Amino acids, proteins and DNA

explain how the anti-cancer drug cisplatin prevents DNA replication

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Figure 6 shows a small part of a single strand of DNA. Some lone pairs are shown. State the name of the sugar molecule that is attached to the bond at X.

2-deoxyribose

C₅H₁₀O₄

2-deoxyribose, is a monosaccharide. It is a very soluble white solid

Structure of a nucleotide.

2-deoxyribose, phosphate group and a nitrogenos base.

How many naturally occurring amino acids are there?

20

Purines

A and G

State the stationary phase in TLC

A coating of powdered silica on a sheet of plastic

What is a disulifde bond?

A disulfide bond, also called an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups.

Mobile phase

A liquid of a gas that moves through stationary phase and carries the components of the mixture with it

Stationary phase

A solid/liquid supported on a solid

Amino acids exists as zwitterions. What does this mean?

Amino acids are dipolar ions- they have both a positive and a negative charge. Zwitterions only exist near an amino acid's isoelectric point

Why is ninhydrin used after the amino acids have dried up.

Amino acids aren't coloured compounds so the ninhydrin solution makes the amino acid spot visible as it turns the spot purple

Basic structure of an amino acid

Amino acids have a basic amino group (NH2) and an acidic carboxyl group (COOH)

What does it mean when amino acids are described as being amphoteric

Amino acids have both acidic and basic properties

Explain why the melting point of aminoethanoic acid is much higher than that of hydroxyethanoic acid

Aminoethanoic acid and hydroxyethanoic acid both have hydrogen bonds. However aminoethanoic acid is also ionic which means it can form ionic bonds which are stronger than the hydrogen bonds in hydroxyethanoic acid.

Messenger RNA is synthesised in cells in order to transfer information from DNA. The bases in one strand of DNA pair up with the bases used to synthesise RNA. Suggest which of the bases A and B forms a pair with guanine in Figure 6 when messenger RNA is synthesised.Explain how the base that you have chosen forms a base pair with guanine.

Base A. Top N-H forms hydrogen bonds to lone pair on O of guanine. The lone pair of electrons on N bonds to H-N of guanine. A lone pair of electrons on O bonds to lower H-N of guanine

Label a diagram of DNA to show the components and the hydrogen bonding between base pairs

Bonds between A and T. N-H--O and N--H-N. Bonds between C and G.O--H-N, N-H--N, N-H--O

Pyrimidines

C,U,T

Explain how drugs, which can be designed with the aid of computers, can act to inhibit enzymes by blocking active sites, but that the correct enantiomer is required.

Chemists now use computer modelling techniques to predict the shapes of proteins even before they have been synthesised., and therefore predict their properties.

Name 2 suitable methods by which the mixture of amino acids formed by hydrolysis of the protein can be separated.

Chromatography and electrophoresis

Evaluate the adverse effects of using drugs such as cisplatin

Cisplatin can bind to DNA in normal cells as well as cancer cells. This is a particular problem for any healthy cells that replicate frequently, such as hair cells and blood cells because cisplatin stops them from replicating in the same way as it does the cancer cells. This means that cisplatin can cause hair loss and supress the immune system. It can also cause kidney damage.

Cisplatin

Cisplatin is a complex of platinum 2 with two chlorides ion ligands and two ammonia ligands in a square planar shape.

Understand the structure of the components of DNA

DNA is made of 2 polynucleotide strands. The two strands spiral together to form a double helix structure which is held together by hydrogen bonds between the bases. Each base can only join with one particular partner. A to T and G to C. This causes the 2 strands of DNA to be complementary.

What is DNA made up of?

DNA is made up from lots of monomers called nucleotides..

Explain why thin-layer chromatography can be used to separate and identify amino acids.

Different amino acids have different R groups so they will have different solubilities in the same solvent. This means different amino acids can be easily separated and identified using thin layer chromatography as each amino acid will move up the plate at a different rate depending on how soluble it is in the solvent used.

