L1: Charge and Shape in Biological Systems

Question 1

What determines the structure and function of biological molecules, cells, organs, and organisms?

Answer 1

Determined by the interactions of the atoms they are made from

Question 2

What is it that nature is able to achieve so well and is so remarkable?

Answer 2

Able to produce many different molecules from very few building blocks - use very similar elements

Question 3

What does the nucleus of an atom consist of?

Answer 3

Protons and neutrons

Question 4

What mass and charge do protons and neutrons have?

Answer 4

Both has a mass of 1
Protons have a charge of +1
Neutrons have a charge of 0

Question 5

What property results from the nucleus having both protons and neutrons?

Answer 5

• The nucleus is very dense - most of the mass is concentrated here
• Accounts for very little of the volume

Question 6

What surrounds the nucleus? How are these arranged?

Answer 6

Cloud of electrons arranged in shells which can contain 2, 8, or 18 electrons

Question 7

What charge and mass do electrons have?

Answer 7

Mass of 0
Charge of 1/1836

Question 8

What do all atoms of an element have in common?

Answer 8

All have the same number of protons (same atomic number)

Question 9

Why are partially filled electron shells not preferable? How is this resolved?

Answer 9

Not as energetically preferable as filled shells
Atoms donate and accept electrons in order to achieve the octet rule, to become more stable

Question 10

What is a cation?

Answer 10

Atoms which have lost electrons from their outer shell to become positively charged

Question 11

What is an anion?

Answer 11

Atoms which have gained electrons in their outer shell to become negatively charged

Question 12

Define ionic bonding

Answer 12

Electrostatic attraction between a metal and non-metal, formed from the transfer of electrons, to form a giant ionic lattice structure

Question 13

Which is the cation and which is the anion? Why?

Answer 13

Na+ is the cation - loses electron to Cl
Cl- is the anion - gains electron Na

Question 14

What ion does hydrogen form? How?

Answer 14

• Loses an electron to form H+
• No electrons so is just a proton

Question 15

What chemical property does H+ cause?

Answer 15

Responsible for acidity - pH is a measure of the concentration of free H+ ions

Question 16

Define covalent bonding

Answer 16

• Localised electrostatic attraction between a shared pair of electrons and the nuclei of the bonded atoms. There is overlap of the atomic orbitals, where the electrons are shared
• Covalent bonding is very strong

Question 17

Why is covalent bonding a favourable process?

Answer 17

By sharing electrons this brings the molecule to a lower energy level overall

Question 18

Why can water form?

Answer 18

• Oxygen has a slight negative charge and hydrogen has a slight positive charge
• Oxygen is more electronegative than hydrogen, meaning the shared pair of electrons are more greatly attracted to oxygen
• This creates a polar bond

Question 19

What type of bonding can form as a result of water being a polar molecule?

Answer 19

Hydrogen bonding between water molecules

Question 20

What two types of bonding are found in liquid water? Where?

Answer 20

• Covalent bonds (sharing electrons between oxygen and hydrogen)
• Hydrogen bonds attraction between non-bonding electrons on oxygen and hydrogens on adjacent water molecules)

Question 21

What is one of the most important functions of hydrogen bonding other than in water?

Answer 21

• Between base pairs in DNA
• Specificity of the base-pairing results from specific hydrogen bonding patterns between A/T and C/G

Question 22

Why does water have a high latent heat capacity?

Answer 22

Lots of hydrogen bonds in water, means it requires a large amount of kinetic energy to break the hydrogen bonds, which gives water stability

Question 23

Why can ice float?

Answer 23

• Ice is less dense than water
• Most substances are more dense in a solid form. The hydrogen bonds in the water molecule fix at lower temperatures, causing the polar molecules to move further apart than in the liquid state to form a lattice structure
• This produces a giant covalent structure, which oxygen atoms at the centre of a tetrahedral structure.

Question 24

Why is ice floating so important?

Answer 24

• Important to evolution
• Allows ice to be an insulator and life to survive underneath, which allowed life to survive and evolve over generations

Question 25

Why is water being a polar molecule beneficial?

