Tutorial Questions W1-4

Question 1

Name the non covalent interactions

Answer 1

• Hydrogen bonds
• charge charge interactions
• van der waals interactions (dispersion forces)
• hydrophobic interactions

Question 2

Explain what allows biological molecules to be flexible and why this is important.

Answer 2

Noncovalent interactions make biological molecules flexible as they are not static, they are dynamic. To allow them to perform their function they must have bonds that are flexible and can be readily made and broken.

Question 3

Give an example of a biological molecule that must have movement to perform its function

Answer 3

Actin/myosin, haemoglobin, ATPase

Question 4

Describe the broad biological functions of the following groups of elements and give a specific example of each.
1. Na, Mg, Cl and Ca
2. B, F, Si, Se
3. V, Cr, Mn, Fe, Co,Ni, Cu, Zn, Mo
4. H, C, O, N, S, P

Answer 4

• Na,Mg,Cl,KandCa  ionic balance: Ca nerve conduction. K extracellular, Na+ intracellular, Mg counter ion to DNA backbone, signal transduction
• B,F,Si,Se  specific specialise functions: I iodine in thyroid, Boron important role in osteogenesis
• V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Mo  trace metals, cofactors, enzymes stability, catalysis
• H,C,O,N, S, P  macromolecules, nucleic acids, proteins, polysaccharides, carbohydrates, lipids

Question 5

How many bonds do these need to satisfy their needs
H
C
O
N
S
P

Answer 5

H -1
C - 4
O - 2
N - 3
S - 2
P - 5

Question 6

What is electronegativity?

Answer 6

a) Electronegativity is a measure of the ability of an atom to attract electrons towards itself in a chemical bond. It is a property of atoms that reflects the degree to which they share or take electrons when they bond with other atoms.

Question 7

What is the most electronegative atom?

Answer 7

Fluorine - 3.98

Question 8

Order the atoms that are found commonly in biological macromolecules in order of decreasing negativity

Answer 8

O > N > C ~ S > H ~ P

Question 9

Name the polar bonds that are important in biochemistry

Answer 9

Water
Hydrogen Fluoride
Sulphur Dioxide
Ammonia

Question 10

What is a hydrogen bond?

Answer 10

Hydrogen bonds are an example of dipole-dipole interaction

Have hydrogen donor and acceptor

Weak bonds

Atoms must be lined up for the hydrogen bond to form - directional

Question 11

What are the alternate names for a charge charge interaction?

Answer 11

Ionic interaction
Salt bridge or
Ion pair

Question 12

Describe the strength of a charge charge interaction compared to other non covalent interactions

Answer 12

Charge-charge interactions are weaker than covalent bonds but are the strongest of the non-covalent interactions with the energy of the bonds ranging from 13-17kj/mol

Question 13

Explain what happens to the strength a lys-Asp interaction if it is found on the surface of an extracellular protein compared to being embedded in the centre of the protein.

Answer 13

Water molecules screening a charge:charge interaction on the surface of a protein shielding the NH3+ from the COO- and preventing them from strongly interacting

Question 14

What is a Van Der Waals interaction?

Answer 14

Van der Waals interactions are driven by induced or permanent electrical interactions (electrostatic) between two or more atoms or molecules that are very close to each other

Question 15

What causes a van der Waal interaction?

Answer 15

Van der Waal forces between dipoles that are either permanent or inducible or something happens to cause them

Question 16

What is and give example of permanent and inducible dipoles

Answer 16

Induced dipole means that something happens to make the dipole happen - asymmetry

Question 17

Is hydrogen bonding a type of Van der Waals interaction?

Answer 17

Since hydrogen bonds involve interactions between permanent dipoles, they can be considered as a type of Van der Waals force (and would fall under the category of Keesom Interactions). However, hydrogen bonds are stronger than other types of Van der Waals forces (such as Debye forces and London dispersion forces).

Question 18

What is the hydrophobic effect?

Answer 18

Non polar molecules tend to self-associate (clump) in water rather than to dissolve individually. The interactions between these hydrophobic molecules are an example of dispersion forces which are a type of van der waals interaction called London dispersion forces

Question 19

What causes the hydrophobic effect?

Answer 19

The clumping of the hydrophobic molecules and the release of water molecules is caused by the properties of the water molecules. Therefore, non polar substances do not dissolve in water, rather, the non polar molecules associate with one another by hydrophobic interactions and are excluded from the water

Question 20

What is entropy?

Answer 20

The disorder of a system

Question 21

Is high or low entropy more favourable?

Answer 21

Water like high entropy = maximum disorder

Question 22

Under what conditions does water have high entropy?

Answer 22

liquid state

Question 23

Explain how the entropy of water increases when hydrophobic molecules clump together

Answer 23

less water becomes ordered when hydrophobic substance clump together

Question 24

Explain how the hydrophobic effect contributes towards protein structure

Answer 24

The arrangement of hydrophobic side chains in a protein determines its folded structure. Because of the hydrophobic effect, hydrophobic side chains (purple) are sequestered to the proteins interior when it folds. Hydrophobic side chains (green) are usually left exposed on the proteins surface.

Question 25

Explain how the hydrophobic effect contributes towards DNA structure

Answer 25

Both purines and pyrimidines are flat in the ring plane. The upper and lower surfaces of the rings are hydrophobic, while the edges are hydrophilic. To reduce their interactions with water, the interactions between hydrophobic surfaces and water need to be minimised and this is achieved by stacking the hydrophobic surfaces of the bases in the centre of the molecule and place the sugars and phosphates at the periphery in contact with water