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Questions and Answers
What is the formula for calculating the isoelectric pH (pI) of an amino acid?
What is the formula for calculating the isoelectric pH (pI) of an amino acid?
Amino acids with uncharged side chains have only one pKa value.
Amino acids with uncharged side chains have only one pKa value.
False
What is the pKa1 value for alanine?
What is the pKa1 value for alanine?
2.35
The pHi for lysine is approximately _____
The pHi for lysine is approximately _____
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Match the amino acids with their pKa values:
Match the amino acids with their pKa values:
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At the isoelectric point (pI), the charge of the amino acid is:
At the isoelectric point (pI), the charge of the amino acid is:
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Amino acids absorb light at various wavelengths.
Amino acids absorb light at various wavelengths.
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What is the pK2 value for glutamic acid?
What is the pK2 value for glutamic acid?
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In a titration curve, the inflection point represents _____
In a titration curve, the inflection point represents _____
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Which amino acid has the following pKa values: pK1=2.18, pK2=8.95, pK3=10.79?
Which amino acid has the following pKa values: pK1=2.18, pK2=8.95, pK3=10.79?
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How many α-amino acids are used to produce proteins?
How many α-amino acids are used to produce proteins?
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All amino acids have an asymmetric carbon atom.
All amino acids have an asymmetric carbon atom.
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What are the two functional groups present in all α-amino acids?
What are the two functional groups present in all α-amino acids?
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Amino acids are known to be __________ molecules because they can act as acids or bases.
Amino acids are known to be __________ molecules because they can act as acids or bases.
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Match the amino acid with its characteristic:
Match the amino acid with its characteristic:
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Which of the following amino acids belongs to the L series?
Which of the following amino acids belongs to the L series?
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Optical isomerism occurs in amino acids with asymmetric carbon atoms.
Optical isomerism occurs in amino acids with asymmetric carbon atoms.
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Name one classification criterion for amino acids.
Name one classification criterion for amino acids.
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The center of chirality in α-amino acids is the __________ carbon.
The center of chirality in α-amino acids is the __________ carbon.
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Which amino acid does not have an asymmetric carbon and is therefore not chiral?
Which amino acid does not have an asymmetric carbon and is therefore not chiral?
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Which amino acid is known as essential and has an isopropyl side chain?
Which amino acid is known as essential and has an isopropyl side chain?
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Serine is classified as an essential amino acid in the human diet.
Serine is classified as an essential amino acid in the human diet.
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What type of side chain does Methionine contain?
What type of side chain does Methionine contain?
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Isoleucine is an isomer of _____ and is classified as an essential amino acid.
Isoleucine is an isomer of _____ and is classified as an essential amino acid.
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Match the following amino acids with their corresponding side chain type:
Match the following amino acids with their corresponding side chain type:
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Which of the following amino acids is known for forming disulfide bridges?
Which of the following amino acids is known for forming disulfide bridges?
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All acidic amino acids are considered non-essential in the human diet.
All acidic amino acids are considered non-essential in the human diet.
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Which amino acid is categorized under 'Imine acid'?
Which amino acid is categorized under 'Imine acid'?
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Phenylalanine absorbs light in the UV around _____ nm.
Phenylalanine absorbs light in the UV around _____ nm.
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Which amino acid has an imidazole side chain?
Which amino acid has an imidazole side chain?
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Which of the following amino acids is considered essential for children?
Which of the following amino acids is considered essential for children?
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All amino acids are non-polar and hydrophobic.
All amino acids are non-polar and hydrophobic.
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Name one amino acid that is classified as non-essential.
Name one amino acid that is classified as non-essential.
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Amino acids with __________ side chains are classified as acidic.
Amino acids with __________ side chains are classified as acidic.
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Match the following classifications of amino acids with their characteristics:
Match the following classifications of amino acids with their characteristics:
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Which amino acid is classified as a non-polar amino acid?
Which amino acid is classified as a non-polar amino acid?
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Zwitterions have a net charge of zero.
Zwitterions have a net charge of zero.
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What occurs to the -COOH group of an amino acid in an aqueous solution at a specific pH?
What occurs to the -COOH group of an amino acid in an aqueous solution at a specific pH?
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At pH < pHi, the amino acid behaves as a __________.
At pH < pHi, the amino acid behaves as a __________.
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What term describes the pH at which an amino acid has a net charge of zero?
What term describes the pH at which an amino acid has a net charge of zero?
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Study Notes
Amino Acids and Proteins
- Amino acids are acidic organic compounds, containing an amine group (NH2).
- The most common amino acids are α-amino acids.
- The carboxyl (COOH) and amino (NH2) groups are attached to the same carbon atom (α-carbon).
- Only 20 α-amino acids are used to produce proteins.
- Amino acids are amphoteric molecules, acting as both acids and bases.
- α-amino acids have a common structural motif: a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R-group).
- Most amino acids are chiral molecules, with an asymmetric α-carbon bonded to four different substituents.
- Glycine is the only achiral amino acid, lacking an asymmetric carbon.
- Proteins in humans generally belong to the L-series.
- The D-series is found in some bacterial components.
