mobile phase over time?
In Affinity Chromatography, what is the binding material that interacts with the desired protein?
In Affinity Chromatography, what is the binding material that interacts with the desired protein?
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Study Notes
Amino Acid Properties
- Aromatic amino acids (tryptophan, tyrosine, phenylalanine) absorb UV light at specific wavelengths, allowing for protein concentration and purity analysis
- UV absorbance graphs show peaks at specific wavelengths, correlating with protein concentration
Amino Acid Types
- Alcohol-containing amino acids: serine, threonine, asparagine, glutamine
- Other amino acids:
- Homoserine: derivative of serine
- Homocysteine: derivative of cysteine
- N-Formylmethionine: used in protein synthesis in prokaryotes and eukaryotic mitochondria
- Selenocysteine: analogue of cysteine with selenium instead of sulfur, involved in antioxidant functions
- Pyrrolysine: uncommon amino acid found in certain archaea and bacteria, used in specific proteins
Amino Acid Ionization
- Amino acids undergo ionization due to acidic (carboxyl) and basic (amino) groups, leading to different forms depending on pH
- Amino acids typically have two pKa values, corresponding to the ionization of their acidic and basic groups
- Isoelectric point (pI) is the pH at which an amino acid carries no net charge, calculated as pI = (pK1 + pK2) / 2
Polypeptides
- Chains of linked amino acids, known as residues, with each residue identified by its 3-letter or 1-letter code
- Amino acids in a polypeptide chain lose most of their charges from their carboxyl and amino groups due to polymerization
- Resulting charges mainly come from the side chains of the amino acids
Ionization of Side Chains
- Side chains of amino acids can undergo ionization, transitioning between protonated (acidic) and deprotonated (basic) forms depending on pH
- Positively charged side chains gain a proton in acidic conditions, becoming neutral
- Negatively charged side chains lose a proton in basic conditions, becoming neutral
Specific Amino Acids
- Glutamate: contains a carboxylic acid group in its side chain, which can be protonated or deprotonated depending on pH
- Arginine: contains a guanidinium group in its side chain, which can be protonated or deprotonated depending on pH
Chromatography Techniques
Size Exclusion Chromatography (SEC) / Gel Filtration Chromatography
- Separates proteins based on size and shape
- Utilizes porous beads in the column that allow smaller molecules to enter and take longer paths, while larger molecules pass through more quickly
- Larger molecules elute first, followed by smaller ones
- Gentle on biomolecules and doesn't require a mobile phase
Affinity Chromatography
- Antibody-antigen interaction: desired protein binds to specific antigen in the column, while non-binding proteins pass through
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