Protein Structure Flashcards
What determines the 3D shape of a protein?
The AA sequence
What forces stabilize the shape?
Non covalent interactions
What mediates interactions between proteins and other substances?
Non covalent interactions
What is a zwitterion?
A positive charge and negative charge on different atoms in a molecule
When the pH is greater than the pKa, the acid exists predominantly as…
the conjugate base form (DEprotonated)
When the pH is less than the pKa, the acid exists predominantly as…
the acid form (protonated)
Define a polypeptide.
Long chain of amino acids (protein)
The sequence of amino acids is the _______ structure.
primary
List the properties of peptide bonds.
- the electrons in peptide bonds are somewhat delocalized generating two resonance forms
- therefore exhibit partial double bond character with no rotation around the C-N bond
- the functional groups in peptide bonds are potential H-bond acceptors or donors
- polar
What two key words describe secondary structure?
Local and backbone
Describe secondary structure.
- local folding of the polypeptide backbone
- allows for H-bonding of the groups in the polypeptide backbone (C=O, N-H)
- “regular” secondary structures occur when each amino acid adopts the same geometry
- alpha helix and beta sheet
Is a loop a part of secondary structure?
Yes
Is a loop a part of regular secondary structure?
No
How does an alpha helix form H-bonds?
The carbonyl oxygen of each residue forms an H-bond with the backbone -NH groups FOUR residues down. (C1…N5)
What forces stabilize alpha helices and beta sheets?
H-bonds between the backbone residues
What is tertiary structure?
Arrangements of all atoms in a single polypeptide (arrangements of secondary structures in relation to one another)
What are the two main protein classes?
Fibrous and globular
Describe globular proteins.
- essentially soluble in aq solutions
- fold into compact structures with non polar cores and polar surfaces
In a globular protein, hydrophobic amino acids are most likely to be found in the ________.
Interior
What is the main stabilizing force for tertiary structure?
Hydrophobic effect
What forces “fine tune” tertiary structure of a protein?
H-bonds
Where will you find disulphide bridges (cys-cys)?
extracellular (reducing conditions)
Define domain.
A polypeptide segment that has folded into a single structural unit with a hydrophobic core. Proteins may encode more than one domain.
Define motif.
A short region of polypeptide with a recognizable 3D shape. A common grouping of secondary structural elements.
Describe a zinc finger.
A single Zn2+ ion is COORDINATED by 2Cys and 2His residues.
What is a coordination bond?
1 atom getting 2 electrons from a single atom.
Define prosthetic group.
A nonprotein component that is permanently incorporated into a protein. These provide structure and reactive groups.
What is quaternary structure?
Proteins composed of more than one polypeptide chain (subunit)
What is the main stabilizing force of quaternary structure?
Hydrophobic effect
