Biochemisty - Part 1

Front 1

How does water influence enzyme activity?

Back 1

Displacement of water makes E-S binding energetically favorable

Front 2

What are the 4 types of Noncovalent Interactions among biomolecules in Aqueous solution?

Back 2

Hydrogen bonds, ionic interactions, hydrophobic interactions, Van der Waals interactions

Front 3

List the nonpolar, aliphatic amino acids.

Back 3

Gly, Ala, Pro, Val, Leu, Ile, Met

Front 4

List the aromatic amino acids.

Back 4

Phe, Tyr, Trp

Front 5

List the polar, uncharged amino acids. What common feature do they share?

Back 5

Ser, Thr, Cys, Asn, Gln.
All contain electronegative atoms

Front 6

What effect does the environment have on Cys residues?

Back 6

Cys amino acids are able to form disulfide bridges in oxidizing environments.

Front 7

List the positively charged/basic amino acids.

Back 7

Lys, Arg, His.

Front 8

List the negatively changed/ acidic amino acids.

Back 8

Asp, Glu.

Front 9

What do the pI, the pKa, and blue boxes represent on the titration curve?

Back 9

(pI) all the H's of the C-terminus are off and now are dealing with the N-terminus; in the Zwitterionic form
(pKa) pt where 1/2 of one terminus has H's on and 1/2 are off
(blue boxes) buffering region, where changes in base concentration has little affect on changing pH

Front 10

How do you form/break a peptide bond?

Back 10

form via condensation and break via hydrolysis

Front 11

What is ion-exchange chromatography? Separates by what? Elute?

Back 11

cation exchange is negatively charged and an anion exchange is positively charged
separates by charge
elute witih 1) varying pH (will change charge) or 2) adding salt concentration to compete for column binding

Front 12

Gel filtration or size-exclusion chromatography

Back 12

separates by size
largest molecules exit first
no need to elute, keep refilling reservoir and all molecules will eventually exit

Front 13

Affinity Chromatography

Back 13

pack column with Ag
pour in solution with Ab
elute by adding 1) more Ag or 2) increasing salt concentration

Front 14

Electrophoresis (SDS PAGE)

Back 14

separate by size
SDS negatively charges all molecules likely, breaks disulfide bonds, and unfolds proteins
smaller proteins move farther towards the + upon induction with electric field
can use to estimate a protein's MW

Front 15

Isoelectric Focusing

Back 15

test tube with decreasing pH
separates by pI (where pI =pH, charge = 0 and v =0)

Front 16

2-D electrophoresis

Back 16

1st do isoelectric focusin
2nd do SDS PAGE

final result has MW decreasing top to bottom and pI decreasing left to right