use the data booklet to help you answer this question...

Use the Data Booklet to help you answer this question.

This question is about amino acids and peptide (amide) links.

(a) Draw the structure of the zwitterion formed by phenylalanine.

(1)

1

(b) Draw the structure of serine at high pH.

(1)

(c) Draw the structures of both dipeptides formed when phenylalanine reacts with serine.

In each structure show all the atoms and bonds in the amide link.

(2)

Page 1 of 21Catalyst Tutors

(d) An amide link is also formed when an acyl chloride reacts with a primary amine.

Name and outline a mechanism for the reaction between CH3CH2COCl and CH3CH2NH2

Give the IUPAC name of the organic product.

Name of mechanism __________________________________________________

Mechanism

IUPAC name of organic product _________________________________________

(6)

(Total 10 marks)


Which structure shows 2-aminobutanoic acid as a zwitterion?

A

B

C

D

(Total 1 mark)

2

The tripeptide shown in the following figure is formed from the amino acids glycine, threonine andlysine.

3

(a) Draw a separate circle around each of the asymmetric carbon atoms in the tripeptide in thefigure.

(1)


(b) Draw the zwitterion of glycine.

(1)

(c) Draw the structure of the species formed when glycine reacts with an excess ofbromomethane.

(1)

(d) Deduce the IUPAC name of threonine.

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(1)

(e) Draw the structure of the species formed by lysine at low pH.

(1)

(Total 5 marks)


The following figure shows a simplified representation of the arrangement of some amino acids ina portion of a protein structure in the form of an α-helix.

4

(a) Name the type of protein structure in the figure.

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(1)

(b) Explain the origin of the interaction represented by the dotted lines in the figure above.

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(4)

(Total 5 marks)


Proteins contain sequences of amino acids joined by peptide links.Amino acid chains (polypeptides) are attracted to each other by hydrogen bonding.

(a) (i) A section of a protein is formed from one molecule of each of the amino acids glycine(H2NCH2COOH) and alanine (H2NCH(CH3)COOH).

Add bonds and atoms to the diagram to complete a structural formula for this sectionof the protein.

(2)

(ii) Draw a diagram to show how an amino acid chain can form a hydrogen bond withanother amino acid chain.Your diagram need only show the relevant atoms from one amino acid in each chain.

(1)

5


(b) Leucine, serine and glutamic acid are naturally-occurring amino acids.

(i) Give the IUPAC name of leucine.

______________________________________________________________

(1)

(ii) Draw the structure of the zwitterion of serine.

(1)

(iii) Draw the structure of the ester formed by two molecules of serine.

(1)

(iv) Draw the structure of the species formed by glutamic acid at low pH.

(1)

(Total 7 marks)


A drug is designed to simulate one of the following molecules that adsorbs onto the active site ofan enzyme.

Which molecule requires the design of an optically active drug?

A

B

C

D

(Total 1 mark)

6

Use the Data Booklet to help you answer these questions.

DNA exists as two strands of nucleotides in the form of a double helix with hydrogen bondingbetween the two strands.

(a) A deoxyribose molecule in a strand of DNA is shown.

Name the types of group attached to 2-deoxyribose at positions X and Y.

X _________________________________________________________________

Y _________________________________________________________________

(2)

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(b) In the DNA double helix, adenine is linked by hydrogen bonds to a molecule in the otherstrand of DNA.

Complete the diagram below to show the other molecule and the hydrogen bonds betweenit and adenine.

(2)

(Total 4 marks)

Use the information in the Data Booklet to help you answer these questions.

A single strand of DNA is made from many nucleotides linked together.

(a) Draw the structure of the nucleotide that contains guanine, showing clearly the bondingbetween the components.

(3)

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(b) Two complementary strands of DNA form a double helix in which one strand is attracted toanother by interactions between pairs of bases.

Complete the base pair diagram showing the interactions.

(2)


(c) State how the interactions in the adenine-thymine base pair differ from those you identifiedin part (b).

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(1)

(d) Urea has the displayed formula

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

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(2)

(Total 8 marks)

The anticancer drug cisplatin operates by reacting with the guanine in DNA.

Figure 1 shows a small part of a single strand of DNA. Some lone pairs are shown.

Figure 1

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(a) The DNA chain continues with bonds at X and Y.

State the name of the sugar molecule that is attached to the bond at X.

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(1)

(b) Messenger RNA is synthesised in cells in order to transfer information from DNA. Thebases in one strand of DNA pair up with the bases used to synthesise RNA.

Figure 2 shows two bases used in RNA.

Figure 2

Suggest which of the bases A and B forms a pair with guanine in Figure 1 whenmessenger RNA is synthesised.Explain how the base that you have chosen forms a base pair with guanine.

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(4)

(c) Cisplatin works because one of the atoms on guanine can form a co-ordinate bond withplatinum, replacing one of the ammonia or chloride ligands. Another atom on anotherguanine can also form a co-ordinate bond with the same platinum by replacing anotherligand.

On Figure 1, draw a ring round an atom in guanine that is likely to bond to platinum.

(1)


(d) An adverse effect of cisplatin is that it also prevents normal healthy cells from replicating.

Suggest one way in which cisplatin can be administered so that this side effect isminimised.

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(1)

(Total 7 marks)

The complex cisplatin acts as an anticancer drug by changing the properties of DNA when itreacts with guanine, a component of DNA.

