Unit 2: 4

Question 1

Van der Waal’s force

Answer 1

arises from an electric dipole in a molecule with no net charge that is induced when the two atoms are brought near each other

• happens in all atoms, regardless of type
• essentially a transient dipole

Question 2

Lennard-Jones potential

Answer 2

E = -A/r^6 + B/r^12

-an equation that approximates the distance dependence of van der waals energy

Question 3

Hydrophobic Effect

Answer 3

the tendency of certain molecules to interact with themselves and not with water

• glue that holds proteins together
• major driving force for proteins interactions with hormones, nucleic acids and other proteins and PROTEIN FOLDING

Question 4

Two misconceptions about the hydrophobic effect

Answer 4

1. hydrophobic groups and water repel each other (still have van der waal’s forces like everything else)
2. hydrophobic groups have a unique mutual attraction

Question 5

Clathrates

Answer 5

• hydrophobic “ice” -water molecules form these structures around hydrophobic components to satisfy their desire to hydrogen bond
• water molecules are more highly ordered in clathrates than in bulk solution -> thus lowering entropy and this is believed to be one of the reasons hydrophobic molecules cluster together to reduce the surfaces exposed to water

Question 6

What stabilizes secondary, tertiary and Quaternary structure?

Answer 6

1. Hydrogen bonding
2. van der waals
3. electrostatic forces
4. hydrophobic effects

Question 7

Which amino acid readily forms alpha helix?

Answer 7

Alanine (because of its lack of side chains suggests its default backbone conformation is helical)

Question 8

Which amino acid(s) are considered strong helical “breakers”?

Answer 8

• Proline- lacks the NH to hydrogen bond

- Glycine - flexible

Question 9

Which amino acid(s) are considered medium helical “breakers”?

Answer 9

Beta branched bulky
Valine, Thr, trp, phe
lose much rotational freedom when in a helix

Question 10

Which amino acid(s) are considered strong helix indifferent?

Answer 10

-long straight chain amino acids (Arg, Lys, Glu)

lose less rotational freedom (alanine loses none)

Question 11

Beta sheets

Answer 11

-fully hydrogen bonded structures, not planar, but has a “pleated” appearance as predicted by pauling bc he’s the man.
two forms:
1. parallel- the strands all point in the same direction (H-bonds slightly bent- less frequently observed)
2. anti-parallel- the strands are head to tail

Question 12

Why beta sheets are stabilized?

Answer 12

• favorable backbone dihedreal angles
• phi psi angles ~ 140 degrees -the chain is nearly fully extended
• rise = 3.5 A
• periodicity = 2
• straight hydrogen bonds between strands
• interaction between adjacent strands (tertiary interaction) -> amyloid

Question 13

The reverse beta turn

Answer 13

• 1/4 of protein structure
• several types
• much sequence variability
• required: glycine (used to avoid steric clashes)
• preferred: proline (because kinked - covalent bond between side chain and main chain puts a kink in backbone)

Question 14

Irregular structure

Answer 14

• sometimes called random coil
• generally only random in the sense that it is not periodic
• usually has specific structures
• surface loops are critical to function
• loops help give proteins their individuality
• not secondary structures
• usually found on the proteins surface and are comprised mostly of hydrophilic residues -they are flexible and often tether globular domains together
• loops are frequently the binding site with another protein or substrate molecule (many examples where proteins only differ in the structure of their loops)

Question 15

motifs

Answer 15

small functional units that are part of larger structures

-motifs consist of short stretches of secondary structure and are usually not stable by themselves

Question 16

Helix turn helix motif

Answer 16

a recognition alpha helix and a support alpha helix connected by a turn. The recognition helix sits in the major groove and binds to specific sequences of nucleotides. The structure of recognition helix is maintained by side-chain-side chain contacts between it and the support helix.

Question 17

zinc finger motif

Answer 17

unlike the helix turn helix motif, zinc fingers bind DNA weakly and transcription factor proteins use 2-40 of these repeats to effectively bind DNA
-the function of the zinc is to hold the structure together without using excessive hydrophobic core -but hydrophobic side chains are used to stabilize the helix which binds to the major groove of DNA

Question 18

Domains

Answer 18

continuous stretches of polypeptides that are linked together by flexible loops
residues within the domain interact more with each other than residues outside of it as a result they tend to be stable in isolation after the rest of the protein has been removed.

Question 19

Coil-coil domains

Answer 19

potentially extremely stable structures- often found in transcription factors and fibrous proteins
-signature ‘heptad repeat’
a-b-c-d-e-f-g (a and d= nonpolar) (e and g = charged, usually opposite one another)
- also function in protein-protein recognition, mechanical force transduction, and viral penetration