Biochem Test 1 memorization

henderson-hasselbalch equation

pH = pKa + log [base]/[acid]

hydrophobic functional group

R-CH3

hydroxyl

-OH (alcohol)

aldehyde

ketone

carboxyl (carboxylic acid)

COOH

amine

R-NH2

phosphate

sulfhydryl

R-SH (Cysteine)

Glycine

Gly, G, Nonpolar (hydrophobic)

Alanine

Ala, A, nonpolar (hydrophobic)

Valine

Val, V, nonpolar, hydrophobic

Leucine

Leu, L, nonpolar, hydrophobic

isoleucine

Ile, I, nonpolar, hydrophobic

Methionine

Met, M, nonpolar, hydrophobic

phenylalanine

Phe, F, nonpolar, hydrophobic

Tryptophan

Trp, W, nonpolar, hydrophobic

Proline

Pro, P, nonpolar, hydrophobic

Serine

Ser, S, Polar, Hydrophilic

Threonine

Thr, T, Polar, Hydrophilic

Cysteine

Cys, C, polar, hydrophilic

Tyrosine

Tyr, Y, polar, hydrophilic

Asparagine

Asn, N, polar, hydrophilic

Glutamine

Gln, Q, Polar, Hydrophilic

Aspartate

Asp, D, polar negatively charged, Acidic, hydrophilic

glutamate

glu, E, polar, negatively charged, acidic, hydrophilic

Lysine

Lys, K, polar, basic, positive, hydrophilic

Arginine

Arg, R, Polar, Basic, positive, hydrophilic

Histidine

His, H, polar, basic, positive, hydrophilic

Nonessential amino acids (11)

alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine

Essential amino acids (9)

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine

R-Group PKA and charge:

Terminal carboxyl

3.1

Acid- Neutral

Base- Negative

R-Group PKA and charge:

Terminal amino group

8.0

acid- positive

base- neutral

R-group PKA and charge:

Aspartic Acid/Glutamic Acid

4.1

acid- neutral

base- negative

R-group PKA and charge:

Histidine

6.0

Acid- positive

base- neutral

R-group PKA and charge:

Cysteine

8.3

Acid- neutral

base- negative

R-group PKA and charge:

Tyrosine

10.9

Acid- neutral

base- negative

R-group PKA and charge: Lysine

10.8

acid- positive

base- neutral

R-group pKA and charge: Arginine

12.5

acid- positive

base-neutral

Enzymatic Cleavage: Trypsin

carboxyl side of lysine and arginine residues

Enzymatic cleavage: Thrombin

Carboxyl side of arginine

Enzymatic cleavage: Chymotrypsin

carboxyl side of tyrosine, tryptophan, phenylalanine, leucine, and methionine

Amino acids in proteins of all organisms on earth are _ isomer

L (clockwise)

isoelectric point

The pH value at which the amino acid exists as a zwitterion (no net charge)

steps to find net charge (4)

1) identify all ionizable groups on AA

2) find pKa of ionizable groups

3) identify dominant group (protonated or deprotonated) based on pH

4)Find overall charge on AA

primary structure bond type

peptide bonds or covalent

secondary structure bond type

hydrogen bonds between peptide -NH and -CO

secondary structure

Either an alpha helix or beta pleated sheet.

Tertiary Structure bond type

hydrophobic effect- hydrophobic side chains are buried and polar/charged chains are on surface

Van der Waals interactions, H bonds as well

quarternary structure bond type

disulfide bonds

denaturation of protein methods

Thermal

Chemical (urea, BME)

molecular exclusion chromatography (gel filtration)

Small molecules enter spaces in beads, large flow through and elute first

Ion exchange chromatography

negatively charged beads will attract positive proteins, negative proteins will flow through (and vice versa)

Affinity chromatography

-uses specific interactions to slow down select molecules

-can make use of receptor-ligand, enzyme-substrate, and antigen-antibody interactions

example: beads with glucose attract glucose-binding protein, proteins attach to beads

glucose is then added into cylinder, releasing glucose binding proteins

gel electrophoresis

The separation of nucleic acids or proteins, on the basis of their size and electrical charge, by measuring their rate of movement through an electrical field in a gel.

SDS-PAGE

sodium dodecyl sulfate polyacrylamide gel electrophoresis

SDS causes proteins to all become negatively charged, and they are then separated purely by mass (smallest travel down to the anode first)