11. Biochemistry

Question 1

oligopeptide

Answer 1

small chain of amino acids

Question 2

polypeptide

Answer 2

long chain of amino acids

Question 3

alpha carbon stereocenter

Answer 3

all human amino acids, due to the 4 substituents (r group, hydrogen, carboxylic acid, and an amine

Question 4

absolute configuration

Answer 4

all native configurations are L- amino acids,

Question 5

L and D configurations

Answer 5

CHO on top with a dash, CH2OH on bottom with a dash, OH to the left on a wedge for L- conformation, and OH on the right with a wedge for D- conformation, the remaining right or left side has a H on a wedge

Question 6

L&D vs. R&S

Answer 6

R&S goes by electro negativity, L&D go by CHO on top and CH2OH on bottom, and placement of OH determines postion

Question 7

order of deprotonation

Answer 7

alpha- COOh group, then acidic R group, then His R group, then alpha NH3+ group then basic R groups

Question 8

COOH groups

Answer 8

pKa 2

Question 9

-R group (acidic)

Answer 9

pKa 4 (Asp 3.7, Glu 4.5)

Question 10

-R group (His)

Answer 10

pKa 6

Question 11

NH3+ group

Answer 11

pKa 9

Question 12

-R group (basic)

Answer 12

pKa 11-12 (Lys 10.7, Arg 12)

Question 13

essential amino acids

Answer 13

body cannot synthesize these

Question 14

non-essential amino acids

Answer 14

body can make its own

Question 15

zwitterion

Answer 15

dipolar amino acid with a positively and negatively charged AA

Question 16

amino acids are weak acids

Answer 16

weak acids, each amino acid has 2 acidic protons (COOH and NH3+), when pH is near pKa of one of the acidic protons the amino acid acts as a buffer.

Question 17

isoelectric point (pI)

Answer 17

pH at which a molecule carries no net charge, (pI for a molecule with two pKa’s the pI is the average of the two pKa’s, pH lower than pI, molecule will have a net positive charge, pH higher than pI the molecule will have a net negative charge. pI is similar to equivalence point but instead of neutral pH it is neutral charge

Question 18

pIneutral

Answer 18

average of pKa-amine group and pKa-carboxyl group.

Question 19

pIacidic

Answer 19

average of pKa-acidic R group and pKa-carboxyl group.

Question 20

pIbasic

Answer 20

average of pKa-amine group and pKa-basic R group.

Question 21

titration curves

Answer 21

aspartic acid into base, buffer, equivalence, end, buffer, equivalence, end. phenylalanine into base, buffer, half eq, equivalence, end

Question 22

peptide bond formation

Answer 22

dehydration synthesis and acyl substitution. The amine group nitrogen (nucleophile) from the NEW amino acid attacks the carbonyl carbon (electrophile) on the C-TERMINUS of the growing peptide chain (aided by the enzymatic function of the ribosome).

Question 23

peptide chain conversions

Answer 23

written, read and synthesized from N-terminus –> C-terminus