Functional Targets for Bioconjugation

Question 1

What are peptides and proteins composed of?

Answer 1

amino acids polymerized together via the formation of amide bonds

Question 2

the backbone of poly peptide structure is the ?

Answer 2

alpha-chain

Question 3

Does the peptide bond possess rotational freedom?

Answer 3

No, basically due to the partial double-bond character of the carbonyl-amino amide bond.

Question 4

Each amino acid is composed of?

Answer 4

amino group and a carboxyl group bound to a central carbon (alpha-carbon)

Question 5

which amino acids have aliphatic side chains (nonpolar and hydrophobic)?

Answer 5

glycine, alanine, valine, leucine, isoleucine, methionine, and proline

Question 6

Simplest amino acid? side chain is just a hydrogen atom?

Answer 6

glycine

Question 7

amino acid with a single methyl group for side chain?

Answer 7

Alanine

Question 8

Which amino acids have three or four carbon branched-chain constituents as their side chains?

Answer 8

Valine, Leucine, Isoleucine

Question 9

Why is Methionine unique?

Answer 9

It is the only reactive aliphatic amino acid that contains a thioether group at the hydro-carbon chain terminus

Question 10

Which is the only imino acid? (IMINO)

Answer 10

proline, its side chain forms a pyrroline ring structure with its alpha-amino group (contains secondary alpha-amino group)

Question 11

Which amino acid causes severe turns in a polypeptide chain?

Answer 11

proline

Question 12

Collagen is enriched with what amino acid?

Answer 12

proline

Question 13

Which amino acids contain aromatic side chains (nonpolar and hydrophobic)?

Answer 13

Phenylalanine and tryptophan

Question 14

Which amino acid contributes more to the (total) absorption of a protein at the 275-280 nm range?

Answer 14

tryptophan

Question 15

Where can you find all (or most) of the aliphatic and aromatic hydrophobic residues of amino acids?

Answer 15

the interior of protein molecules or in areas that interact with other nonpolar structures such as lipids (not very accessible to water)

Question 16

Which amino acids contain relatively polar constituents and are hydrophilic?

Answer 16

Asparagine, glutamine, threonine, and serine

Question 17

Where do you usually find polar, hydrophilic amino acids?

Answer 17

At or near the surface where hydration can occur with the aqueous environment

Question 18

Which amino acids are usually found post-translationally modified with carbohydrate in N-glycosidic and O-glycosidic linkages?

Answer 18

Asparagine, Threonine, and serine. N-glycosidic (asp) and O-glycosidic (thr and ser)

Question 19

Which amino acids are most significant for modifying and conjugating purposes?

Answer 19

the ones with ionizable side chains, aspartic acid, glutamic acid, lysine, arginine, cysteine, histidine, and tyrosine

Question 20

What is the theoretical pKa of B-carboxyl of aspartic acid?

Answer 20

3.7-4.0

Question 21

What is the theoretical pKa of gamma-carboxyl on glutamic acid?

Answer 21

4.2-4.5

Question 22

What is the pKa of the alpha-carboxyl groups at the C-terminal of a polypeptide chain

Answer 22

2.1 - 2.4

Question 23

Which amino acid chains have ionizable amine-constaining constitutents that contribute to the overall positive charge with the N-terminus?

Answer 23

Lysine, arginine, histidine

Question 24

When do amino acids like lysine, arginine, and histidine protonate? (what conditions)

Answer 24

In pH environments lower than their pKa (9.3-9.5 for lysine, 7.6-8.0 for alpha amines)

Question 25

Which amino acid is virtually always protonated and has a pKa higher than 12.0?

Answer 25

Arginine

Question 26

What determines the resultant three-dimensional structure of protein molecules?

Answer 26

Ionic charge, hydrogen bonding capability, and hydrophobicity

Question 27

What holds together alpha-helices and B-sheets?

Answer 27

the hydrogen bonding of carbonyl oxygens from peptide bonds interacting with other peptide bonds

Question 28

What does Cre recombinase do?

Answer 28

It is a tyrosine recombinase enzyme that catalyzes the site specific recombination of the loxP sites…introduces inducible deletions

Question 29

What is Cre-lox recombination?

Answer 29

system that can be used to introduce gene deletions, inversions, and translocations on specific target sites.

Question 30

What are the components of Cre-lox recombination?

Answer 30

Cre recombinase, and LoxP sites

Question 31

What do the loxP sites act as?

Answer 31

they flank the target gene of interest