Biochemistry

Front 1

What sorts of interactions stabalize a protein's folded structure?

Back 1

Weak interactions: H bonds, hydrophobic interactions, ionic pairs, Vander waals, disulfide bonds

Front 2

Name and briefly describe the four levels of protein structure

Back 2

1-linear amino acid sequence
2-local conformation: alpha helicies, beta pleat sheets, beta turns etc.
3- overall 3D structure: fibrous and globular
4- combined polypeptide subunits(if they exist) in 3D conformation

Front 3

The peptide bond is rigid and planar. Why is this?

Back 3

The peptide bond is a resonance hybrid. The oxygen shares electrons with the nitrogen on the other side of the Beta carbon--> this gives a negative dipole to the oxygen and a positive one to the nitrogen.
This gives the peptide bond partial double bond character, so it cannot rotate freely anymore.

Front 4

Where does a Hydrogen bond occur in an alpha helix?

Back 4

The oxygen of the carbonyl next to a residue will H bond to a hydrogen on the nitrogen 3. amino acids away.

Front 5

All peptides have what conformation? what is the exception?

Back 5

Usually trans except for sometimes when proline is involved.

Front 6

What two amino acids are only rarely found in alpha helices?

Back 6

Glycine-It is too flexible
Proline-It is too rigid, and causes a destabalizing kink. Also, since its Nitrogen is in a ring, it has one fewer H's to bond.

Front 7

Why are Glycines and Prolines particularly well suited to beta turn structure?

Back 7

Glycines are small and flexible for turns
Prolines can be in cis conformation, where the ring causes a tight 180 degree turn

Front 8

What stabalizes a Beta turn?

Back 8

An h-bond is created at the ends of the hairpin and the amino acids in the hairpin often H-bond with outside water

Front 9

Stable clusters of 2 structure can form motifs (supersecondary structure). Give some examples

Back 9

alpha alpha corners (90 degree turn), beta-alpha beta loops, beta barrels

Front 10

What is a protein domain?

Back 10

A stable globular unit within a polypeptide.

Front 11

Globular proteins usually contain more than one kind of secondary structure whereas fibrous proteins usually contain only one kind. Name a fibrous protein and it's 2ndary structural unit

Back 11

Alpha keratin- alpha helicies form coils
-an intermediate filament protein
Collagen-alpha chains (not helicies) formed from repeated 3 aa units of gly-x-pro

Front 12

How do you use X-ray diffraction to predict a protein's structure?

Back 12

1) crystallize extremely pure protein and dry onto a slide
2) put into an X-ray beam, which have a wavelength around the size of an atom.
3) use diffraction angles to see concentrations of different types of atoms

Front 13

Which covlent bonds stabalize 3 structure? Why are they particularly important in smaller proteins/?

Back 13

Disulfide linkages occurring between cysteine residues
-since smaller proteins do not have as many weak interactions, disulfide linkages play a greater relative role in structure.

Front 14

Can long range interactions be predicted from amino acid sequence?

Back 14

No, linear aa sequence cannot predict tertiary structure because we cannot predict the long range interactions.