PL 1 - Structure and Bonding

Question 1

What is an amino acid?

Answer 1

An organic compound that contains both an amine (-NH2) and carboxylic acid (-COOH) functional group

Question 2

What is the general structure of an amino acid?

Answer 2

Contains an amine group, a carboxylic acid group, a hydrogen atom and an R group (which is different for every amino acid)

Question 3

What is a protein?

Answer 3

A protein is a condensation polymer formed from amino acid monomers

Question 4

How is a peptide link formed?

Answer 4

When two amino acids react in a condensation reaction, a molecule of water is released and a peptide link/bond is formed

Question 5

How is a peptide link broken?

Answer 5

The hydrolysis of a peptide bond requires a water molecule so that the amine and carboxylic acid groups can be fully reformed. A concentration acid and heat is usually required too

Question 6

What is paper chromatography and why is it used?

Answer 6

Is it the separation of a mixture into its constituent components on filter paper for further analysis. This allows identification by the calculation and comparison of Rf values

Question 7

How do you carry out paper chromatography?

Answer 7

1. Add solvent to a jar. Seal to create a saturated environment
2. Draw a pencil line on filter paper. Spot samples along this line using a capillary tube
3. Add paper to jar. Make sure solvent is below pencil line
4. The solvent rises up the filter paper, bringing components of the samples with it
5. Draw a pencil line where the solvent finishes (don’t allow it to travel to the top of the paper). Allow to dry

Question 8

How do you calculate an Rf value?

Answer 8

Rf value = (distance travelled by component) / (distance travelled by solvent)

Question 9

Why must any lines drawn on the paper be in pencil?

Answer 9

Because if drawn in ink, this will dissolve in the solvent and run up the paper with the other components, contaminating them

Question 10

Why should the solvent be below the pencil line?

Answer 10

if above the pencil line, the solvent will dissolve all samples and they will not run up the paper

Question 11

What is the primary, secondary and tertiary structure of proteins?

Answer 11

1. Primary structure: The sequence of amino acids in the polypeptide chain
2. Secondary structure: The twisting and folding of the polypeptide chain due to hydrogen bonding
3. Tertiary structure: The further folding/twisting of the chain due to disulfide bridges, ionic bonds and further hydrogen bonds

Question 12

What determines secondary and tertiary protein structure?

Answer 12

Intermolecular bonds (hydrogen, ionic and disulfide bonds) between the R groups of amino acids

Question 13

What are DNA and RNA?

Answer 13

DNA and RNA are polymers formed from condensation reactions between nucleotide monomers

Question 14

What is a nucleotide?

Answer 14

A nucleotide has a phosphate group, a pentose sugar and a nitrogen containing base

Question 15

What is the structure of DNA?

Answer 15

• DNA is made from two antiparallel polynucleotide chains that are held together by hydrogen bonds between complementary base pairs. This causes it to twist into a double helix
• Pentose sugar = Deoxyribose
• Bases are A, T, G and C

Question 16

What is the structure of RNA?

Answer 16

• Single stranded polynucleotide chain
• Bases are A, U, G and C
• Pentose sugar = Ribose

Question 17

What happens when two nucleotides react?

Answer 17

• When two nucleotides react in a condensation reaction, a bond forms between the pentose sugar of one nucleotide and the phosphate group of the other nucleotide
• For DNA and RNA, many nucleotides join in this way to create a long chain. The section of the chain containing the sugar-phosphate bonds is called the sugar-phosphate backbone

Question 18

Why is hydrogen bonding important in the structure and function of DNA?

Answer 18

• In DNA, hydrogen bonds hold the two polynucleotide strands together
• Without hydrogen bonding, this structure would not occur and DNA wouldn’t be able to replicate by semi-conservative replication

Question 19

How does DNA base sequence code for a protein?

Answer 19

• For coding regions of DNA, the base sequence is read in terms of triplets (a sequence of three bases), whereby each triplet codes for a corresponding amino acid
• Hence a sequence of triplets codes for a corresponding sequence of amino acids, which will be joined later in condensation reactions to form a protein

Question 20

What is molecular recognition?

Answer 20

The interaction between multiple molecules through bonding that is not covalent e.g. hydrogen bonding, hydrophobic forces, van der Waals (id-id) forces etc.

Question 21

What is a pharmacophore?

Answer 21

The part of the molecule that is responsible for a particular interaction, either biological or pharmacological

Question 22

What are the ways that species interact in three dimensions?

Answer 22

Size, shape, bond formation or orientation