Protein Structure Flashcards
What is the conformation of a protein?
The final folded structure of a protein. Proteins typically have a limited number of stable conformations
What determines a protein’s conformation
Amino acid sequence
Is proper folding of protein guaranteed? Why or why not?
No. Sometimes protein misfold, sometimes they require help from chaperone proteins
What makes a protein conformation stable?
Gives the protein the lowest free energy.
Can protein conformation change?
Yes, protein conformation can change when interacting with different molecules.
List the four protein structures.
Primary, secondary, tertiary, quaternary
What is the primary structure of a protein?
The linear amino acid sequence
What is the secondary structure of a protein?
Small segments of peptide backbone folding to form simple structures like a helix and beta sheet.
What is the tertiary structure of a protein?
The entire peptide backbone folds into the full 3D structure of the protein.
What is the quaternary structure of a protein?
More than one protein combining to form a larger structure.
In reality, does protein folding occur sequentially, with each stage occurring at their own moments in time?
No, typically it is all occurring simultaneously.
Give an example of how a single amino acid change in a protein sequence can have catastrophic effects.
Sickles cell anemia: glutamic acid is switched for hydrophobic valine, which completely changes the shape of hemoglobin.
What creates and stabilizes secondary structures?
Intramolecular hydrogen bonds between backbone
In which ways can beta sheets be arranged?
Parallel, antiparallel, a combination
Where does the R group point in an alpha helix?
Outwards
What type of helix is an alpha helix?
Right handed
How many amino acids per turn of an alpha helix?
3.6
Explain exactly how the N-C-C backbone forms hydrogen bonds in the alpha helix.
Every backbone C=O group forms a hydrogen bond with the N-H group of the amino acid residue 4 residues downstream of the peptide.
Is the primary sequence of an amino acid actually random?
Frequently, hydrophobic/hydrophilic amino acids are grouped on the same side of an alpha helix, resulting in one side of the helix being hydrophobic and one side hydrophylic.
How are beta sheets held together?
Adjacent chains held together by hydrogen bonds between backbone residues. Hydrogen bonding occurs one every two amino acid pairs.
How many amino acids are in one beta strand? How many strands per sheet?
5-10 amino acids; 2-15 strands/sheet
How are the side chains oriented in beta sheets?
Alternating up and down
What determines the folding of the tertiary structures?
Amino acid residues
What is a protein domain? How many domains can a single protein have?
unit of protein that can fold and perform a function on its own without the help of outside molecules. There can be multiple domains within one protein.
What happens to a protein domain when you remove it from the parent protein?
It retains its function.
What is meant by domain shuffling?
Evolution doesn’t have to reinvent new domains for new functions, oftentimes they simply recombines previously selected domains.
