peptides and peptide bonds

Question 1

Ala

Answer 1

hydrophobic

Question 2

Arg

Answer 2

free amino group makes it basic and hydrophilic

Question 3

Asn

Answer 3

carbohydrate can be covalently linked to its -NH

Question 4

Asp

Answer 4

free carboxyl group makes it acidic and hydrophilic

Question 5

Cys

Answer 5

oxidation of their -SH groups link 2 Cys (S-S)

Question 6

Glu

Answer 6

free carboxyl group makes it acidic and hydrophilic

Question 7

Gln

Answer 7

moderately hydrophilic

Question 8

Gly

Answer 8

so small it is amphiphilic (can exist in any environment)

Question 9

His

Answer 9

base/acid and hydrophilic

Question 10

Ile

Answer 10

hydrophobic

Question 11

Leu

Answer 11

hydrophobic

Question 12

Lys

Answer 12

strongly basic and hydrophilic

Question 13

Met

Answer 13

hydrophobic

Question 14

Phe

Answer 14

very hydrophobic

Question 15

Pro

Answer 15

causes kinks in the chain

Question 16

Ser

Answer 16

carbohydrate can be covalently linked to its -OH

Question 17

Thr

Answer 17

carbohydrate can be covalently linked to its -OH

Question 18

Trp

Answer 18

scarce in most plant proteins

Question 19

Tyr

Answer 19

-OH group makes it moderately hydrophilic

Question 20

Val

Answer 20

hydrophobic

Question 21

proteome

Answer 21

post-translational modifications of amino acids in proteins

Question 22

peptide bond

Answer 22

a molecule of water is eliminated (dehydration) for each peptide bond formed and the product is called a peptide

Question 23

what is the remaining portion of the AA in the peptide called?

Answer 23

amino acid residue

Question 24

what reaction is catalyzed by the ribosome?

Answer 24

condensation reaction

Question 25

C-N bond length

Answer 25

10% shorter than found in usual amines

Question 26

why is the peptide bond short?

Answer 26

C-N bond has some double bond character (40%) due to resonance with the C=O

Question 27

what is true about peptide bonds?

Answer 27

all are approx. coplanar and the rigidity of the peptide bonds reduces the degrees of freedom during folding

Question 28

what are the 3 main torsion angles?

Answer 28

phi, psi, and omega (peptide bond)

Question 29

in rare case, omega=0 degrees for a cis peptide bond which usually involves which AA?

Answer 29

proline

Question 30

what allows the proline side chain have both cis and trans configurations with nearly equivalent energies?

Answer 30

its cyclic nature

Question 31

because the formation of a peptide bond is not favored thermodynamically, what allows it to be favored?

Answer 31

the reverse reaction, hydrolysis of the peptide bond

Question 32

what is the orientation of a polypeptide?

Answer 32

N-terminus on the left and C-terminus on the right

Question 33

how do you name a polypeptide?

Answer 33

name the individual AAs in order starting with the N-terminus with the name of every AA ending in -yl, except for the C-terminal AA, which takes its full name

Question 34

what are short peptides of a few residues called?

Answer 34

oligopeptides

Question 35

what are the longer chain peptides called?

Answer 35

polypeptides

Question 36

what is the average molecular weight of an amino acid?

Answer 36

about 138

Question 37

when accounting for abundance of AAs in known proteins, what is the average molecular weight?

Answer 37

about 128

Question 38

peptide bond formation removes a water molecule (mw 18) so what is the average weight of an amino acid residue?

Answer 38

110

Question 39

how can you estimate the number of residues in a protein?

Answer 39

divide the molecular weight by 110

Question 40

what do the amino acid side chains do?

Answer 40

direct folding of nascent polypeptide into a function protein and stabilize its final conformation