Charge and shape in biological molecules

Question 1

What is the structure of the nucleus in the atom?

Answer 1

Protons have a mass of 1, charge of +1.
Neutrons have a mass of 1, charge of 0.
The nucleus is very dense.

Question 2

Where are electrons in the atom?

Answer 2

The nucleus is surrounded by a cloud of electrons which exist in shells that can contain 2,8,18 electrons.
Electrons have a mass of 0 and charge of -1.

Question 3

What is the atomic number?

Answer 3

All atoms of the same element have the same number of protons.

Question 4

What are cations?

Answer 4

Atoms with few electrons in their outer shell will lose electrons readily to form positively charged cations - these are metals.

Question 5

What are anions?

Answer 5

Atoms with nearly full outer shells take electrons from metals to form negative anions.
These are non-metals.

Question 6

What is ionic bonding?

Answer 6

The electrostatic attraction between oppositely charged ions.

Question 7

What are hydrogen ions?

Answer 7

Hydrogen loses its one electron to form H+, which is a proton.
It is responsible for acidity.

Question 8

What is pH?

Answer 8

The measure of concentration of free H+.

Question 9

What are covalent bonds?

Answer 9

A chemical bond involving the sharing of electron pairs between atoms.
Sharing electrons brings the molecule to a lower energy level overall.

Question 10

What is the strength of covalent bonds?

Answer 10

Covalent bonds are very strong.

Question 11

Why is water polar?

Answer 11

Oxygen is electronegative - the electrons shared in the covalent bonds are attracted to it - so electrons are more towards oxygen than hydrogen.

Question 12

What are hydrogen bonds?

Answer 12

There is a partial negative charge on oxygen and partial positive charge on hydrogen.
This attraction between oxygen on one molecule of water and hydrogen on another is hydrogen bonds.

Question 13

What is the order of strength of intermolecular interactions?

Answer 13

Single covalent bond
Cation-anion
Hydrogen bond
Pi-cation
Pi-Pi
Dipole-dipole
Van der Waals
This is dependent on the solvent - strength is likely to be less in an aqueous environment.

Question 14

What is the function of hydrogen bonds in DNA?

Answer 14

Hydrogen bonds control base-pairing.
Specificity of base-pairing results from specific hydrogen bonding patterns between A/T and C/G.

Question 15

Why is it unusual hydrogen bonding can control base pairing?

Answer 15

Nucleobases have a relative hydrophilicity - which means they are good at dissolving water.

Question 16

What are features of water due to hydrogen bonding?

Answer 16

High latent heat capacity
Ice is less dense than water
Water expands when it feezes
Heat breaks hydrogen bonds.

Question 17

How is water a polar environment?

Answer 17

Water is good at solubilising polar regions of molecules or polar ions.
It does not solubise non-polar regions well.

Question 18

What are hydrophilic qualities?

Answer 18

Areas of molecules with charge, good hydrogen-bonding potential and low proportion of carbon atoms sit in or face water.

Question 19

What are hydrophobic qualities?

Answer 19

Also lipophilic.
Areas of molecules with a high proportion of carbons tend to be pushed out of the aqueous phase.

Question 20

What are the features of the phospholipid membrane?

Answer 20

The phosphate head group is hydrophilic.
The fatty acid tails are hydrophobic/lipophilic.

Question 21

What is a phospholipid bilayer?

Question 22

What is a phospholipid liposome?

Question 23

What is a phospholipid micelle?

Question 24

What are acids?

Answer 24

Compounds that lose a proton and become negatively charged.
e.g. HCl, H2SO4

Question 25

Is HCl strong?

Answer 25

HCl completely dissociates to its atomic ions in aqueous solution. HCl --> Cl- + H+ In less polar solvent it remains associated as the covalent molecule.

Question 26

What are weak acids?

Answer 26

Weak acids partially dissociate. The energy difference between the two states can be relatively small and going back and forth between the forms is possible in the physiological pH range.

Question 27

What are bases?

Answer 27

Compounds that can form covalent bonds with a proton to become positively charged.

Question 28

What are weak bases?

Answer 28

In weak amine bases, the equilibrium between dissociation is possible at physiological pH range.

Question 29

Which acids are ionised?

Answer 29

Acids with low pKa (<7.4) are predominantly ionised at physiological pH. E.g. Glutamic acid, aspartic acid

Question 30

Which bases are ionised?

Answer 30

Bases with high pKa (>7.4) are predominantly ionised at physiological pH. e.g. lysine, arginine. When charged, these residues (acids as well) are very hydrophilic.

Question 31

What are amides?

Answer 31

In peptides, amines and carboxylic acids combine to form amides. Amides are neutral across the physiological pH range - do not ionise.

Question 32

What determines the tendency for water of proteins?

Answer 32

The different R-groups within the amino acids, which is greatly influenced by the ionisation state of the peptide side chains, determines the hydrophilic or hydrophobic nature.

Question 33

What is basic primary structure of proteins?

Answer 33

The order of amino acids - is responsible for the structure and function of the protein.

Question 34

What is the basic secondary structure of proteins?

Answer 34

Arrangement of primary structure into defined regions - alpha helix or beta sheet. Can be predicted from primary structure.

Question 35

How can secondary structure be determined?

Answer 35

Secondary structure is determined by the shape of the residues due to the hydrophicity/hydrophilicity preference. It is then maintained by regular hydrogen bonding pattern.

Question 36

What is the basic tertiary structure of proteins?

Answer 36

Higher order folding of secondary structure - gives the overall shape of a protein chain. Conformation of residues influences structure.

Question 37

What bonds form in tertiary structure?

Answer 37

Ionic and hydrogen bonding is important. Some new covalent bonds can be made between chains - disulphide bonds.

Question 38

How does hydrophilicity affect tertiary structure?

Answer 38

Lipophilic residues prefer to be at the centre of the protein and so influences structure.

Question 39

What is the basic quarternary structure of proteins?

Answer 39

How the chains come together and arrange to form complexes. Lipophilic residues prefer to be at the centre so affect structure.