When cisplatin is absorbed into the human body, it undergoes a ligand substitution reaction andone chloride ligand is replaced by a water molecule forming a complex ion Q.

(a) Write an equation for this substitution reaction to form the complex ion Q.

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(2)

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(b) The complex ion Q can bond to guanine in two different ways.

(i) The first way involves a hydrogen atom, from one of the ammonia ligands on Q,bonding to an atom in a guanine molecule. State the type of bond formed to guanineand identify an atom in guanine that could form a bond to this hydrogen atom.

Type of bond ___________________________________________________

Atom in guanine _________________________________________________

(2)


(ii) The second way involves a ligand substitution reaction in which an atom in a guaninemolecule bonds to platinum by displacing the water molecule from Q.State the type of bond formed between guanine and platinum when a water moleculeis displaced and identify an atom in guanine that could bond to platinum in this way.

Type of bond ___________________________________________________

Atom in guanine _________________________________________________

(2)

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

Risk _______________________________________________________________

Explanation _________________________________________________________

(2)

(Total 8 marks)


Mark schemes

(a)

Allow −CO2−

Allow +H3N− and NH3+−1

1

(b)

(c)

1

1

If same wrong amino acid twice – max 1


(d) (nucleophilic) addition-elimination

Not electrophilic addition-elimination.M1

M2 for arrow from lp on N to C

(or to space half way between N and C)

Ignore δ+ and δ− unless wrong

M3 for arrow from C=O bond to O

Not score M3 as an independent first step, but can allow M2 forattack on C+ produced

If Cl lost at this stage, Max 1 for mechanism for M2

M4 for structure of ion including 2 charges

(+ on N must be correct in both cases if drawn twice)

M5 for 3 arrows and lp on O

- may be scored in two steps

Ignore use of RNH2 to remove H+ in M5, but penalise use of Cl−

M2-5

N-ethylpropanamideM6

[10]

B

[1]2


(a)

1

3

(b)

1

(c)

Allow

1

(d) 2-amino-3-hydroxybutanoic acid1

(e)

1

[5]

(a) Secondary14

(b) Nitrogen and oxygen are very electronegative1

Therefore, C=O and N–H are polar1

Which results in the formation of a hydrogen bond between O and H1


In which a lone pair of electrons on an oxygen atom is strongly attracted to the δ+H1

[5]

(a) (i)

Only one molecule of each used

M1 for 2 amide links

M2 CH2 and CH(CH3)

Allow 1 mark after one error

Dipeptide max 1

Treat both trailing bonds missing as one error

Ignore n2

5

(ii)

No need to show lp

The covalent bond and the hydrogen bond either side of the H mustbe linear.

1


(b) (i) 2-amino-4-methylpentan(-1-)oic acid

Ignore hyphens, commas, spaces1

(ii)

Allow -NH3+

1

(iii)

1

(iv)

Allow -NH3+

1[7]

C

[1]6

(a) X – base1

Y – phosphate (group)1

Ignore organic

Any mention of sugar in either loses that mark

7


(b) If not Thymine CE=0

Correct structure scores 2, penalise by 1 each error in• structure of thymine• orientation of thymine• hydrogen bonding

Ignore lp on N and O

Don’t penalise non-linear H bonds

on RHS of thymine – allow with or without H or – [DNA strand]2

[4]

(a)

CE=0 if nucleotide does not contain one base, one sugar and onephosphate.

Max 2 for any slips in structures.

Correct phosphate-sugar link on C3.

Allow phosphate attached to C5.1

Correct sugar-guanine link on C1.1

Remainder of molecule correct.1

8


(b)

Correct diagram of cytosine (base pair with guanine).

CE=0 if wrong base shown.1

Three hydrogen bonds drawn.

Allow M2 if slip in M1.1

(c) There are only two H-bonds in the adenine-thymine base pair.

Allow there is one fewer H-bond in the AT base pair.1

(d) The amino/-NH2 groups in urea1

are able to substitute for the H–bonds in the double helix.

Allow H bonds will form between the urea and the DNA strands.1

[8]

(a) 2-deoxyribose19

(b) Base A

If Base B stated, allow 1 mark only for response including hydrogenbonding

1

Top N–H forms hydrogen bonds to lone pair on O of guanine1

The lone pair of electrons on N bonds to H–N of guanine1

A lone pair of electrons on O bonds to lower H–N of guanine

Allow all 4 marks for a correct diagram showing the hydrogenbonding

Students could also answer this question using labels on thediagram

1


(c) Allow either of the nitrogen atoms with a lone pair NOT involved in bonding tocytosine

1

(d) Use in very small amounts / target the application to the tumour1

[7]

(a) Pt(NH3)2Cl2 + H2O → [Pt(NH3)2Cl(H2O)]+ + Cl–

Correct product1

Balanced equation1

10

(b) (i) Hydrogen bond1

Oxygen (or nitrogen)

Only score this mark if type of bond is correct1

(ii) Co-ordinate1

Nitrogen (or oxygen)

Bond type must be correct to score this mark but allow M2 if bond iscovalent

1

(c) Killing them or causing damage (medical side effects)

Allow any correct side effect (e.g. hair loss)Allow kills healthy (or normal) cells

1

May attach to DNA in normal cells1

[8]


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