Metabolism: 1.4 Protein Structure & Function

Front 1

4 levels of protein structure

Back 1

1. Primary: aa sequence
2. Secondary: alpha-helices, beta-strant, beta, turn
3. Tertiary: fold of single peptide
4. Quaternary: complexes containing more than 1 peptide

Front 2

What is the level of protonation and charge on each of the groups of amino acids at pH = 7.0?

Acidic?

Basic?

Back 2

Zwitterion: both positive & negative charg = net charge 0

protonated (positive)

deprotonated (negative)

Front 3

Characteristics of Amino Acids.

Back 3

-amino group
-carboxyl group
-chiral
-20 aa are L-isomer (counter clockwise)
-linked via peptide bonds = protein (bw amino and carboxl group)

Front 4

Describe how an aa sequence is put together.

Back 4

-peptide bonds
-backbone is identical
-different sequence aa, yield unique proteins
-side chains w/ only H & C are hydrophobic
-side chains w/ only O or N are hydrophilic
-side chains w/ aromatic groups are hydrophobic

Front 5

What is the tertiary structure of a protein driven by?

Back 5

hydrophobi forces (especially large aromatic side-chains)

Front 6

Peptide bond

Back 6

-amide bonds
-planar
-limit # of possible conformations of peptide backbone
-lone pair e- on N resonates w/ carbonyl bond pair of e-
-resonance constrains peptide conformation cause polarity
-atoms adjacent to resonance are constrained in plane by pancake of e- density above & below plane
-backbone composed of a line of planar groups
-planar groups rotate around the alpha-carbon

Front 7

Beta-strands

Back 7

-can interact systematically to form beta-sheets
-antiparallel: L to alpha carbon is N & R to alpha carbon is C (the next row is opposite)
-parallel: both rows are going in same direction

Front 8

What conformation of aa is inhibited?

Back 8

-cannot rotate alpha-carbon 180
-sterically hindered by R-group and hydrogens
-and atoms don't interact w/ another to form a bond

Front 9

alpha-helix secondary structure

Back 9

formed from less extended backbone
-folds back and wraps around itself to form a rod
-helices: view from above = hole in tube (not solid)
-helices or rods

Front 10

tertiary structure

Back 10

alpha-helices and beta-strands fold together to form a sphere (globules)
-then can bind together to form quaternary structures

Front 11

Hydrophobic aa

Back 11

**Phenylalanine

-tyrosine
-tryptophan

-valine, leucine, isoleucine, methionine

-solvent exposed: proline (ster. hindered, cannot rotate = kink) the "turns"

-cystine: used in metal binding (catalysis) & constrain structures w/ disulfide bonds

Front 12

Amiguous aa

Back 12

hydrophobic or hydrophilic:
-glycine and alanine
-small side chains
-found in turns

Front 13

Hydrophilic aa

Back 13

polar, outside protein
-serine, threonine (form H-bonds)
-asparagine and glutamine

charged aa and very polar
-aspartate & glutamate

Front 14

Charged and basic:

Back 14

lysine
argenine
histidine

Front 15

Typical pKa values of ionizable groups in aa

Back 15

3-4:
-terminal alpha-carbon carboxyl group
-aspartic & glutamic acid

6: histidine

8:
-terminal amino group
-cysteine

10-12:
-lysine & arginine