export_aa

Question 1

Hydrophobic amino acids

Answer 1

* GAV LIMP TP * Gly, ala, val, leu, I le, pro, phe, met, trp

Question 2

Polar amino acids

Answer 2

* Polar CATTS G rowl * Cysteine, asparagine, threonine, tyrosine, serine, glutamine

Question 3

Polar uncharged amino acids

Answer 3

* Thre e TAGS * Threonine, tyrosine, asparagine, glutamine, serine

Question 4

Acidic amino acids

Answer 4

Asp and glu

Question 5

Basic amino acids

Answer 5

* His lys ar e basic * Arg, his, lys

Question 6

3 AA that contribute to UV absorbance at λ=280 nm

Answer 6

1. Trp (ε ~5000 M -1 cm -1 ) 2. Tyr (ε ~1000 M -1 cm -1 ) 3. Phe (ε ~250 M -1 cm -1 )

Question 7

Structures at half and full E.P. (equivalence point)

Answer 7

https://s3.amazonaws.com/classconnection/833/flashcards/4068833/gif/half_and_full-153E2F7BA226388E880.gif

Question 8

Iso (pI) electric point

Answer 8

Characteristic pH where net charge of a protein is 0

Question 9

To calculate pI of asp/glu

Answer 9

Take an average of sidechain pKa + α-COOH pkA

Question 10

To calculate pI of basic amino acids

Answer 10

= (side chain pKa + α-NH3)/2

Question 11

Excluding basic/acidic side chains, for other ionizable groups, how do we calculate pI

Answer 11

1. Determine middle pKa 2. Add with α-COOH 3. Divide by 2

Question 12

pKa range for ammonium (NH3+)

Answer 12

8.8-11.0

Question 13

pKa range for -COOH

Answer 13

1.8-2.4

Question 14

Primary protein structure

Answer 14

* Series of aa joined by peptide bonds * Most important aspect of 1° structure is sequence of aa

Question 15

Secondary protein structure

Answer 15

* Classified (α-helix, β-sheet, β-turn) according to how the polypeptide folds upon itself

Question 16

Alpha helix

Answer 16

* 3.6 residues per turn * Hydrogen bonding stabilizes the structure (between N-H and O=C)

Question 17

Beta sheet

Answer 17

* Parallel: β-strands line N-N and C-C terminals * Anti parallel: β-strand folds upon itself, lining N with C * Stabilized by H bonds

Question 18

Beta turn

Answer 18

* 5 amino-acid residues or less * Lye on the protein surface because they are hydrophilic

Question 19

Tertiary structure

Answer 19

* Higher order of folding * Stabilized by H-bonds, VDW interactions, disulfide bridge formation (only in cys), and hydrophobic packing

Question 20

Quaternary structure is described by

Answer 20

* Interaction between tertiary polypeptides * Named according to # of sub-units

Question 21

What is unique about C-N bond

Answer 21

Has partial double bond character, cannot rotate freely

Question 22

Rotation is permitted about the

Answer 22

N-Cα and Cα-C bonds

Question 23

Ramachandran plot

Answer 23

* Determines stable configurations of phi and psi angles * Only a few configurations are energetically favorable, therefore polypeptide chain flexibility is limited

Question 24

3 characteristic areas on a Ramachandran plot

Answer 24

https://s3.amazonaws.com/classconnection/833/flashcards/4068833/gif/ram-153E35363B36F397A88.gif

Question 25

Hydrophobic effect

Answer 25

* CH3 (non-polar) does not interact well with H20 * Interaction decreases entropy * When contact is minimized entropy increases due to clustering of non-polar groups

Question 26

Stabilizing interactions: hydrogen bonding

Answer 26

NH and OH groups form H bonds

Question 27

Stabilizing interactions: ionic interactions

Answer 27

* In the 2 acidic aa (asp, glu), occurs in non α-COOH * Also occur in a molecule (ie lys) with an extra NH2 group * Ionic bonds form between +&- groups

Question 28

Stabilizing interactions: disulfide bond

Answer 28

Form only when 2 cysteine residues bond

Question 29

Gel filtration (size-exclusion) chromatography

Answer 29

Small proteins are trapped first in the beads within the column, while the biggest proteins travel the farthest/fastest

Question 30

Ion exchange chromatography

Answer 30

* Separation based on charge and the pH of the matrix

Question 31

SDS PAGE

Answer 31

* SDS binds to protein, giving them all - charge * smaller proteins move fastest * polyacrylamide has bigger pores than agarose

Question 32

Affinity chromatography

Answer 32

* Separate based on affinity to bind to ligand * Unwanted proteins exit while protein of interest is held in the column

Question 33

Basic idea of Solid Phase Peptide Synthesis

Answer 33

* since protecting group for C-terminus does not need to be removed, attach C-terminus to resin (solid support or bead) * Add each additional amino acid to free N-terminus of growing peptide chain * Cleave peptide product off solid support as final deprotection