With reference to your answer to part (d)(i), explain why the melting point of the amino acid X is higher than the melting point of CH3CH2CH(OH)COOH

Electrostatic forces between ions in X are stronger than the hydrogen bonding between CH3CH2CH(OH)COOH

Explain why the melting point of 2-aminobutanoic acid is higher than the melting point of CH3CH2CH(OH)COOH

Electrostatic forces between ions in the amino acid is stronger than hydrogen bonding between CH3CH2CH(OH)COOH

Why are enzymes stereospecific?

Enzymes are made up of amino acids so they contain chiral centres. This makes their active sites stereospecific which means they'll only work on one enantiomer of a substrate. The other enantiomer won't fit properly in the active site so no ES complexes will be formed.

Describe the tertiary structure of proteins

Further infold of the peptide chain now consisit of both intra and inter molecular forces such as h-bond inc bonds disulphide bridges and van der Waals forces

Describe the ways in which the side effects of cisplatin can be lessened.

Give the patients very low dosages of cisplatin. Target cisplatin to the tumour using a method that delivers the drug only to the cancer cells, so that it doesn't get the chance to attack healthy cells.

All amino acids are chiral molecules except glycine. Why is this?

Glycine doesn't have 4 different groups attached to the centre carbon atom

Describe the importance of hydrogen bonds and S-S bonds

Hydrogen bonds hold the protein in shape by stabilising both the secondary and tertiary structure. The SS bonds link together different parts of the protein chain and help to stabilise the tertiary strucutre

Process by which peptide links in proteins are broken to form amino acids

Hydrolysis

A pencil line is drawn near the bottom of the plate and a small drop of a solution of the dye mixture is placed on it. Any labelling on the plate to show the original position of the drop must also be in pencil. Explain why.

If any of this was done in ink, dyes from the ink would also move as the chromatogram developed.

The dipeptide in Question 6(d) is hydrolysed in acid conditions and the mixture produced is analysed by column chromatography. The column is packed with a resin which acts as a polar stationary phase. Suggest why lysine leaves the column after alanine

In acid conditions, the amino acids would become protonated. Lysine has a double positive charge so the lysine ion has a greater attraction to the stationary phase so it sticks better to it.

State and explain one risk associated with the use of cisplatin as an anticancer drug.

Killing them or causing damage (medical side effects). May attach to DNA in normal cells and kill healthy cells.

General structure of amino acids in alkaline solution

NH₂-CHR-COO⁻ (carboxylic acid group has deprotonated)

General structure of amino acids in acidic solution

NH₃⁺-CHR-COOH (amino group has protonated)

General structure of amino acids as zwitterions.

NH₃⁺-CHR-COO⁻

The strucuture of the species present in solid aminoethanoic acid

NH₃⁺-CH₂-COO⁻ ZWITTERION

Figure 3 shows a simplified representation of the arrangement of some amino acids in a portion of a protein structure in the form of an α-helix.Explain the origin of the interaction represented by the dotted lines in

Nitrogen and oxygen are very electronegative therefore, C=O and N-H are polar which results in the formation of a hydrogen bond between O and H in which a lone pair of electrons on an oxygen atom is strongly attracted to the δ+H.

Identify the components of DNA

Nitrogen bases pentose sugar phosphate

Understand the nature of nucleotides.

Nucleotides are made up of a phosphate group, a pentose sugar which in DNA is called 2deoxyribose, and a nitrogenous base

Covalent bonds

Nucleotides join together to form a polynucleotide chain. Covalent bonds form between the phosphate group of one nucleotide and the sugar of another. This makes the sugar phosphate backbone of the chain.

The chemist showed, using infrared spectroscopy, that the propan-2-ol was contaminated with propanone. The chemist separated the two compounds using column chromatography. The column contained silica gel, a polar stationary phase. The contaminated propan-2-ol was dissolved in hexane and poured into the column. Pure hexane was added slowly to the top of the column. Samples of the eluent (the solution leaving the bottom of the column) were collected. Suggest the chemical process that would cause a sample of propan-2-ol to become contaminated with propanone. State how the infrared spectrum showed the presence of propanone. Suggest why propanone was present in samples of the eluent collected first (those with shorter retention times), whereas samples containing propan-2-ol were collected later.

