Charge & Shape in Biological Systems

Question 1

Summarise atomic structure

Answer 1

• Contains a dense nucleus which consists of protons and neutrons
• Protons and neutrons have a nominal mass of 1
• protons have a charge of +1 and neutrons 0.
• The nucleus is very dense
  
  • accounts for 99.99% of the mass.
  • The nucleus is surrounded by a cloud of electrons in which exist is shells that can contain 2, 8, 18 electrons which have a nominal mass of 0 and a charge of -1.
• All atoms of an element have the same number of protons (atomic number).
• Partially filled electron shells are not as energetically preferable as filled shells so atoms swap or share electrons in order to fill (or empty) their electron shells

Question 2

Summarise Ionic bonding

Answer 2

• Atoms with few electrons in their outer shell will lose these quite readily to form cations
  
  • we know these elements as metals.
• Atoms with nearly full outer shells can take these electrons to fill their shells and form anions.
• This results in an electrostatic attraction between the ions, bringing them together through ionic bonding interactions.

Question 3

What are hydrogen ions and what are they a measure of?

Answer 3

• Hydrogen can also lose its electron to form H+
• The H+ion has no electrons and is therefore just a proton–it is 1/100,00ththe size of an atom
• H+is the species responsible for acidity
  
  • the measure of pH actually describes the concentration of free H+

Question 4

Summarise covalent bonding

Answer 4

• Molecules contain covalently bonded atoms
• A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms
• this brings the molecule to a lower energy level overall
  
  • a favourable process
• Most covalent bonds are very strong

Question 5

Discuss the structure and bonding within and between water molecules

Answer 5

• Oxygen is ‘electronegative’
  
  • the electrons shared in the covalent bonds are attracted to it, pulling electrons away from the H, polarising the bond → partial -vecharge on O & partial +vecharge on each H.
  • This leads to an attraction between oxygen on one molecule of water and the hydrogens on another which is known as hydrogen bonding
• 2 types of bonding in liquid water:
  
  • Covalent bonds(sharing electrons between oxygen and hydrogen)
  • Hydrogen bonds (attraction between non-bonding electrons on oxygen and hydrogens on adjacent water molecules)
• Water is a POLAR environment
  
  • It is good at solubilising polar regions of molecules (or polar species such as ions).
  • It does not solubilise non-polar regions well.
  • Areas of molecules with charge, good hydrogen-bonding potential and/or a low proportion of carbon atoms tend to sit in (or facing) water known as hydrophilic
  • areas of molecules with high proportion of carbons tend to be pushed out of the aqueous phase
    –known as hydrophobic or lipophilic

Question 6

What is the strongest bond?

Answer 6

Covalent

Question 7

What is the weakest bond?

Answer 7

Van der Waals

Question 8

How is hydrogen bonding relevant to DNA?

Answer 8

• Specificity of base-pairing results from specific hydrogen bonding patterns between A/T C/G
• Hydrogen bonding controls base pairing and occurs despite the relative hydrophilicity of the nucleobases

Question 9

What are acids?

Answer 9

Acids are compounds that can lose a H+ ion becoming -vely charged

Question 10

Give an example of an acid that completely dissociates to atomic ions in aqueous solution

Answer 10

HCL

in a less polar solvent it remains associated as a covalent molecule

Question 11

Give an example of an acid that completely dissociates to an ionic molecule in aqueous solution

Answer 11

H2SO4

Question 12

What are weak acids?

Answer 12

Compounds that can exist in two states and can go between the forms at physiological pH
- Equilibrium

Question 13

What are bases?

Answer 13

• Bases are compounds that can (reversibly) form covalent bonds with an H+ion to become positively charged
  
  • For weak amine bases, this equilibrium is also possible at physiological pH ranges.

Question 14

What happens to acids with a low pKa?

Answer 14

They are predominently ionised (anionic) at physiological pH

Question 15

What happens to bases with a high pKa?

Answer 15

They are predominently ionised (cationic) at physiological pH

Question 16

What happens to acids and bases when they are ionised?

Answer 16

Become very hydrophilic. The extent to how hydrophilic varies with pH but at physiological pH they are very hydrophilic

Question 17

How are amides formed from peptides?

Answer 17

Peptide bond forms between amines and carboxylic acids to form an amide

Question 18

How is the hydrophilic/phobic nature of a protein determined?

Answer 18

Determined by the R group as the amide is neutral across the physiological pH range

Question 19

What is the primary protein structure?

Answer 19

• The order of the amino acids

- entirely responsible for both structure and function of protein

Question 20

What is the secondary protein structure?

Answer 20

• Arrangement of primary structure into defined regions, e.g alpha helix and beta sheet
• Determined by the shape (conformational preference) of the residues due to their hydrophobicity/hydrophilicity preference, and maintained by regular hydrogen bonding pattern.Can be predicted from primary structure.

Question 21

What is the tertiary protein structure?

Answer 21

• Higher order folding of these secondary structures
  
  • gives the overall shape of a protein chain
• Bonding interactions (ionic, hydrogen-bonding) are important
• Some new covalent bonds can be made between chains (di-sulphidebonds between cysteines)
• Conformation of residues influences structure (most common example is proline-induced turns)
• Hydrophilicity plays an important role. Lipophilic residues prefer to be at the centreof the protein (away from water) and so will influence structure.

Question 22

What is the quarternary protein structure?

Answer 22

• How chains come together and arrange to form complexes
• Bonding interactions between chains are important
• Lipophilic residues prefer to be at the centre of the protein (away from water) and so will influence structure, function and where protein will be found in cells (cellular distribution)