Exam 2 - Ch 5, 6 + Antibodies (Ch 7) Flashcards
Charge on Arginine at pH 7?
+1
Charge on Aspartic Acid at pH 7?
-1
Charge on Cysteine at pH 7?
0
Charge on Glutamic Acid at pH 7?
-1
Charge on Histidine at pH 7?
0
Charge on Lysine at pH 7?
+1
Charge on Tyrosine at pH 7?
0
pH < pI
What is the net charge on the protein?
Net + charge
pH > pI
What is the net charge on the protein?
Net - charge
1st amino acid the N-terminus or C-terminus?
N-terminus
last amino acid the N-terminus or C-terminus?
C-terminus
What is a conservative mutation?
a mutation that conserves chemical properties (size, polarity, and charge similar for both amino acids)
What is a nonconservative mutation?
a mutation where the properties of the amino acids are different
Explain what affinity chromatography (IMAC, His-tag) is and what its uses are
a separation method based on a specific binding interaction between an immobilized ligand and its binding partner.
High efficiency for removing bulk contaminants, usually 1st step in purification process
Explain IEC (Ion-Exchange Chromatography)
Ion-Exchange Chromatography separates proteins based on charge.
important to match the pH of the buffer with the pI of the protein, and the charge on the resin
often an early step in the purification process
Explain SEC (Size Exclusion Chromatography)
Separates proteins based on their size.
Large protein elutes first, Small protein elutes last.
Size difference needs to be significant (at least a factor of 2).
Which terminus does the arrow point at in a beta-strand?
always C-terminus
What dictates primary structure?
Genes
What is secondary structure? What dictates it?
Alpha helices and beta sheets
Amino Acids dictate
What is tertiary structure?
When secondary structures pack against each other
What is quaternary structure?
multiple protein subunits associated with each other
How can you predict if a protein will fold into an alpha helix based on amino acid sequence?
it will show repeating patterns of side chain polarity every 3-4 amino acids
How can you predict if a protein will fold into a beta sheet based on amino acid sequence?
it will show repeating patterns of side chain polarity every other residue
Explain the structure of fibrous proteins
extended regions of secondary repeating structures
Which amino acid has the greatest entropy of conformation? (Sconf)
Glycine
Which amino acid has the lowest entropy of conformation? (Sconf) Why?
Proline
it has very limited conformation around the phi angle
What type of interaction stabilizes secondary structure?
H-bonding
(intramolecular for alpha helices and intermolecular for beta sheets)
What are some examples of fibrous proteins?
Keratin, Fibroin, and Collagen
Explain Globular proteins
Have compact structures which arise from specific packing interactions between short secondary structure motifs
define a domain
a region of a protein that is associates with a specific function, and is typically able to fold independently of the rest of the protein structure
What are the 4 main classes of structure of globular proteins?
- mostly alpha
- mostly beta
- mixture of alpha/beta
- relatively unstructured (few secondary structures)
Which type of secondary structure will usually form fastest (alpha helices or beta sheets) and why?
Alpha helices - all residues are continuous, local, and uninterrupted. Once the first 4 residues come together, there are more places for H-bonds to form and it folds up quickly
Which folds quicker: parallel beta sheet or antiparallel beta sheet?
antiparallel beta sheet
is the change in enthalpy usually more favorable or less favorable in the folded state?
Usually favorable (delta H < 0 ) (U–>F)
Is delta S conf favorable or unfavorable for the folded state?
Unfavorable (delta S conf < 0) (U–>F)
Is delta S solvent favorable or unfavorable for the folded state?
Favorable (delta S solvent > 0 ) (U–>F)
Do disulfide bonds increase or decrease protein stability?
Generally increase protein stability
(disulfides reduce the # of conformations possible in the unfolded state)
Will the binding of a metal ion or cofactor increase or decrease stability?
Generally increase protein stability
In a folding funnel, what does the width of the funnel represent?
the # of possible conformations
In a folding funnel, what does the depth of the funnel represent?
Free energy (higher free energy at the top of the funnel)
Are amide bonds more stable in the cis or the trans conformation?
Trans
What do Peptide prolyl isomerases (PPI) do?
catalyze the isomerization of cis-pro conf to trans-pro conf
(Increase the folding rate)
What do protein disulfide isomerases do?
Catalyze the reduction and re-oxidation of native disulfide bonds (correct the formation of non-native S-S bonds)
What is the role of chaperonins?
Help prevent intermolecular interactions that lead to aggregation of proteins (help prevent off-pathway events)
What amino acids are favored in globular protein turns?
Pro and Gly
What is the function of turns in a globular protein
they allow the peptide chain to fold back on itself and adopt a compact tertiary structure
For alpha helices, what is the length in Angstroms between amino acids? How many residues per turn?
5.4 A in length
3.6 amino acids per turn
For beta sheets, what is the length in Angstroms between amino acids? How many residues per turn?
6.4 A for parallel
6.8 A for antiparallel
2 residues per turn
a-keratin features?
coiled-coil
found in hair
fibroin features?
extended beta-structure
found in silk
collagen features?
triple-strand
most abundant human protein
What is the Fab for IgG?
the antigen binding fragment
What is the Fc for IgG?
The constant fragment
How many chains in IgG?
4
How many domains in IgG?
12 Beta sandwich domains
How many CDRs per antigen binding site?
6
How many antigen binding sites per IgG?
2
How many antigen binding sites per Fab?
1
