BIS 102 conceptual

What experiments were done on Euglena

Euglena was placed in one flask containing Zn2+ and another with no Zinc media. Both conditions were than placed into light and Euglena in Zinc swam perfectly and seemed mobile. The Euglena in with no zinc seems nonmotile and was about 10x its original size and had in increase in iron, magnesium and calcium. when zinc was added to media, the euglena returned to normal state.

what is the amino acid with an indole group

tryptophan

what is the amino acid that is the most hydrophobic

isoleucine because of its molecule orientation. The water will wrap around the side chain and form a clathrin

what are the two chemicals to reduce disulfide bonds

mercaptoethanol (BME) and dithiothreitol (DTT)

• DTT can be lower in concentration and stronger

what does 280 nm wavelength measure

used to measure absorbance of W, Y, and F in A280 protein assay

what does 440nm of wavelength measure

wavelength used to detect amino acid exchange column (P only)

what wavelength is 570 nm used to measure

this wavelength is used to detect aa in an exchange ion (all acids except for P)

what are the special properties a compound wil have pH=pI

• net charg of molecule = 0

• no movement in electric field

• bind electrostatically to another molecule

what are ionic bonds

(±) ionic bridges, force of attraction between opposite charges, increases with distance decrease strength, pH matters

what is hydrophobic effect

tendency of water molecules to not bind with nonpolar molecules. flickering clusters, doesn’t care about shape or pH, temp is important

what are hydrogen bonds

Donors: ONS, binding of hydrogen with ONS. pH matters, distance matters (straight line is good)

what are Van der Waals

happens between two touching molecules, pH does not matter

what kind of bonds will be affected by pH

hydrogen and ionic bonds

what bonds are affected by distance

hydrogen bonds, van der waals bond and ionic bonds

affected by polarity/hydrophobicity of solvent

all but ionic bonds are most affected by constant

which bonds are affected by temperature

hydrophobic effect and hydrogen bond

what is affected by hydrogen direction

hydrogen bonds

what is mainly based on entropy change

hydrophobic effect

which bond affects one or more water molecules

hydrophobic effect or hydrogen bonds

what is the goal of performing amino acid analysis

to identify and qualtify each and every amino acid present

what catalyst is used to preak pepetide bond and how does it work

HCl adds proton to every C double bond O including side chains. This makes the C is now much more electrophilic and H2O is now able to attack which breaks CN peptide bods

what is a typical protein. how many peaks do you expect

19, 20 aa, two can’t be seen, and plus another peak from Nh4 so 19 peaks in total

which amino acid peaks twice as large as most other acids per mole

Lysine (K) since it ahs 2 amino groups

which aa elutes with 0.35 N citrate buffer and why?

Arginine and has positive charge at every charge at any pH. citrate salt concentration must be increased so salt counter ion outcompete arginine to bind to column instead allowing arginine to run off

what is the pH of the resin in the column to work correctly.

it has to be between 1.5 and 3 because anything below 1.5 protonates sulfonic acid resuidues. Aspartic acid D is the easiest to elute and has pI=3. to keep D with (+) charge, must have pH below pI

in hydrophobic effect what happens when temperature is changed

in hydrophobic effect, a clathrate structure around hydrophobe. lower temp, hydrophobic effect is not going to show. since entropy is a big part of hydrophobic effect, a lower temp means more positive Gibbs free energy meaning not spontaneous act

which amino acid has a side chain bound to its amino group

proline

which side chain is considered hydrophobic

G, A, V, L, I, M, F, W, P

which side chains contain amide functional group

N, Q

which side chain contain hydroxyl group

S, T Y

which side chain have positive charge in acidic form

H K R

which side chain has a negative charge in basic form

D E C Y

which side chain is amino acid achiral

G

which side chain can form ionic bonds in protein at pH 7

D E K R H C

what is the side chain that contains at least one sulfur atom

M, C

side chain that contains at least one nitrogen atom

S T Y D E N Q

what side chain can be detected by A280 assay

Y W T

which side chain is the heaviest molecular weight

W

what side chain can act as hydrogen bond donor or acceptor

S T N Q W

what side chain appears yellow when analyzed with minhydrin durin aa analysis

P

what side chain has a positive charge at pH 7

H R K

what is a side chain that has a negative charge at pH 7

D E C

which side chain is only compromised of carbon and hydrogen atoms

P F A V L I

side chain is in resonance in its basic form

D E R H Y

what side chain is reasonance in acidic form

D E R H Y

in the elution profile what is at pH 3

B and Z

at pH 5 what is the seen aa

H K R NH4+

what is B and Z

B is when N changes to D + NH4+

Z is when Q changes to E + NH4+