Oxidation Absorption at 1680 -1750 due to C=O Propan-2-ol is more polar. It has hydrogen bonding about attraction to stationary phase or solubility in moving phase Propan-2-ol has greater affinity for stationary phase or vice versa OR propanone is more soluble in solvent/moving phase or vice versa

Equation used to find the Rf value of an amino acid

Rf= Distance travelled by spot/Distance travelled by solvent

A tripeptide was heated with hydrochloric acid and a mixture of amino acids was formed. This mixture was separated by column chromatography. Outline briefly why chromatography is able to separate a mixture of compounds. Practical details are not required

Solvent is mobile stationary phase separation depends on balance between solubility of compounds in each phase amino acids have different Rf values because amino acids travel at different speeds.

Explain that enzymes are proteins which act through a stereospecific active site that binds to a substrate

The active site of an enzyme is very specific so it takes a lot of effort to find a drug molecule that will fit into an active site because the active sites of enzymes are stereospecific.

Describe how disulfide bridges are formed

The amino acid cysteine contains a thiol group (SH_. Thiol groups on different cysteine residues can lose their hydrogen atoms and join together to form disulfide bonds.

Suggest why urea is effective at separating the complementary strands in DNA

The amino groups in urea are abe to substitute for the hydrogen bond in the double helix. Hydrogen bonds are able to form between the urea and the DNA strands.

Zwitterions are dipolar and only exist near an amino acids isoelectric point. What is the isoelectric point.

The isoelectric point is the pH where the average overall charge on the amino acid is zero

Despite the side effects of cisplatin, it is still uses as a chemotherapy drug. Explain why

The long term positive effects outwiegh the negative short term effects.

Cancer is caused by uncontrolled cell division of body cells which form tumours. In order for a cell to divide DNA must be replicated. Cisplatin binds to DNA causing kinks in the DNA helix which stops the proteins that replicate the DNA from copying properly. Explain how cisplatin works?

The nitrogen atom on a guanine base in DNA forms a co ordinate bond with cisplatin's platinum ion replacing one of the chloride ion ligands. This is called ligand substitution. A second nitrogen atom from a nearby guanine either on the same strand of the DNA or opposite strand, can bond on the platinum and replace the second chloride ion. The presence of the cisplatin complex bound to the DNA strands causes the strands to kink. This means that the DNA strand can't unwind and be copied properly so they can't replicate.

Isoelectric point

The pH where the average overall charge on the amino acid is zero

TM

The temperature of which the DNA helix separates into two strands.

SS bond

These bonds are responsible for the stabilizing the globular structure and are the strongest type of bond that a protein can possess and are one of the major forces responsible for holding proteins in their respective conformations, and therefore have an important role in protein folding and stability

What can you use to identify unknown amino acids

Thin-layer chromatography can be used to identify different amino acids in a mixture. The rate at which the amino acid will move up the thin-layer chromatography plate depends on the solubility of the amino acids in the solvent

Explain how cytosine forms a base pair with guanine

Top N-H forms hydrogen bonds to lone pair on O of guanine. The lone pair of electrons on N bonds to H-N of guanine. A lone pair of electrons on O bonds to lower H-N of guanin

An adverse effect of cisplatin is that it also prevents normal healthy cells from replicating. Suggest two ways in which cisplatin can be administered so that this side effect is minimised.

Use in very small amounts or target the application to the tumour.

Describe the secondary structure of proteins

chain of amino acids folds forming either an alpha helixor a beta pleated sheet

Describe how DNA replicates in simple terms

semi- conservative reapplication. DNA helicase

What is chromatography used for?

separate mixtures of substances into their components

Describe the primary structure of proteins

sequence of amino acids

What if the substances you are interested in are colourless?

spray ninhydrin

State 3 properties of a typical amino acid

white crystalline solids at room temperature. Dissolve readily in water but not non polar organic solvents Have a high melting point