Functional Targets for Bioconjugation Flashcards
What are peptides and proteins composed of?
amino acids polymerized together via the formation of amide bonds
the backbone of poly peptide structure is the ?
alpha-chain
Does the peptide bond possess rotational freedom?
No, basically due to the partial double-bond character of the carbonyl-amino amide bond.
Each amino acid is composed of?
amino group and a carboxyl group bound to a central carbon (alpha-carbon)
which amino acids have aliphatic side chains (nonpolar and hydrophobic)?
glycine, alanine, valine, leucine, isoleucine, methionine, and proline
Simplest amino acid? side chain is just a hydrogen atom?
glycine
amino acid with a single methyl group for side chain?
Alanine
Which amino acids have three or four carbon branched-chain constituents as their side chains?
Valine, Leucine, Isoleucine
Why is Methionine unique?
It is the only reactive aliphatic amino acid that contains a thioether group at the hydro-carbon chain terminus
Which is the only imino acid? (IMINO)
proline, its side chain forms a pyrroline ring structure with its alpha-amino group (contains secondary alpha-amino group)
Which amino acid causes severe turns in a polypeptide chain?
proline
Collagen is enriched with what amino acid?
proline
Which amino acids contain aromatic side chains (nonpolar and hydrophobic)?
Phenylalanine and tryptophan
Which amino acid contributes more to the (total) absorption of a protein at the 275-280 nm range?
tryptophan
Where can you find all (or most) of the aliphatic and aromatic hydrophobic residues of amino acids?
the interior of protein molecules or in areas that interact with other nonpolar structures such as lipids (not very accessible to water)
Which amino acids contain relatively polar constituents and are hydrophilic?
Asparagine, glutamine, threonine, and serine
Where do you usually find polar, hydrophilic amino acids?
At or near the surface where hydration can occur with the aqueous environment
Which amino acids are usually found post-translationally modified with carbohydrate in N-glycosidic and O-glycosidic linkages?
Asparagine, Threonine, and serine. N-glycosidic (asp) and O-glycosidic (thr and ser)
Which amino acids are most significant for modifying and conjugating purposes?
the ones with ionizable side chains, aspartic acid, glutamic acid, lysine, arginine, cysteine, histidine, and tyrosine
What is the theoretical pKa of B-carboxyl of aspartic acid?
3.7-4.0
What is the theoretical pKa of gamma-carboxyl on glutamic acid?
4.2-4.5
What is the pKa of the alpha-carboxyl groups at the C-terminal of a polypeptide chain
2.1 - 2.4
Which amino acid chains have ionizable amine-constaining constitutents that contribute to the overall positive charge with the N-terminus?
Lysine, arginine, histidine
When do amino acids like lysine, arginine, and histidine protonate? (what conditions)
In pH environments lower than their pKa (9.3-9.5 for lysine, 7.6-8.0 for alpha amines)
Which amino acid is virtually always protonated and has a pKa higher than 12.0?
Arginine
What determines the resultant three-dimensional structure of protein molecules?
Ionic charge, hydrogen bonding capability, and hydrophobicity
What holds together alpha-helices and B-sheets?
the hydrogen bonding of carbonyl oxygens from peptide bonds interacting with other peptide bonds
What does Cre recombinase do?
It is a tyrosine recombinase enzyme that catalyzes the site specific recombination of the loxP sites…introduces inducible deletions
What is Cre-lox recombination?
system that can be used to introduce gene deletions, inversions, and translocations on specific target sites.
What are the components of Cre-lox recombination?
Cre recombinase, and LoxP sites
What do the loxP sites act as?
they flank the target gene of interest
