Amino Acids, Proteins & DNA

Question 1

Do amino acids exist as optical isomers?

Answer 1

Yes apart from glycine (2-aminoethanoic acid) because the central carbon in these amino acids is bonded to four different groups

Question 2

Why can amino acids act as both a weak acid and a weak base?

Answer 2

They are bifunctional molecules with a -COOH group at one end, which is weakly acidic and can donate its proton to water, and an -NH2 group at the other end, which is weakly basic and can accept a proton from water via the nitrogen lone pair

Question 3

What is the zwitterion of an amino acid?

Answer 3

Where the amino acid exists as both an anion and cation simultaneously. Happens at some intermediate pH

Question 4

What happens when an amino acid is dissolved in highly acidic solution?

Answer 4

It is protonated and becomes a cation

Question 5

What happens when an amino acid is dissolved in highly alkaline solution?

Answer 5

It is deprotonated and exists as its anion

Question 6

What is the Isoelectric pH of a specific amino acid?

Answer 6

The pH at which the zwitterion occurs. In solution, the zwitterion exists at a unique pH value for each different amino acid

Question 7

What is the pH called where the zwitterion of a specific amino acid occurs?

Answer 7

The amino acid’s isoelectric pH

Question 8

What is the isoelectric pH for glycine? Cysteine?

Answer 8

1) 6.1

2) 5.0

Question 9

Why do amino acids have relatively high melting points compared to their corresponding amines and acids which are similar in size?

Answer 9

Because the zwitterion also exists in crystalline structure form of an amino acid. Therefore there is an electrostatic attraction between oppositely charged parts of the ion

Question 10

What is a protein? How is a protein formed?

Answer 10

1) A condensation polymer of two amino acids
2) The -NH2 group of one amino acid can undergo a condensation reaction with the -COOH group of another, eliminating a water molecule and forming a dipeptide bond

Question 11

What is a peptide bond? What is a peptide link?

Answer 11

1) The amide group that links the two amino acids
(-CONH-)
2) The C-N bond within the peptide link

Question 12

What is the primary structure of a protein?

Answer 12

The sequence of amino acids in the chain of the protein

Question 13

Describe an α-helix structure. Give an example of a protein that forms this structure

Answer 13

1) H bonds can form between an N-H group from one peptide link and an C=O group from another peptide link four amino acids further down the protein chain. This forms a helical shape which is held in place by a regular pattern of H bonds. In an α-helix all the R groups attached to the protein are pointed towards the outside of the helix. The helix itself its elastic and flexible
2) Keratin (the protein that makes up human hair) contains α-helices and each hair can support about 100g before it will break

Question 14

Describe the β-pleated sheet structure

Answer 14

This is where two or more parallel regions of a protein line up so that H bonds form between an N-H group from one peptide link and a C=O from another peptide link much further along the chain in another parallel region. Many parallel strands can interact side by side, leading to a flat sheet-like structure. This arrangement is similar to the interaction between chains in polymeric nylons

Question 15

What is the tertiary structure of a protein? How determines the tertiary structure of a protein?

Answer 15

1) The overall three-dimensional shape of the whole protein. Only in this structure are they capable of carrying out their characteristic biochemical functions
2) How different regions of the secondary structure interact which is due to the various electrostatic or covalent interactions between the R side chains of amino acid residues in the protein

Question 16

When does a disulphide bridge form? What is the importance of this bond? How can it be broken?

Answer 16

1) When a protein contains cysteine amino acids that are positioned close in space then the side chain S-H groups can react to from a strong S-S bond (cystine link)
2) This bond helps to fix the tertiary structure of a protein
3) If the protein is heated, reduced or treated with a base

Question 17

What happens when bonds in a protein are broken down, e.g. A cystine link?

Answer 17

The biologically active tertiary structure can collapse causing the protein to denature

Question 18

Why are many proteins biologically active over a very narrow pH range?

Answer 18

A change in pH can cause different interactions and bonds to break, changing the tertiary structure of the protein and making it biologically inactive

Question 19

What interactions and bonds are contribute to the tertiary structure of a protein?

Answer 19

• Disulphide bridge (cystine link)
• H binding interactions
• Ionic interactions

Question 20

Explain TLC (thin layer chromatography)

Answer 20

A small spot of a mixture is added near the bottom of a TLC plate which is dipped into a solvent, making sure the spot is above the solvent line. As the solvent moves up the TLC plate different amino acids move up ye plate at different rates. The TLC plate is removed when the solvent has nearly reached the top of the plate and the compounds are revealed using an appropriate technique

Question 21

How are amino acids revealed from TLC?

Answer 21

The plate is sprayed with an ethanol solution of ninhydrin. The ninhydrin reacts with the amine groups of the amino acids and produces a blue-purple colour. The retention factor (Rf) can then be calculated for each amino acid and used to identify the amino acid composition of the protein by comparison with known data

Question 22

How is Rf calculated?

Answer 22

The distance moved by the compound divided by the distance moved by solvent

Question 23

How can proteins be broken up? What happens to the protein?

