Podcast Beta
Questions and Answers
What type of protein includes a heme unit as its prosthetic group?
Which of the following interactions is primarily responsible for protein stability?
What describes the spatial arrangement of the polypeptide backbone?
Which characteristic of a peptide bond contributes to its rigidity and resistance to conformational change?
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Which of the following statements about conformational changes in proteins is true?
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Which of the following amino acids is classified as nonpolar?
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What is a common characteristic of polar uncharged amino acids?
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Which amino acid is considered semi-essential for children?
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Which groups of amino acids are positively charged at physiologic pH?
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What best describes zwitterions in amino acids?
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Which amino acid is categorized as acidic?
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Which amino acids are classified as branched-chain amino acids?
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What is the primary structure of a protein composed of?
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What is the primary function of the side chain group (R-group) in an amino acid?
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Which of the following amino acids is classified as a polar basic amino acid?
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Which chemical group in an amino acid can accept a proton?
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Which amino acid is the simplest and achiral?
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In the context of protein structure, what is an oligopeptide?
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Which class of amino acids possesses both a carboxyl and an amino group?
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What is a characteristic feature of enantiomers in amino acids?
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Which of the following is not a common function of proteins?
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What element is not commonly found in proteins?
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What role does chirality play in amino acids?
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What type of amino acids are commonly found in beta turns?
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Which type of protein is characterized by a rounded, spherical shape and typically functions in a biochemical capacity?
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Which of the following statements about keratin is true?
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What characterizes a supersecondary structure?
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What type of keratin is known for being less pliable and is found in structures like hair and nails?
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Which structure is described as having irregularities within antiparallel beta-sheets?
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What type of forces are primarily involved in maintaining the tertiary structure of proteins?
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Which of the following is an example of a fibrous protein?
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What definition best describes configuration in the context of molecular structure?
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Which of the following does NOT affect the stability of a protein's conformation?
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In the alpha helix structure, how many amino acids are typically found per turn?
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What is the pitch of an alpha helix in angstroms (Å)?
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Which statement regarding the beta-pleated sheet is correct?
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What is a primary function of torsional angles in protein folding?
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Which of the following amino acids is known to act as an alpha-helix breaker?
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What type of beta sheet features hydrogen bonding chains running in opposite directions?
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Study Notes
Proteins and Peptide Bonds
- Proteins are the most abundant organic molecules in the human body.
- Composed of carbon, hydrogen, oxygen, nitrogen, and some contain sulfur and phosphorus.
- Monomer unit of proteins is an amino acid.
- Peptide bonds (amide bonds) form between amino acids.
- Peptide: unbranched chain of amino acids.
- Oligopeptide: 10-20 amino acid residues.
Functions of Proteins
- Structural support
- Enzymes
- Hormones and receptors
- Immunity
- Fluid and acid-base balance
Amino Acid
- Building block of protein.
- Contains both an amino group and a carboxyl group.
- α-amino acid: amino group and carboxyl group are attached to the α-carbon atom.
- R denotes a side chain group.
Amino Acid Classification
-
Non-polar amino acids:
- Zero net charge
- Form hydrophobic interactions
- Found in the interior of the protein
- Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline
-
Polar uncharged amino acids:
- Zero net charge
- Form hydrogen bonds
- Found on the surface of the protein
- Serine, Threonine, Tyrosine (contain -OH), Cysteine (-SH), Asparagine, Glutamine (amides)
-
Charged amino acids:
- Positive (acidic) or negative (basic) net charge
- Form ionic interactions
- Found on the surface of the protein
- Acidic: Aspartate, Glutamate
- Basic: Arginine, Lysine, Histidine
Essential Amino Acids
- Cannot be synthesized in the body.
- Semi-essential amino acids: required for growth in children, but not for adults.
-
Barone Essential Amino Acid Mnemonic: PVT.TIM HALL
- Phenylalanine, Valine, Tryptophan
- Threonine, Isoleucine, Methionine
- Histidine, Arginine, Lysine (ketogenic), Leucine (ketogenic)
Zwitterion
- Has a positive charge on one atom and a negative charge on another atom with no net charge.
- Amino acids can serve as buffers in aqueous solutions.