- Amino acids are classified based on side chain properties, polarity, and dietary importance.
- Several classifications are used: chemical nature of the side chain and groups, polarity of the side chain, and dietary importance.
Structure of α-Amino Acids
- α-amino acids have a common structural motif.
- The R group is variable and determines the specific properties of each amino acid.
Stereochemistry of α-Amino Acids
- Most amino acids are chiral molecules.
- The α-carbon is chiral, linked to four different substituents.
- Glycine is the only achiral amino acid.
Optical Isomerism
- The amino acids in human proteins belong to the L-series.
- Enantiomers, spatial conformations, and mirrored forms are possible but have different properties.
- D-amino acids are found in bacterial components and some bacterial peptides.
Classification of Amino Acids
- Amino acids can be classified according to the chemical nature of their side chains.
- These include aliphatic, hydroxylated, sulfur-containing, basic, aromatic, acidic, and imine acids.
- Different amino acids exhibit different properties due to the variations in the side chain.
- Specific categories include hydrophobic/nonpolar, hydrophilic/uncharged polar, and hydrophilic/charged polar groups, categorizing them accordingly.
Amino Acids with Aliphatic Side Chains
- Glycine (G or Gly), Alanine (A or Ala), Valine (V or Val), Leucine (L or Leu), and Isoleucine (I or Ile) all have aliphatic side chains with specific chemical structures.
- Glycine is the simplest, with a single hydrogen atom as the side chain.
- Dietary importance varies among these amino acids.
Glycine (G or Gly)
- Simplest structure; only a hydrogen atom in the side chain.
- Not essential in human diets.
Alanine (A or Ala)
- Methylated side chain (CH3).
- Not essential in human diets.
Valine (V or Val)
- Isopropyl side chain.
- Essential in human diets.
Leucine (L or Leu)
- Isobutyl side chain.
- Essential in human diets.
Isoleucine (I or Ile)
- Isobutyl side chain (same chemical formula as leucine), but a different structure.
- Essential in human diets.
Amino Acids with Hydroxylated Side Chains
- Serine (S or Ser) and Threonine (T or Thr).
- Both have a hydroxyl (-OH) group in their side chains.
Serine (S or Ser)
- Side chain with a hydroxyl group (-OH).
- Phosphorylation site in many proteins.
- Nonessential amino acid.
Threonine (T or Thr)
- Side chain with a hydroxyl group (-OH).
- Phosphorylation site in many proteins.
- Essential amino acid.
Amino Acids with Sulfur Side Chains
- Cysteine (C or Cys) and Methionine (M or Met).
- Both have sulfur atoms in their side chains.
Cysteine (C or Cys)
- Side chain with sulfhydryl group (-SH).
- Forms disulfide bridges, important in protein structure.
- Not essential in human diets.
Methionine (M or Met)
- Side chain with thioether group.
- First amino acid in protein synthesis.
- Essential amino acid.
Amino Acids with Basic Side Chains
- Arginine (R or Arg), Histidine (H or His), and Lysine (K or Lys).
- All have positively charged functional groups in their side chains at physiological pH.
Histidine (H or His)
- Imidazole side chain (aromatic).
- Essential amino acid.
Lysine (K or Lys)
- Amino side chain.
- Essential amino acid.
Arginine (R or Arg)
- Guanidine group at the end of the side chain.
- Positively charged at physiological pH.
- Essential amino acid.
Amino Acids with Aromatic Side Chains
- Phenylalanine (F or Phe), Tyrosine (Y or Tyr), and Tryptophan (W or Trp).
- All have aromatic rings in their side chains.
Phenylalanine (F or Phe)
- Aromatic side chain (phenyl).
- One of the most hydrophobic amino acids.
- Essential amino acid.
Tyrosine (Y or Tyr)
- Aromatic side chain (phenol).
- Phosphorylation site in many proteins.
- Nonessential amino acid in human diets.
Tryptophan (W or Trp)
- Aromatic side chain (Indol).
- Absorption of light in the UV around 280 nm.
- Essential Amino acid.
Amino Acids with Acidic or Amide Side Chains
- Aspartic acid (D or Asp), Asparagine (N or Asn), Glutamic acid (E or Glu), and Glutamine (Q or Gln).
- All have acidic or amide groups in their side chains.
Aspartic Acid (D or Asp)
- Acidic side chain.
- Not essential.
Asparagine (N or Asn)
- Side chain with amide group.
- Not essential.
Glutamic Acid (E or Glu)
- Acidic side chain.
- Not essential.
Glutamine (Q or Gln)
- Side chain with amide group.
- Most abundant amino acid in blood.
- Not essential.
Imine Acid (Proline)
- Cyclic side chain.
- Bond between R group and N-H.
- Not essential.
Classification of amino acids according to polarity:
- Nonpolar (hydrophobic) R groups: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, and Proline.
- Uncharged polar R groups: Serine, Threonine, Cysteine, Asparagine, and Glutamine.
- Charged polar R groups: Acidic (Aspartic acid, Glutamic acid) or Basic (Lysine, Arginine, Histidine).
