Charge and shape in biological molecules Flashcards
What is the structure of the nucleus in the atom?
Protons have a mass of 1, charge of +1.
Neutrons have a mass of 1, charge of 0.
The nucleus is very dense.
Where are electrons in the atom?
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.
What is the atomic number?
All atoms of the same element have the same number of protons.
What are cations?
Atoms with few electrons in their outer shell will lose electrons readily to form positively charged cations - these are metals.
What are anions?
Atoms with nearly full outer shells take electrons from metals to form negative anions.
These are non-metals.
What is ionic bonding?
The electrostatic attraction between oppositely charged ions.
What are hydrogen ions?
Hydrogen loses its one electron to form H+, which is a proton.
It is responsible for acidity.
What is pH?
The measure of concentration of free H+.
What are covalent bonds?
A chemical bond involving the sharing of electron pairs between atoms.
Sharing electrons brings the molecule to a lower energy level overall.
What is the strength of covalent bonds?
Covalent bonds are very strong.
Why is water polar?
Oxygen is electronegative - the electrons shared in the covalent bonds are attracted to it - so electrons are more towards oxygen than hydrogen.
What are hydrogen bonds?
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.
What is the order of strength of intermolecular interactions?
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.
What is the function of hydrogen bonds in DNA?
Hydrogen bonds control base-pairing.
Specificity of base-pairing results from specific hydrogen bonding patterns between A/T and C/G.
Why is it unusual hydrogen bonding can control base pairing?
Nucleobases have a relative hydrophilicity - which means they are good at dissolving water.
What are features of water due to hydrogen bonding?
High latent heat capacity
Ice is less dense than water
Water expands when it feezes
Heat breaks hydrogen bonds.
How is water a polar environment?
Water is good at solubilising polar regions of molecules or polar ions.
It does not solubise non-polar regions well.
What are hydrophilic qualities?
Areas of molecules with charge, good hydrogen-bonding potential and low proportion of carbon atoms sit in or face water.
What are hydrophobic qualities?
Also lipophilic.
Areas of molecules with a high proportion of carbons tend to be pushed out of the aqueous phase.
What are the features of the phospholipid membrane?
The phosphate head group is hydrophilic.
The fatty acid tails are hydrophobic/lipophilic.
What is a phospholipid bilayer?
What is a phospholipid liposome?
What is a phospholipid micelle?
What are acids?
Compounds that lose a proton and become negatively charged.
e.g. HCl, H2SO4
Is HCl strong?
HCl completely dissociates to its atomic ions in aqueous solution.
HCl –> Cl- + H+
In less polar solvent it remains associated as the covalent molecule.
What are weak acids?
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.
What are bases?
Compounds that can form covalent bonds with a proton to become positively charged.
What are weak bases?
In weak amine bases, the equilibrium between dissociation is possible at physiological pH range.
Which acids are ionised?
Acids with low pKa (<7.4) are predominantly ionised at physiological pH.
E.g. Glutamic acid, aspartic acid
Which bases are ionised?
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.
What are amides?
In peptides, amines and carboxylic acids combine to form amides.
Amides are neutral across the physiological pH range - do not ionise.
What determines the tendency for water of proteins?
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.
What is basic primary structure of proteins?
The order of amino acids - is responsible for the structure and function of the protein.
What is the basic secondary structure of proteins?
Arrangement of primary structure into defined regions - alpha helix or beta sheet.
Can be predicted from primary structure.
How can secondary structure be determined?
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.
What is the basic tertiary structure of proteins?
Higher order folding of secondary structure - gives the overall shape of a protein chain.
Conformation of residues influences structure.
What bonds form in tertiary structure?
Ionic and hydrogen bonding is important.
Some new covalent bonds can be made between chains - disulphide bonds.
How does hydrophilicity affect tertiary structure?
Lipophilic residues prefer to be at the centre of the protein and so influences structure.
What is the basic quarternary structure of proteins?
How the chains come together and arrange to form complexes.
Lipophilic residues prefer to be at the centre so affect structure.