Types of Conjugated Proteins
-
Hemoproteins:
- Prosthetic group: heme unit
- Hemoglobin, myoglobin
- Carrier of O2 in blood, oxygen binder in muscles
Protein Stability
-
Chemical Factors:
- Disulfide bonds
- Hydrophobic interactions (predominant)
- Hydrogen bonding
- Van der Waals interactions
- Increase in IMF, more stable due to decreased Gibbs free energy change (ΔG)
Peptide Bond
- Rigid planar trans configuration
- Partial (about 40%) double bond character between α-amino nitrogen of one amino acid to the carbonyl carbon of the next.
- Keeps peptide links relatively resistant to conformational change
Torsional Angles
- Ψ (psi): allowed rotation for –Cα–C=O
- Ф (phi): allowed rotation for –N–Cα–
- Limited rotation due to steric and torsional strains
- Ramachandran diagram indicates allowed conformations of polypeptides
Conformation & Configuration
-
Conformation: Spatial relationship of every atom in a molecule.
- Interconversion between conformers occurs with retention of configuration.
-
Configuration: Geometric relationship between a given set of atoms.
- Interconversion of configurational alternatives requires breaking and reforming covalent bonds.
Protein Conformation
- Spatial arrangement of atoms in a molecule (protein).
- Native proteins: functional and folded conformation.
- Folding must achieve a decrease in Gibbs free energy change for a protein to be stable.
- Stability is the tendency to maintain a native conformation.
Secondary Structure
- Conformation of the polypeptide backbone
- Spatial arrangement of the polypeptide backbone.
- Alpha helix:
- Right-handed coiled spring shape (helix).
- Stabilized by intramolecular hydrogen bonds.
- Hydrogen bonds are parallel to the axis of the helix.
- 3.6 amino acid residues per turn.
- Pitch: 5.4 Å (0.54nm) rise per turn.
- Amino acid side chains (R groups) project outward from the helix.
- Beta pleated sheet:
- Highly extended polypeptide backbone.
- Zigzag or pleated pattern.
- R groups of adjacent amino acid residues project in opposite directions.
- Hydrogen bonds occur between neighboring polypeptide chains.
- Parallel β sheet: H-bonded chains run in the same direction.
- Antiparallel β sheet: H-bonded chains run in the opposite direction.
- β-Loops:
- Short segments of amino acids that join two units of the secondary structure (e.g., two adjacent strands of an antiparallel β sheet).
- 180° turn involving 4 amino acid residues.
- Structural role.
- β-Bulge:
- Irregularity in antiparallel β-sheets.
- Hydrogen bonding between 2 residues from one strand with 1 residue from the other.
Super Secondary Structure
- Also known as motifs.
- Intermediate in scale between secondary and tertiary structures.
- A recognizable folding pattern involving 2 or more elements of secondary structure and the connection/s between them.
- Examples:
- β-α-β loop
- α-α unit (helix-turn-helix)
- β-meander
- Greek key motif
Fibrous and Globular Proteins
- Fibrous: - Long narrow rod. - Structural role. - Mostly insoluble in water. - Repetitive amino acid sequence. - Examples: collagen, keratin
- Globular: - Rounded/spherical. - Functional role. - Mostly water soluble. - Irregular amino acid sequence. - Examples: hemoglobin, enzymes, immunoglobulins
Keratin
- Occurs in all higher vertebrates.
- Found in hair, nails, claws, wool, quills, feathers, horns, hooves, and skin.
-
α-Keratins: found in mammals.
- Right-handed α-helix.
- Two α-helices coil each other to form a left-handed supercoil.
- Rich in Cys residues that form disulfide bonds, linking filaments.
- Hard keratin: hair, horn, nail (less pliable).
- Soft keratin: skin, callus.
-
β-Keratins: occur in birds and reptiles.
- Provides waterproofing and prevents drying.
- β-sheet pattern in native state.
Permanent Wave in Hair
-
Forces Involved in 3° Structure:
- Disulfide bonds.
- Hydrophobic interactions.
- Hydrogen bonding.
- Van der Waals interactions.
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Description
This quiz explores the structure, function, and classification of proteins and peptides, focusing on amino acids and their roles in biological systems. Test your knowledge on how peptide bonds form and the diverse functions proteins serve in the human body.
