Chemistry - 3.3.13: Amino Acids, Proteins and DNA

Amino acids

The building blocks of proteins

How many functional groups do amino acids have? What are they?

2 - a carboxylic acid and a primary amine

How many naturally-occurring amino acids are there?

20

Zwitterions

Ions that have a permanent positive and negative charge - overall, the molecule is neutral

Why are amino acids found as zwitterions?

The carboxylic acid group has a tendency to lose a proton to form COO^-, while the amine group has a tendency to accept a proton to form NH₃⁺

Describe the melting points of amino acids and why they are like that.

High melting points - they are ionic

Describe the solubility of amino acids and why they are like that.

Dissolve well in water but poorly in non-polar solvents - they are ionic

What happens to amino acids in strongly acidic conditions?

The amine group gains a proton (is protonated) to form a positive ion (NH₃⁺)

What happens to amino acids in strongly alkaline solutions?

The carboxylic acid group loses a proton (is deprotonated) to form a negative ion (COO^-)

Proteins

Sequences of amino acids joined by peptide bonds

Dipeptide

A peptide with two amino acids

What forms when proteins are hydrolysed?

A mixture of its constituent amino acids

What bonds may be present between the amino acids of a protein chain?

Hydrogen bonds, ionic attractions and sulfur-sulfur bonds

In amino acids, what do hydrogen bonds form between?

The C=O and N-H groups

In amino acids, what do ionic attractions form between?

Between groups on the side chains of amino acids (if a COO^- or NH₃⁺ are present)

What amino acid can form disulfide bridges?

Cystine

What are the levels of protein structure?

Primary, secondary, tertiary and quaternary

Primary structure of a protein

The sequence of amino acids along a protein chain

How might the primary structure of a protein be represented?

With drawings of the amino acids or their 3 letter abbreviations

What holds together the primary structure of proteins?

Covalent bonds between the amino acids (peptide / amide links)

Secondary structure of a protein

The folding of a protein chain into an alpha helix or beta pleated sheet

What holds together the secondary structure of proteins?

Hydrogen bonds between C=O and N-H

Tertiary structure of proteins

The folding of the secondary structure into a three dimensional shape

What holds together the tertiary structure of proteins?

Hydrogen bonds, ionic interactions and sulfur-sulfur bonds

How can amino acids be separated and identified?

By thin-layer chromatography

What developing agents would you use when separating amino acids with TLC?

Developing agents like ninhydrin or UV light

Enzymes

Protein-based catalysts (biological catalysts)

How do enzymes work? (4)

1. They have a stereospecific active site

2. The reacting molecule is complementary to the active site and binds to it

3. The active site holds the reacting molecules in the right orientation to react

4. The products are released so the process may repeat.

What type of proteins are enzymes?

Globular proteins

Active site

A cleft/crevice in an enzyme where the reaction takes place and where the reacting molecule binds to the enzyme

What are some active sites described as?

Stereospecific

Why are some active sites stereospecific?

They can only catalyse reactions of one or other of a pair of enantiomers

How do drugs inhibit enzymes?

They have a similar shape to the substrate so bind to the active site instead, blocking it

How might the action of enzymes be reduced?

By denaturing them or by blocking their active sites

How might drugs used to reduce the action of enzymes be designed and why?

By using computer modelling - can predict the shapes of proteins, enabling them to predict their properties

What is DNA? What is it made up of?

It is a polymer made up of monomers called nucleotides

What are nucleotides made up of?

A phosphate ion, a 2-deoxyribose sugar and an organic base

What does DNA stand for?

Deoxyribonucleic acid

What are the four inorganic bases of DNA?

Adenine, thymine, cytosine and guanine

How does DNA exist as?

2 complementary strands arranged as a double helix

How do nucleotides join together?

In a condensation reaction between the OH groups of the phosphate ion on one nucleotide and the OH group on the deoxyribose sugar on another nucleotide - this eliminates a molecule of water

What bonds are present in DNA?

Covalent bonds between the phosphate of one nucleotide and deoxyribose sugar of another + hydrogen bonds between the complementary bases of the 2 strands

What are the complementary base pairings of DNA?

A-T, C-G

What happens to DNA during cell division?

The hydrogen bonds of the double helix break and the strands unravel so the DNA may be replicated

Cisplatin

An anti-cancer drug

What is the structure of cisplatin?

Square planar

What is the formula of cisplatin?

PtCl₂(NH₃)₂

How does cisplatin work? (4)

1. It bonds to the the nitrogen atoms on 2 adjacent guanine bases on a strand of DNA

2. A ligand substitution reaction takes place - the chloride ions on cisplatin are displaced by water, while the water molecules are then displaced by the nitrogen on guanine

3. The nitrogen atoms of the guanine molecules form dative covalent bonds with platinum

4. This distorts the shape of DNA so cell replication cannot take place

Why does cisplatin have side effects?

It also bonds to the DNA in healthy cells, not just cancerous ones, so healthy cells that replicate quickly are significantly affected

Why does cisplatin have a greater effect on cancerous cells than healthy ones?

The cancerous cells are replicating faster

Complementary

The two strands must have base sequences that all match A to T and C to G

Draw a phosphate bonded to a 2-deoxyribose

Why do hydrogen bonds form in the secondary structure of proteins? (4)

1. Nitrogen and oxygen are very electronegative

2. So C=O and N-H are polar

3. This means hydrogen bonds form between O and H

4. As the lone pair of electrons on O is strongly attracted to the positive dipole on H

What makes amino acids more polar?

They have a more positive charge