Answer 25

- Makes water a good solvent - Able to solubilise polar regions of molecules (or polar species like ions) - Driver of the conformation of biological structures

Question 26

What can water not solubilise? Why?

Answer 26

- Non-polar molecules - Because water is polar and repels non-polar molecules so H bonding does not occur

Question 27

What is meant by hydrophilic/lipophobic?

Answer 27

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

Question 28

What is meant by hydrophobic/lipophilic?

Answer 28

Areas of molecules with high proportion of carbons tend to be pushed out of the aqueous phase

Question 29

What is one of the biggest examples of a structure formed due to differences in polarity?

Answer 29

Phospholipid bilayer - negatively charged polar head which is hydrophilic and a neutrally charged non-polar fatty acid tail which is hydrophobic/lipophilic

Question 30

What are two other examples of phospholipid structure which are determined by polarity?

Answer 30

Liposome - bilayer of phospholipids in a sphere Micelle - monolayer of phospholipids in a sphere

Question 31

Define what an acid is

Answer 31

- Acids are compounds that can lose an H+ ion (proton), in the process they become negatively charged - Fully dissociate in an aqueous solution but will remain associated as the covalent molecule in a less polar solvent

Question 32

Name some strong inorganic acids

Answer 32

Hydrochloric acid Sulphuric acid

Question 33

Why can equilibrium occur in a weak organic acid?

Answer 33

The energy difference between the two states can be relatively small, allowing a shift in equilibrium between each side of the reaction, and a back and forth between the form, possible in the physiological pH range

Question 34

What is an example of a weak organic acid?

Answer 34

Any carboxylic acid

Question 35

Define what a base is

Answer 35

Bases are compounds that can (reversibly) form covalent bonds by taking an H+ ion to become positively charged

Question 36

Can equilibrium occur in weak bases like with with acids?

Answer 36

- Yes - At a physiological pH - Energy difference between the two states is relatively small

Question 37

Which two acidic amino acids are predominantly ionisable at a physiological pH?

Answer 37

Glutamic acid and aspartic acid

Question 38

What charge do acidic amino acids have at a physiological pH? What is the pKa value?

Answer 38

Negatively charged Low pKa - less than 7.4

Question 39

Which two basic amino acids are predominantly ionisable at a physiological pH?

Answer 39

Lysine and Arginine

Question 40

What charge do basic amino acids have at a physiological pH? What is the pKa value?

Answer 40

Positively charged High pKa above 7.4

Question 41

What property do the acidic and basic amino acids have when charged?

Answer 41

VERY hydrophilic When something is charged it is very soluble in water

Question 42

What structure do the backbone amines and carboxylic acids combine to form in peptides?

Answer 42

Amides /amide linkages

Question 43

Giver an overall equation for the formation of an amide

Answer 43

Question 44

What property is significant about amides?

Answer 44

Neutral across the physiological pH range, so DO NOT ionise

Question 45

What groups have an impact on the structure of the protein?

Answer 45

Side/ R-groups

Question 46

What can influence the side/R-group structures?

Answer 46

The ionisation states on the amino acids

Question 47

What is the primary structure of a protein?

Answer 47

The order of the amino acids - the polypeptide sequence

Question 48

How does the primary structure of a protein influence the secondary structure?

Answer 48

- Arrangement of primary structure into defined regions, e.g. alpha helix and beta sheets - Determined by the shape (conformational preference) of the residues due to their hydrophobicity/hydrophilicity preference (determined by the R groups) and maintained by regular hydrogen bonding pattern

Question 49

What is the tertiary structure of a protein?

Answer 49

- Higher order of folding from secondary structure which gives the overall shape of a protein - Conformation of residues influences the structure ( the most common is proline-induced turns) - More bonding interactions (ionic and H bonding are the most important) and disulfide bridges/bonds between cysteines

Question 50

How does hydrophilicity play a role in the folding of a protein?

Answer 50

Lipophilic/hydrophobic residues prefer to be at the center of the protein (away from water) and will influence structure