p.2
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What is the structure formed by hydrogen bonds between peptide chains in beta-pleated sheets?
A zigzag structure that is perpendicular to the direction of the protein chain.
p.2
Tertiary Structure and Protein Folding
What role does proline play in reverse turns?
Proline's cyclic structure provides the correct geometry for reverse turns, typically occurring as the second residue.
p.2
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What is a beta-bulge?
A common non-repetitive irregular secondary motif in antiparallel beta-sheets.
p.1
Introduction to Proteins
What are proteins composed of?
Polymers consisting of amino acids linked by covalent peptide bonds.
p.4
Introduction to Proteins
What is the role of alpha-lactalbumin in the body?
It is a regulatory component of the lactose synthase enzyme.
p.4
Denaturation and Refolding of Proteins
What is the purpose of beta-mercaptoethanol in protein studies?
It reduces disulfide bridges to two sulfhydryl groups.
p.3
Tertiary Structure and Protein Folding
What type of bonds are involved in the stability of collagen helices?
Hydrogen bonds involving hydroxyproline and hydroxylysine.
p.3
Levels of Protein Structure
What are fibrous proteins characterized by?
Polypeptide chains organized approximately parallel along a single axis, forming long fibers or large sheets.
p.5
Hemoglobin and Myoglobin Functionality
What happens to hemoglobin's O2 affinity when H+ concentration increases?
The O2 affinity of hemoglobin decreases.
p.2
Tertiary Structure and Protein Folding
What are supersecondary structures?
Structures resulting from the combination of alpha and beta strands, such as βαβ and αα.
p.3
Factors Affecting Protein Structure
What types of interactions are involved in tertiary structures?
Non-covalent interactions, including hydrogen bonding, hydrophobic interactions, and electrostatic attractions.
p.1
Primary Structure and Amino Acid Sequencing
What can changes in one amino acid residue affect?
Biological functions of the protein.
p.4
Hemoglobin and Myoglobin Functionality
How does the affinity of free heme for carbon monoxide compare to oxygen?
It is 25,000 times greater for carbon monoxide than for oxygen.
p.2
Factors Affecting Protein Structure
What causes strong electrostatic repulsion in proteins?
Proximity of several side chains of like charges, such as lysine and arginine or glutamic and aspartic.
p.1
Introduction to Proteins
What do native conformations refer to?
The 3D shapes of proteins with biological activity.
p.3
Levels of Protein Structure
How do globular proteins differ from fibrous proteins?
Globular proteins fold on themselves to produce a spherical shape and are generally soluble in water.
p.4
Hemoglobin and Myoglobin Functionality
At what partial pressure of O2 is myoglobin 50% saturated?
1 torr partial pressure of O2.
p.5
Predicting Protein Structure Using Bioinformatics
What is fold recognition in protein modeling?
A method used to model proteins with the same fold as known structures.
p.1
Primary Structure and Amino Acid Sequencing
What is the primary structure of a protein?
The order in which amino acids are covalently linked together.
p.2
Tertiary Structure and Protein Folding
How do collagen triple helices differ from alpha-helices?
All three individual collagen chains are helices that differ from the alpha-helix.
p.1
Quaternary Structure and Protein Interactions
What defines quaternary structure?
The arrangement of subunits with respect to one another.
p.1
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What is the role of hydrogen bonds in secondary structure?
They stabilize the arrangement of the polypeptide chain.
p.5
Tertiary Structure and Protein Folding
How does the structure of oxygenated hemoglobin differ from deoxygenated hemoglobin?
Oxygenated hemoglobin undergoes conformational changes that affect its function.
p.5
Hemoglobin and Myoglobin Functionality
What is the significance of BPG in fetal oxygen supply?
BPG plays a role in the supply of O2 to the growing fetus.
p.2
Tertiary Structure and Protein Folding
What are the two types of reverse turns?
Type I, where the side chain lies outside the loop, and Type II, where the side chain is rotated 180 degrees and lies inside the loop.
p.2
Quaternary Structure and Protein Interactions
What is the significance of protein domains with similar conformations?
