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What type of secondary structure is primarily formed by keratin?
What type of secondary structure is primarily formed by keratin?
What role do disulfide bonds play in proteins?
What role do disulfide bonds play in proteins?
In Anfinsen's experiment, what was concluded about protein structure?
In Anfinsen's experiment, what was concluded about protein structure?
Which protein is primarily responsible for oxygen transport?
Which protein is primarily responsible for oxygen transport?
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What proteins are involved in transporting cholesterol in the body?
What proteins are involved in transporting cholesterol in the body?
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What is the main function of myoglobin in the body?
What is the main function of myoglobin in the body?
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Which type of protein structure do β sheets belong to?
Which type of protein structure do β sheets belong to?
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What is the relationship between myoglobin and hemoglobin?
What is the relationship between myoglobin and hemoglobin?
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What is the primary role of proteins within a cell?
What is the primary role of proteins within a cell?
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What does a pKa value indicate about a group in relation to pH?
What does a pKa value indicate about a group in relation to pH?
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When are groups primarily protonated?
When are groups primarily protonated?
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What structural feature accounts for peptide bonds maintaining a planar configuration?
What structural feature accounts for peptide bonds maintaining a planar configuration?
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What form of amino acids are found in all life on Earth, apart from glycine (G)?
What form of amino acids are found in all life on Earth, apart from glycine (G)?
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Which level of protein structural organization refers to the amino acid sequence?
Which level of protein structural organization refers to the amino acid sequence?
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Under what condition do disulfide bonds typically form?
Under what condition do disulfide bonds typically form?
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In protein structure, what does the term 'dihedral angle' refer to?
In protein structure, what does the term 'dihedral angle' refer to?
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What is the main characteristic of Van der Waals forces?
What is the main characteristic of Van der Waals forces?
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What is the typical length of a hydrogen bond?
What is the typical length of a hydrogen bond?
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What is the typical value of the dihedral angle Ω in peptide bonds?
What is the typical value of the dihedral angle Ω in peptide bonds?
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Which structure encompasses multiple subunits folded into a complex?
Which structure encompasses multiple subunits folded into a complex?
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What role do reducing agents play in laboratory protocols concerning disulfide bonds?
What role do reducing agents play in laboratory protocols concerning disulfide bonds?
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What is the significance of the dihedral angles Φ and Ψ in polypeptides?
What is the significance of the dihedral angles Φ and Ψ in polypeptides?
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Which structural motifs are well-represented when plotting dihedral angles Φ against Ψ?
Which structural motifs are well-represented when plotting dihedral angles Φ against Ψ?
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What allows proline to have a unique twist in the peptide bond configuration?
What allows proline to have a unique twist in the peptide bond configuration?
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What characterizes the secondary structure of proteins?
What characterizes the secondary structure of proteins?
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How many residues are involved in one complete turn of an α-helix?
How many residues are involved in one complete turn of an α-helix?
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What percentage of β-sheets are typically found in a mixed parallel and anti-parallel configuration?
What percentage of β-sheets are typically found in a mixed parallel and anti-parallel configuration?
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What is the primary structural level of protein organization?
What is the primary structural level of protein organization?
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Which statement about α-helices is true?
Which statement about α-helices is true?
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What term refers to the structural organization level involving multiple subunits?
What term refers to the structural organization level involving multiple subunits?
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What is the distance between consecutive rungs of an α-helix turns?
What is the distance between consecutive rungs of an α-helix turns?
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Which of the following describes the pleated nature of β-sheets?
Which of the following describes the pleated nature of β-sheets?
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What is the main characteristic of hemoglobin's affinity for oxygen at low pH?
What is the main characteristic of hemoglobin's affinity for oxygen at low pH?
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How does the structure of hemoglobin affect its function?
How does the structure of hemoglobin affect its function?
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What happens to oxygen binding in hemoglobin when oxygen pressure increases?
What happens to oxygen binding in hemoglobin when oxygen pressure increases?
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What term is used to describe hemoglobin when it is bound to oxygen?
What term is used to describe hemoglobin when it is bound to oxygen?
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Which of the following statements is true about myoglobin and hemoglobin?
Which of the following statements is true about myoglobin and hemoglobin?
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What role do prolines play in the structure of myoglobin?
What role do prolines play in the structure of myoglobin?
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According to Le Chatelier’s principle, how does low pH affect hemoglobin's behavior?
According to Le Chatelier’s principle, how does low pH affect hemoglobin's behavior?
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What is the significance of the first crystal structures of myoglobin and hemoglobin being solved?
What is the significance of the first crystal structures of myoglobin and hemoglobin being solved?
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Study Notes
Protein Structure and Function
- Proteins are essential components of cells; their shapes, functions, and responses to the environment determine cellular behavior.
Review of Basic Concepts
- The pKa of a group is the pH at which it is 50% protonated.
- A group is primarily protonated at pH values lower than its pKa.
