Molecular bio 3: Molecules of Life

What are the four most abundant elements in the human body, in order?

Hydrogen, Oxygen, Carbon and Nitrogen

Why are the biological molecules vary reactive?

They have incomplete outer electron shells

A-DNA

B-DNA becomes A-DNA in 75% relative humidity

It is also right handed but has a slightly increased helical diameter and reduced vertical rise

Features of B-DNA

The standard type of DNA

Right handed

Found in 92% relative humidity

Z-DNA

Found in high salt concentrations

Left-handed

Has a slightly decreased helical diameter and increased vertical rise

Covalent bonds

Two or four electrons (single or double covalent bond) are shared between molecules, restricting movement around the axis and creating a very strong bond

Give three types of noncovalent bonds

Van der Waals attractions, electrostatic attractions, and hydrogen bonds

Van der Waals attractions

If two atoms are too close together they repel each other very strongly. The distance at which this happens is dependant of the radii of the atoms. The contact distance between any two non-covalently bonded atoms is the sum of their van der Waals radii.

Electrostatic attractions

The attraction between one positively-charged ion and one negatively-charged ion.

Very strong WHEN NOT IN SOLUTION (so don’t tend to be strong within the body, which is mostly water).

Give an example of the importance of electrostatic bonds in biochemistry

In the active site of an enzyme that binds a positively-charged substrate, there will often be a negatively-charged amino acid

What is a dipole?

A partial charge, or polarity, on an atom.

Hydrogen bonds

Weak bonds formed between the positive dipole and the negative dipole of water molecules

What does it mean that Oxygen is a very electronegative molecule?

It has a strong propensity to pull electrons towards it (on the scale of 1 to 4, Oxygen is 3)

Is oxygen a hydrogen bond donor or receptor in water?

Acceptor

What is the hydrophobic effect?

When hydrophobic substances coalesce because they are pushed together by water, minimizing the disruption to the water molecule lattice

Give two types of bonds that are weaker when the molecules involved are in solution

Hydrogen and ionic bonds

What two functional groups are common between all amino acids?

Carboxyl terminus and amino terminus

What are the three ‘special’ amino acids and what are their interesting properties?

Glycine (very small)

Cystine (forms sulphic bonds, which are very restrictive)

Proline (has a ring structure and is known as a helix breaker)

How are hydrophilicity and acidity related?

More acidic molecules tend to be more hydrophilic, because their acidity allows them to form hydrogen bonds with water and become readily soluble in it

What type of bond joins adjacent amino acids?

A peptide bond between the carboxy terminus of one and the amino terminus of the next

What type of reaction forms a peptide bond?

Condensation

What is meant by the alpha carbon in an amino acid?

The carbon that the R group is bound to

How is an alpha helix formed?

The carbonyl oxygen in the peptide bond forming hydrogen bonds with the amino hydrogen in the amino acid four positions along

What type of bonds are responsible for beta pleated sheets?

Hydrogen bonds

How many amino acids comprise a beta turn?

4

Which amino acids are usually found in beta turns?

Glycine and proline

What percentage of an average protein is comprised of alpha helices and beta sheets?

60%

What name is given to the regions of proteins that do not form alpha helices or beta sheets?

Disordered regions

What are the four tertiary structural categories of proteins?

Globular, fibrous, integral membrane proteins and intrinsically disordered proteins

Give an example of a protein with both fibrous and globular regions

Haemagglutinin

Give four examples of macromolecules

DNA, RNA, proteins and polysaccharides (ie. any biological polymer)

How many base pairs are there per ‘turn’ of the DNA double helix?

10.4

What is the helical diameter of DNA?

2.4nm

What is the average rise per base pair of DNA?

0.34nm

How many hydrogen bonds form between A and T in DNA?

2

How many hydrogen bonds form between C and G in DNA?

3