They are associated with a particular function.
p.4
Denaturation and Refolding of Proteins
What causes denaturation of proteins?
Breakdown of noncovalent interactions due to heat, pH changes, detergents, urea, and beta-mercaptoethanol.
p.2
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What are the two types of arrangements for polypeptide chains in beta-pleated sheets?
Parallel and antiparallel.
p.3
Tertiary Structure and Protein Folding
What happens to collagen helices with age?
They become cross-linked by covalent bonds formed by reactions of lysine and histidine residues.
p.2
Tertiary Structure and Protein Folding
What is a β-barrel?
A repetitive supersecondary structure created when beta sheets fold back on themselves.
p.3
Tertiary Structure and Protein Folding
What is the tertiary structure of a protein?
The 3D arrangement of all atoms in a molecule, including side chains and prosthetic groups.
p.4
Quaternary Structure and Protein Interactions
What defines the quaternary structure of a protein?
Proteins that consist of more than one polypeptide chain, called subunits.
p.5
Hemoglobin and Myoglobin Functionality
What is the Bohr effect?
The effect of H+ on reducing the O2 affinity of hemoglobin.
p.5
Hemoglobin and Myoglobin Functionality
What is the role of 2,3-Bisphosphoglycerate (BPG) in hemoglobin function?
BPG binding reduces the oxygen-binding capacity of hemoglobin.
p.5
Predicting Protein Structure Using Bioinformatics
What is the principal application of bioinformatics in protein structure prediction?
Searching databases for sequence homology.
p.5
Predicting Protein Structure Using Bioinformatics
What is de novo prediction in protein structure modeling?
An algorithmic process predicting tertiary structure from primary amino acid sequence.
p.3
Levels of Protein Structure
What is an example of a fibrous protein?
Keratin in hair and wool, and collagen in connective tissue.
p.1
Primary Structure and Amino Acid Sequencing
How is the primary structure read?
From the N-terminal end to the C-terminal end.
p.4
Introduction to Proteins
What is alpha-lactalbumin and where is it expressed?
A protein expressed exclusively in the lactating mammary gland.
p.1
Tertiary Structure and Protein Folding
What is tertiary structure?
The 3D arrangement of all atoms in a protein, including side chains and prosthetic groups.
p.4
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What stabilizes the alpha-helical regions in myoglobin?
Hydrogen bonding in the polypeptide backbone.
p.3
Predicting Protein Structure Using Bioinformatics
What techniques are used to determine tertiary structure?
X-ray crystallography and nuclear magnetic resonance spectroscopy.
p.4
Hemoglobin and Myoglobin Functionality
What is the function of the heme group in myoglobin?
It binds oxygen in the bloodstream.
p.1
Factors Affecting Protein Structure
What is the significance of proline in alpha-helix structure?
It disrupts the alpha-helix due to its cyclic structure and restricts rotation.
p.4
Hemoglobin and Myoglobin Functionality
What is positive cooperativity in hemoglobin?
When one O2 is bound, it becomes easier for the next O2 to bind.
p.5
Predicting Protein Structure Using Bioinformatics
What is the goal of modeling algorithms in protein structure prediction?
To fold a primary amino acid sequence into a protein structure for novel function and behavior.
p.1
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What are the two main types of secondary structure?
Alpha-helix and beta-pleated sheets.
p.1
Secondary Structure: Alpha Helix and Beta-Pleated Sheets
What characterizes secondary structure in proteins?
The ordered 3D arrangement in space of the backbone atoms in a polypeptide chain.
p.4
Levels of Protein Structure
What is the structure of myoglobin?
Consists of a single polypeptide chain of 153 amino acid residues and a heme prosthetic group.
p.3
Factors Affecting Protein Structure
What role do disulfide bonds play in protein structure?
They restrict folding patterns available to polypeptide chains.
p.4
Hemoglobin and Myoglobin Functionality
What are the primary functions of myoglobin and hemoglobin?
Myoglobin is for oxygen storage, while hemoglobin is for oxygen transport.
