1.2 Flashcards
What kind of amino acids make proteins?
L amino acids
What is an L amino acid?
The amino group (NH3) comes before the carboxyl group (coo-)
What is the pKa of Lysine and Argentine?
10-12
What is the pKA of histidine?
6
What is the pKa of aspartic acid and glutamine?
3-4
What is a zwitterion? (Ampholyte)
A dipolar ion that acts as an acid or base
What does 2 zones of buffer mean in a titration curve?
The amino acid is not charged
What does 3 zones of buffer in a titration curve mean?
Look at middle pKa to see which amino acid it is
How are peptide bonds made?
Two amino acids join and water is lost to form the bond a
Phosphorylation
Adds a phosphate group to Ser, Thr, and Tyr
Enzyme activity
Sulfation
Only happens to Tyr
Hormones
Methylation
Adds methyl group to Lys or Arg
Are cysteine sulfhydryl groups oxidized or reduced?
Oxidized
What purpose do disulfide bridges serve?
Helps link amino acid chains together and helps with structure
Are the interior of beta barrels hydrophilic or hydrophobic
Hydrophobic
How many residues are there per turn in an alpha helix
3.6
How many residues are there per turn in a coiled-coil alpha helix
3.5
On average how many hydrogen bongs are there per turn in an alpha helix
3 to 4 hydrogen bonds
At which end is an alpha helix is the partial positive charge of the overall dipole
Amino end
What is the structure of a keratin fiber?
Staggered coiled coil structures that have protofilament, protofibril, and filaments
What are the 3 amino acids repeated in the collage helix?
Proline, Glycine, Hydroxyproline
Is the collagen helix right handed it left handed?
Left handed
What is the difference between an alpha/beta motif and an alpha + beta motif? Which is more common?
Alpha/beta motifs alternate frequently between an alpha and beta strand
-alpha + beta does not alternate frequently
-alpha/beta is more common
What is the function of the barrel versus the loops in alpha/beta (TIM) barrel proteins such as RuBisCo or DNA Endonuclease IV
-the barrel is a tightly hydrophobic core
-loops are used for ligand/substrate binding,flexible, orients protein the right way
What secondary structure is the EF hand composed of? What molecules do EF hands bind? What are the functions of charged residues vs hydrophobic residues?
-2 alpha helixes separated by a flexible loop
-bind to DNA(short), calcium(long)
-charged/polar located in loop directly interact with ligand
-hydrophobic stabilize structure and properly orient loop for binding
What is the structure of neuramindase? What enzymatic activity goes it have? Where is the enzyme active site?
-4 beta propellers
-cleaves off sialic acid bonds which allows for it to infect other cells
-hydrophobic core with loops in between
Glycosylation O linked adds to
Serine, threonine, tyrosine
Glycosylation N linked adds to
Asparagine
Glycosylation C linked
Tryptophan
Acetylation adds to
Lysine
How to separate proteins by charge?
-Ion exchange chromatography
-Electrophoresis
-negative charge comes out first
How to separate by protein size?
-Gel filtration chromatography
-large proteins come out before small proteins
How to separate proteins by polarity?
-hydrophobic interaction chromatography/reverse phase
-hydrophilic comes out before hydrophobic
