Protein Structure Flashcards
In all cases, how is a protein’s function determined?
By its structure.
What is a zwitterion?
A neutral ion with an equal number of positive and negative charges.
What is pKA?
The strength of the weak acid; as pKA becomes smaller, the conjugate strong acid becomes stronger (more likely to be present in a solution).
What happens when pKA is less than pH
The base form of the ion is more present in a solution. The molecule will be deprotonated.
What happens when pKA>pH?
The acid form of the ion is more present in a solution.
What is the pKA of COO-?
pKA = 2
What is the pKA of NH3+?
pKA = 9.5
Why are amino acids chiral? Which amino acid is the exception? Why is it important that amino acids are chiral?
- They are chiral because the alpha carbon always has 4 different substituents.
- Glycine is achiral.
- Amino acids occur in L- and D- conformations based on their chirality (enantiomers). While L-isomers are present in living organisms and are the most common isomer, D- conformations are present in pharmacological substances and have vastly different functions from their L-type conformers.
Which amino acids are nonpolar?
[A] Alanine [V] Valine [L] Leucine [F] Phenylalanine [W] Tryptophan [P] Proline [I] Isoleucine [M] Methionine
Which amino acids are polar uncharged?
[G] Glycine [S] Serine [T] Threonine [C] Cysteine [N] Asparagine [Q] Glutamine [Y] Tyrosine
Which amino acids are polar charged?
[D] Aspartate [E] Glutamate [K] Lysine [R] Arginine [H] Histidine
What is the pKA of cysteine?
8.5
What is unique about cysteine?
It is able to form disulphide bonds with other cysteine molecules in oxidizing environments.
What is the pKA of Tyrosine?
10.5
What is the pKA of Histidine?
6
What is the pKA of Aspartate?
4
What is the pKA of Glutamate?
4
What is the pKA of Lysine?
10
What is the pKA of Arginine?
12.5
Where are polar side chains typically found within a protein? Why?
On the surface; these groups can interact with water.
Where are nonpolar side chains typically found within a protein? Why? What is the exception?
In the core to minimize interaction with water. Alanine is the exception.
How are peptide bonds formed?
Peptide bonds are formed when two hydrogens from the N-terminus are accepted by an oxygen atom at the C-terminus. The result is an amide bond at the expense of a water molecule.
What are peptides/oligopeptides?
A general term for a larger number of amino acids that are generally synthetically synthesized.
What is a polypeptide?
A long chain of amino acids that is usually produced naturally.
What is a protein?
A large polypeptide or group of polypeptides with a biological function.
What is the primary structure of a protein? What interactions are present?
The basic sequence of amino acids in a polypeptide. Peptide/amide bonds between amino acids.
What is the secondary structure of a protein? What interactions are present?
The local folding of the polypeptide backbone driven by hydrogen bonding between carbonyl and amino groups.
What are the two most regular patterns of secondary structure in a protein?
Alpha-helix and Beta-sheet.
How many residues downstream can carbonyl and amino groups interact in an alpha-helix?
4 residues downstream.
What forces stabilize beta-sheets?
Hydrogen bonds between backbone CO and NH groups of neighbouring strands.
What forces stabilize alpha-helices?
Hydrogen bonds between backbone CO and NH groups in the same helices.
What is an irregular structure?
Polypeptide loops of varying sizes that link together regular secondary structures.
What is the tertiary structure of a protein? What interactions are present?
The arrangement of all atoms in a single polypeptide; the arrangement of secondary structures in relation to one another.
The structure is determined by non-covalent interactions between amino acid R-groups, as well as interactions with prosthetic groups. In some cases, salt bridges form between ionizable amino acid chains.
What are the two classifications of tertiary structures?
Fibrous and Globular.
What are fibrous proteins?
Insoluble in aqueous, long-filament proteins that contain limited residues with many repeats. Their primary function is structure or connectivity.
What are globular proteins?
Soluble in aqueous solutions, folded into compact structures with nonpolar cores and polar surfaces.
How is the hydrophobic effect relative in protein folding?
The hydrophobic effect drives soluble globular proteins to maintain a tertiary structure in which their hydrophobic cores remain compacted in the internalized structure.
What are salt bridges?
Ionic interactions that form between closely-positioned charged amino acids that stabilize secondary and tertiary structure.
What is a domain?
A polypeptide segment that has folded into a single structural unit with a hydrophobic core. There may be more than one present in a protein.
What is a motif?
A short region of polypeptide with a recognizable 3D shape (Zinc fingers).
What is a prosthetic group?
A non-peptide component in a protein that is permanently incorporated.
What is the function of a prosthetic group?
To provide structure and function in different proteins.
How are globular proteins stabilized? Are they easily denatured?
- Weak noncovalent forces.
2. Easily denatured.
What can disrupt a disulphide bond?
Reducing agents (DTT)
What is the quaternary structure of a protein?
The association of multiple polypeptides, stabilized by same forces as in tertiary.
