Nap Attack 6

Question 1

Anfinsen’s dogma

Answer 1

at least for small globular proteins, tertiary structure is determined exclusively by primary structure (based on study of addition and removal of mercaptoethanol)

Question 2

native structure represents

Answer 2

a unique, stable and kinetically accessible minimum of the free energy

Question 3

chemical interactions that stabilize polypeptides

Answer 3

covalent bonds, disulfide bonds, salt bridges, hydrogen bonds, long-range electrostatic interactions, Van der Waals interactions

Question 4

How is stabilization from these weak bonds possible

Answer 4

strength in numbers, many weak bonds can make a large stable structure

Question 5

Advantages of stabilization through weak interactions

Answer 5

allow for dynamic interactions and permit energy and information to more about the cell (pulling apart dna)

Question 6

biological covalent bond strengths

Answer 6

200-460 kJ/mol (stable but can be broken under physiological conditions)

Question 7

biological weak interactions strength

Answer 7

0.4-30 kJ/mol (continuously broken and reformed)

Question 8

disulfide bond fun facts

Answer 8

• proteins on the extracellular surface are no longer exposed to the reducing environment inside a cell
• non-reducing environment disulfide bonds can form between the side chains of cysteine residues
• found primarily in secreted extracellular proteins(eukaryotes)
• uncommon in prokaryotes

Question 9

four primary types of non-covalent forces that promote and stabilize protein structure

Answer 9

• hydrogen bonds
• electrostatic interactions(Ionic)
• hydrophobic interactions
• van der waals interactions

Question 10

Second law of thermodynamics

Answer 10

the total entropy (disorder) of a system and it’s surroundings always increases in a spontaneous process

Question 11

when a non polar molecule is introduced into water

Answer 11

• a cavity is created
• displaced water molecules reposition to form hydrogen bonds because there are less ways of forming hydrogen bond
• decrease in entropy
• non polars collect to release water molecules

Question 12

The presence of other molecules in aqueous solution

Answer 12

disrupts the hydrogen-binding of water

Question 13

when water surrounds a hydrophobic molecule

Answer 13

• results in a highly structure shell, or solation layer, of water around the molecule (decreased entropy)

Question 14

when non-polar groups cluster together

Answer 14

the extent of the solation layer decreases bc each group no presents its entire surface to the solution

• less energy required to encage clumps of molecules than individually
• favourable increase in entropy major thermodynamic driving force for association of hydrophobic groups in aqueous solutions

Question 15

water is a

Answer 15

dynamic loose network of hydrogen bonds

Question 16

hydrogen bond features in common with covalent and non-covalent bonds

Answer 16

• charge-charge interaction using the partial positive charge on the hydrogen and negative charge on the electron pair
• electron pair sharing between the hydrogen and the electron pair (reflected in bond length (in the middle of van der walls and covalent bond length)

Question 17

hydrogen bond

Answer 17

an electrostatic interaction between an electronegative atom with a hydrogen linked (donor) to another electronegative atom with a free electron pair (acceptor)

• covalently bonded hydrogen atom, pair of non bonded electrons
• highly directional (points directly at the electron acceptor pair

Question 18

most common hydrogen bond donors and acceptors (within biomolecules)

Answer 18

oxygen and nitrogen

Question 19

intramolecular hydrogen bonds

Answer 19

groups within the same molecule

Question 20

intermolecular hydrogen bonds

Answer 20

groups within other molecules

Question 21

significance of hydrogen bonding in biomolecular interactions

Answer 21

• are a critical determinant of specificity
• not a force of formation(could just bond with water)
• little to be gained from a hydrogen bonding perspective with the formation of higher order structures

Question 22

the strength of a hydrogen bond depends on

Answer 22

its geometry

Question 23

polarizable

Answer 23

a molecule in which a dipole can be induced(from electric fields)

Question 24

induced dipole interactions

Answer 24

iteractions of polarizable molecules, shorter range than permanent dipole interactions

Question 25

fluctuations in the electronic charge distribution cause

Answer 25

molecules with neither a net charge nor permanent dipole moment to attract one another(happens if their close enough)

Question 26

when two molecules approach a very close distance

Answer 26

they synchronize their charge fluctuations so as to give a net attractive force (their surrounding electron clouds influence each other) ( their outer electron orbitals are overlapping and there is repulsion)

Question 27

van der waal attraction maximal when

Answer 27

two atoms are seperated by the sum of the van der Waal radii (theres a wall barring approach closer than distance rv)

Question 28

van der waals common in _____

Answer 28

core of protein, because of the close packing of hydrophobic side chains

Question 29

in a cell charges are surrounded by

Answer 29

dielectric medium that screens charges from one another

Question 30

E =

Answer 30

k* (q1*q2)/£r

Question 31

prion diseases

Answer 31

transmissible spongiform encephalopathies

- novel paradigm of infectious disease based on misfolding of self protein into a pathological, infectious conformation

Question 32

When a protein misfolds

Answer 32

new regions are surface exposed for antibody binding

- these misfolding dependent epitopes termed Disease-Specific epitopes (ideal vaccine targets)