MODULE 3: Chapter 4.2 Flashcards
What determines protein structure and function?
The amino acid sequence
The chemical properties of the amino acid side chains contribute to the protein’s fold and function.
What types of interactions stabilize the structure of folded proteins?
Weak noncovalent interactions
These include hydrogen bonding, van der Waals forces, ionic interactions, and hydrophobic effects.
What is an advantage of weak interactions in biological systems?
They permit flexibility
Proteins can change shape by breaking and re-forming weak interactions.
True or False: Proteins are rigid, crystalline-like structures.
False
Proteins are flexible and undergo conformational changes.
What is the primary (1°) structure of a protein?
The amino acid sequence
It determines how the polypeptide backbone folds into a stable three-dimensional structure.
What is the secondary (2°) structure of a protein?
The regular repetitive arrangement of local regions of the polypeptide backbone
Major secondary structures include β strands, α helices, and β turns.
What are the three major secondary structures in proteins?
- α helices
- β strands
- β turns
These are stabilized by hydrogen bonding and geometry.
What is the tertiary (3°) structure of a protein?
The spatial location of all the atoms in the polypeptide chain
This includes the path of the polypeptide and the positions of the side chains.
What defines the quaternary (4°) structure of a protein?
The organization of multiple polypeptide chains in a protein complex
This can involve multiple copies of the same polypeptide or different polypeptides.
What is a characteristic of the α helix structure?
It is a right-handed helix
The α helix is stabilized by intrastrand hydrogen bonds.
How many residues per turn does an α helix typically have?
3.6 residues
Each residue corresponds to a 100° turn of the helix.
What role does proline play in the α helix structure?
Proline disrupts hydrogen bonding
It lacks a hydrogen on its nitrogen and has a rigid ring structure.
Who first predicted the structure of the α helix?
Linus Pauling and Robert Corey
Their model was validated by the structure of whale myoglobin determined by John Kendrew.
What creates a dipole moment in a peptide bond?
The separation of charge between the carbonyl oxygen and the amide nitrogen
This dipole moment contributes to the overall dipole moment in α helices.
What can be found at the termini of α helices to stabilize them?
Compensating charged amino acids
Negatively charged residues at the N-terminal end and positively charged residues at the C-terminal end.
Fill in the blank: The three major types of secondary structure in proteins are _______.
[α helices, β strands, β turns]
What can neutralize the charge on protein surfaces?
Interactions with H2O or charged ions such as phosphate or Mg2⁺
What is the dipole moment in α helices?
A partial positive charge on the N-terminal end and a partial negative charge on the C-terminal end
What does it mean for an α helix to be amphipathic?
One side of the helix is hydrophobic and the other side is hydrophilic
How is an amphipathic α helix generated?
When amino acids with hydrophilic or hydrophobic properties are positioned every three to four residues along the polypeptide backbone
What is the sequence of residues in an amphipathic α helix from phosphofructokinase-1?
Hydrophilic: Thr145, Glu148, Asp151, Arg153, Arg155, Asp156, Thr157; Hydrophobic: Val146, Val147, Ala149, Ile150, Leu154
What tool can be used to predict the existence of an amphipathic α helix?
A helical wheel representation
Describe the arrangement of hydrophobic and hydrophilic residues in apolipoproteins.
Hydrophobic residues oriented inward, hydrophilic residues facing outward
Describe the arrangement of hydrophobic and hydrophilic residues in rhodopsin.
Hydrophobic residues pointing outward toward the lipid membrane, hydrophilic residues facing inward