- Carboxylic acids are considered acidic due to their low pKa, meaning they are deprotonated at neutral pH.
- Basic groups have a high pKa.
- Elements towards the upper right of the periodic table are more electronegative.
- Peptide bonds form via dehydration reactions and have a partial double bond character, contributing to their planar nature.
- Cysteines can be oxidized to form disulfide bonds - a process favored in oxidizing environments, such as the extracellular space; reducing environments, like the cytosol, prevent disulfide bond formation.
- Hydrogen bonds have lengths between 1.6 and 2.0 Angstroms.
- Van der Waals forces between nonpolar groups are weak; the aggregation of hydrophobic domains in proteins is driven primarily by entropy of water molecules, not by Van der Waals forces.
- All amino acids, except glycine, are chiral and exist in the levorotary (L) form in all known life.
Levels of Structural Organization
- Proteins have four levels of structural organization:
- Primary: Amino acid sequence
- Secondary: Alpha-helices, beta-sheets, and loops
- Tertiary: Entire polypeptide chain, bundles of helices and sheets, domains
- Quaternary: Multiple subunits folded into a complex
Amino Acids
-
Dihedral angle: The spatial arrangement of amino acids is defined by three dihedral angles:
- Φ (phi): angle along the N-Cα bond
- Ψ (psi): angle along the Cα-C bond
- Ω (omega): angle along the C-N bond
Peptide Bond
-
Dihedral angles in a polypeptide:
- The Ω angle is always 0 or +180 degrees.
- Analyzing Φ and Ψ angles reveals preferred conformations:
- Alpha-helix combinations
- Beta-sheet configurations
- A less common structure called Lα (left-handed alpha-helices)
- The trans conformation of Ω is favored due to steric hindrance between consecutive side chains.
- Proline's unique structure allows for a cis conformation because it is anchored to the backbone.
Secondary Structure
-
α-helix:
- Forms due to hydrogen bonding between the backbone NH and C=O groups.
- Contains 3.6 residues per turn, with each residue spanning 100 degrees of rotation.
- Consecutive α-helix turns are separated by 5.4 Angstroms.
- Almost exclusively right-handed.
- Amphipathic helices have hydrophobic residues on one side and hydrophilic residues on the other.
- Fully buried helices consist of hydrophobic residues, and fully exposed helices are composed of hydrophilic residues.
-
β-sheet:
- Also forms through hydrogen bonds between backbone NH and C=O groups.
- All potential hydrogen bonds are satisfied, except for the flanking strands at the sheet ends.
- About 20% of beta-sheets are mixed parallel and anti-parallel, the other 80% are purely one type or the other.
- β-sheets are not flat, but pleated.
Disulfide Bonds
-
Ribonuclease:
- Contains disulfide bonds.
- Illustrates Anfinsen's experiment, which suggested that primary sequence determines structure (current understanding is more nuanced).
-
Insulin:
- Also contains disulfide bonds.
-
Immunoglobulins:
- Chains are held together by disulfide bonds.
Protein Carriers
-
Cholesterol:
- Transported by high-density lipoprotein (HDL) and low-density lipoprotein (LDL) particles.
- Apolipoproteins within these particles play a crucial role.
-
Solute Lipid Carriers (SLC family):
- Transport carboxylic acids and small molecules.
-
Myoglobin (Mb) and Hemoglobin (Hb):
- Transport oxygen.
Hemoglobin
-
Oxygen-carrying team:
- Hemoglobin: carries oxygen (transport function).
- Myoglobin: stores oxygen (repository function).
-
Saturation curves:
- Myoglobin: exhibits a parabolic curve, indicating simple binding.
- Hemoglobin: displays a sigmoidal (S-shaped) curve, reflecting cooperative binding between heme units in the tetrameric structure.
-
Hemoglobin and oxygen:
- Hemoglobin's affinity for oxygen increases with rising oxygen pressure.
- Oxyhemoglobin: Hemoglobin with bound oxygen.
- Deoxyhemoglobin: Hemoglobin without bound oxygen.
- HbO2 is a stronger acid than Hb.
- In acidic environments, Le Chatelier's principle dictates that the equilibrium shifts towards the weaker acid (Hb), releasing oxygen - an adaptation crucial for oxygen delivery to tissues with high oxygen consumption.
-
Crystal structures:
- X-ray diffraction structures solved by Perutz and Kendrew (1961 Nobel Prize).
- Myoglobin (Mb): contains seven helical chains, with heme nestled in the middle, secured by histidines; prolines create bends between helices.
- Hemoglobin (Hb): similar amino acid sequence to Mb; its structure prevents oxidation of Fe(II) to Fe(III), which would render the molecule incapable of binding oxygen.
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Description
This quiz explores the fundamental concepts of protein structure and function, including key principles like pKa, peptide bonds, and molecular interactions. Understand how proteins interact within cellular environments and the significance of structural features in their functionality. Test your knowledge on the essential roles that proteins play in biological systems.
