Charge and shape in biological molecules Flashcards
The nucleus consists of…
…protons and neutrons
What are the mass and charges of neutrons and protons
Mass: 1 for both
Proton charge: +1
Neutron charge: 0
What volume of the atom does the nucleus account for?
1/100,000th
What surrounds the nucleus?
A cloud of electrons
Give the nominal mass and charge of an electron
0 and -1
What is atomic number?
The number of protons in an atom
How are cations formed?
Loss of electrons
How are anions formed?
Gain of electrons
What is a covalent bond?
A bond that involves the sharing of electron pairs between atoms
How strong are covalent bonds?
Very strong
What is a hydrogen bond?
An attraction between N, O or F and a H on another molecule
What type of bonding is present in liquid water?
Covalent bonds: sharing electrons between oxygen and hydrogen
Hydrogen bonds: between adjacent molecules
What kind of environment is water?
Polar
What will water easily solubilise?
Other polar molecules, regions of molecules or ions
What makes something hydrophilic?
Charge
Hydrogen bonding potential
Low proportion of carbon atoms
What makes something hydrophobic
No charge
High proportion of carbon atoms
What is an acid?
A compound that can lose an H+ ion
What is a base?
A compound that can form covalent bonds with a H+ ion
What will happen to amino acids with low pKa at physiological pH?
They will be negatively charged and anionic
Predominantly ionised
What will happen to amino acids with high pKa at physiological pH?
They will be positively charged and cationic
Predominantly ionised
What happens to amides at physiological pH?
Amides are neutral at physiological pH
What determines secondary structure?
Shape and conformation preference of the residues
Maintained by regular hydrogen bonding pattern
Can be predicted from primary structure
What is tertiary structure?
The overall shape of a protein chain
What determines tertiary structure?
Bonding interactions:
Ionic & hydrogen
Conformation of residues e.g. proline-induced turns