Answer 23

1) By heating a protein with 5 mol/dm^3 HCl for about 24 hours
2) The secondary and tertiary structures of the protein are rapidly broken down causing the polyamide chain to unravel the chain is then hydrolysed at each of the peptide links and liberated the component amino acids

Question 24

Enzymes are very specific, give an example of this

Answer 24

The enzyme DOPA decarboxylase only catalyses the loss of CO2 from L-DOPA but not from its enantiomer D-DOPA

Question 25

What is a substrate?

Answer 25

The reactant in an enzyme-catalysed reaction

Question 26

What is formed when a substrate enters an active site?

Answer 26

The enzyme-substrate complex

Question 27

Why can enzymes only catalyse specific reactions?

Answer 27

Only molecules that have the right shape can fit into the active site. This is known as the lock and key hypothesis

Question 28

Explain how the side chains in the amino acid that make up an enzyme play an important role in the attraction and binding of the substrate?

Answer 28

The side chains may contain -OH groups which can H bond to the substrate, or ionic groups such as NH3+ or COO- which can attract the substrate by electrostatic forces. Hydrocarbon side chains also contribute to the binding of the substrate by van der Waals forces. The substrate must have the correct functional groups displayed in the correct orientation in space to he capable of interacting with side chains of the active site efficiently

Question 29

Why are enzymes chiral molecules?

Answer 29

They are made from L-amino acids

Question 30

What is the result of enzymes being chiral molecules?

Answer 30

Enantiomers of chiral substrates can interact differently with the active sites of enzymes

Question 31

What is a stereospecific active site? Give a. Example of where this occurs

Answer 31

1) An active site that will only bind with one enantiomer of a racemate
2) The D-isomer of ibuprofen is far more active as a painkiller than its optical isomer

Question 32

What is an enzyme inhibitor?

Answer 32

A molecule that binds to an enzymes active site and decreases its activity. Many drugs that treat disease are enzyme inhibitors

Question 33

For an inhibitor to be active it must…

Answer 33

… bind more strongly to the active site than the natural substrate does

Question 34

What information is necessary to design a drug which acts as an enzyme inhibitor?

Answer 34

The three-dimensional structure as well as the amino acid side chains present in the enzyme active site. Then a molecule of the correct shape with the appropriate functional groups must be synthesised

Question 35

How does the shape of drugs compare to that of the natural substrate they inhibit?

Answer 35

They are often similar in structure which is not surprising as they must bind to the same active site

Question 36

What are enzymes?

Answer 36

Proteins that act as biological catalysts. They work by providing an alternative reaction pathway of lower activation energy so more reactants have sufficient energy to react

Question 37

What are the monomers that make up DNA called?

Answer 37

Nucleotides which consist of a phosphate a sugar and a base

Question 38

What sugar is in the nucleotides that make up DNA?

Answer 38

2-deoxyribose, a modified version of the sugar ribose with a missing hydroxyl group on carbon number 2

Question 39

How is the polymer DNA made?

Answer 39

By linking nucleotides via the phosphate at the 5 position of one nucleotide with the hydroxyl group on the 3 position of a different nucleotide. This produces a polynucleotide with a backbone of sugars and phosphates and with the various bars attached to the backbone

Question 40

Who first came up with the double helix shape of DNA?

Answer 40

Chemists James Watson and Francis Crick in 1953, was formed as a result of the H-bonding between bases in one polynucleotide strand and bases in a second strand (the complementary strand)

Question 41

Why do the bases thymine and adenine only bind with each other and guanine and cytosine only bind with each other?

Answer 41

The H-bonding is very specific because the base pairs fit exactly in terms of size and shape. The AT base pair makes two H-bonds, the GC bond makes three H-bonds

Question 42

Why do a lot drugs used to treat cancer have side effects such as nausea, hair loss and susceptibility to infection?

Answer 42

They work by targeting cells that divide rapidly, a characteristic of cancer cells. However other cells e.g the ones in the gastrointestinal tact, hair follicles and bone marrow also replicate quickly so these are also usually affected

Question 43

What is the structure of the anticancer drug cisplatin (cis-diamminedichloridoplatinum(II))?

Answer 43

A central platinum atom with two NH3 groups in one side and two Cl groups on the other

Question 44

How does the anticancer drug cisplatin work?

Answer 44

When it enters a cell one of the chlorides is initially replaced by water and then by one of the nitrogen atoms of a guanine base in DNA. This forms a nitrogen-platinum bond and fixes the drug to one strand of the DNA double helix. The second chloride is then lost in the same way and this allow a second guanine base to bind. This distorts the shape of the DNA molecule and prevents replication

Question 45

What are some of the side effects of the anticancer drug cisplatin?

Answer 45

Nausea, kidney damage and nerve damage

Question 46

What isn’t transplatin an effective anticancer drug?

Answer 46

The two chlorides are on opposite sides, therefore only one can bind to a guanine base on the DNA strand. This doesn’t affect the shape of the DNA molecule and therefore it doesn’t prevent replication

Question 47

During chemotherapy how is damage to healthy cells minimised?

Answer 47

Chemotherapy doses are given in small quantities at regular intervals to allow the body to recover

Question 48

During DNA replication what dictates the base sequence on the complementary strand?

Answer 48

The sequence of bases on the original strand