Zwitterions
- Amino acids exist as zwitterions in aqueous solutions at a specific pH (isoelectric pH, pHi).
- At the pHi, the positive and negative charges balance out, and the amino acid has a net zero charge.
Isoelectric pH (pHi)
- The pH at which an amino acid exists predominantly as a zwitterion.
- The pH of the solution determines whether the amino acid will be in the cationic or anionic form.
- This pH is important for the proper functioning and interactions of proteins.
Determination of pKa
- pKa values are essential for determining the ionization constants of amino acids.
Titration Curves (e.g., Glycine, Alanine)
- Titration curves help to visualize the ionization states of amino acids.
Absorbance of Amino Acids
- Aromatic amino acids (Tryptophan, Tyrosine, Phenylalanine) absorb light at around 280 nm.
Electrical properties of Amino Acids (Electrophoresis)
- Electrophoresis separates amino acids based on their charge in an electric field.
- Different amino acids will migrate toward the electrodes differently depending on their net charge at the pH of the solution.
Protein Separation: SDS-PAGE
- Denaturing technique used to separate proteins based on their molecular weight.
- SDS coats proteins with negative charges, making their migration solely dependent on size.
Estimation of Molecular Weight of Proteins
- By analyzing the migration of protein bands on a gel containing standardized sized proteins , you can determine the molecular weight of the unknown substance.
The Proteins
- Proteins are macromolecules composed of amino acids linked by peptide bonds. Different structures lead to differing properties and functions.
Peptides and Proteins
- Oligopeptides (2-10 amino acids), Polypeptides (10-100 amino acids), and Proteins (more than 100 amino acids) are structural components with a peptide bond linking the amino acids.
Classification of Proteins (based on composition, form, and function)
- Holoproteins: consist only of amino acids.
- Heteroproteins: contain a non-protein component (prosthetic group) besides amino acids (e.g., glycoproteins, lipoproteins).
- Fibrous proteins: extended, insoluble structures (e.g., keratin, collagen).
- Globular proteins: folded, soluble structures (e.g., enzymes, transport proteins).
- Different protein classifications can be based on their functions, such as structural, catalytic, transport, or regulatory roles.
Classifications of proteins based on their functions
- Structural proteins (ex. Keratin, Collagen)
- Catalytic proteins (enzymes-ex. Oxidoreductases, Transferases)
- Transport proteins( ex. Hemoglobin)
- Defense proteins(ex. Immunoglobulins)
- Regulatory proteins
- Reserve proteins
- Hormones
Peptide Bond
- A covalent bond formed between the carboxyl group of one amino acid and the amino group of another.
- Water is eliminated during the formation of each peptide bond.
Stereochemistry of Peptide Bond
- Peptide bonds have a rigid planar structure, due to resonance.
Conformation of Peptide Bond
- The peptide group, with few exceptions, has a trans conformation, with the alpha carbons on opposite sides of the bond.
Primary Structure of Proteins
- The linear sequence of amino acids in a polypeptide chain.
- The primary structure determines the shape and properties of the protein, which in turn determines its function.
- By convention, the amino acid sequence starts at the N-terminus and ends at the C-terminus.
Post-translational Modifications of Proteins
- Processes that modify proteins after their synthesis on the ribosome.
- These modifications can alter the protein's activity, stability, and localization. Some post-translational modifications are: glycation, glycosylation (N-glycosylation and O-glycosylation), acetylation, phosphorylation, and acylation.
Glycation
- A non-enzymatic process where sugars attach to proteins.
- This is largely related to blood glucose, and in particular, can result in prolonged hyperglycemia, which results from poorly controlled diabetes.
Protein Glycosylation
- A common post-translational modification involving the attachment of sugars (glycans) to proteins.
N-glycosylation
- Co-translational modification, attaching sugars in the endoplasmic reticulum.
O-glycosylation
- Post-translational modification adding sugars to the oxygen atoms of serine or threonine residues in the Golgi apparatus; involves N-acetylgalactosamine(GalNAc) as the first sugar in the chain.
Acylation of Proteins
- A post-translational modification involving the attachment of fatty acids to proteins.
Properties of Proteins: Solubility
- Solubility varies greatly between different proteins (fibrous vs. globular), and the factors influencing the solubility of protein molecules include:
- The geometry of the protein structure (size and shape)
- The nature of interactions between proteins (H-bonds etc)
- The concentration of ions or salts and the solution's pH level.
- Organic molecules in the solvent (alcohols etc).
Influence of environmental factors: salt, pH, and organic solvents.
- Changes in these factors can impact protein solubility and interactions.
Applications for protein purification
- Methods for extracting and separating proteins from other biological components, such as extracting a protein from a tissue sample.
Conclusion
- These detailed notes summarize amino acids, proteins, their structures, properties, and functions. Understanding these fundamentals is crucial for any further study in molecular biology or other relevant sciences.
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Description
Explore the fundamentals of amino acids and proteins in this quiz. Learn about the structural motifs, classifications, and the significance of different amino acids within proteins. Test your knowledge of the unique properties that make amino acids crucial for biological functions.
