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non polar aliphatic R-group

GAPVLIM

Aromatic R-groups

FYW

Uncharged polar R-groups

STCNQ

Polar positively charged R-groups

KRH

Polar Negative R-groups

DE

Ionic interaction

• KRH

• DE

Hydrogen bond acceptors

DE

Hydrogen bond donors

KRH

Positively charged at pH7.4

KRH

Hydrophilic

STCNQ

Hydroxyl, Amide, and Thiol

STCNQ

Non-polar

FYW

hydrophobic

GAPVLIM

Carbons and hydrogens

GAPVLIM

if pk> pH

protonated

pk < pH

deprotonated

how many residues per turn

3.6

distance per turn

5.4 angstrom

motif

small groupings of secondary structure found repeatedly in unrelated globular proteins

domains

distinct folded areas of an extended polypeptide chain

amino acids essential for collagen

glycine and proline

separation techniques

1. salting out

2. ion exchange chromatorgraphy

3. hydrophobic interaction chromatography

4. gel filtration chromtagrophy

5. affinity chroma

salting

solubility

ion exchange chromatography

charge

hydrophobic interaction chromatography

polarity

gel filtration chromatography

size

affinity chromatography

binding affinity

2-mercaptoethanol

reductively cleaves disulfide bond

iodoacetate

prevents reformation of disulfide bonds

dansyl chloride

reacts with primary amines (used in identification of N-term)

CNBr

cleaves the C-term side of methionine residues

phenylisothiocyanate

reacts with N-term amino acids (edmans reagent-PTC)

edman degredation procedure

1. separate polypeptide chains

2. cleave disulfide bonds

3. determine amino acid composition

4. determine end groups

5. cleave chain into smaller fragments using proteases or chemicals

6. repeat step 5 with different protease or chemical

7. sequence peptides by edman degradation using PTC

8. reconstruct fragments by comparing sequences of overlapping fragments

trypsin

arg, lys except near proline

chymotrypsin

phe, trp, tyr except near pro

elastase

ala, gly, ser, val except near pro