Organic Chemistry

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2021.pdf

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Organic and Biological Chemistry (OBC) 2020-21

SAT

14 June 2021

Name (please print)

Student number

Please do not write in this table.

Q Mark

1 /25

2 /25

3 /25

4 /25

5 /25

6 /25

Total /150

1. Upon consideration of the reaction R1 to R11 below answer the following questions [20 marks].

1.1. Write the line-bond formula of compounds 1a, 1c, 1g, 1h, 1i, 1j, 1k and 1m

1.2. What type of reaction (addition, elimination, hydrolysis, nucleophilic substitution, condensation or acid-base)

are reaction R1, R2, R4, R5, R6, R7, R9 and R10?

2. Upon consideration of the compounds 2a to 2o below answer the following questions [30 marks].

2.1. Classify the compounds below as alkanes, alkenes, alkynes, alcohols (primary, secondary and tertiary), ethers,

ketones, aldehydes, amines (primary, secondary and tertiary), acids, esters and amides (primary, secondary and

tertiary). If no compound of a particular class is present answer n/a in the corresponding box.

2.2. Identify all the isomers of compounds 2a, 2b, 2c, 2d and 2e

2.3. Identity a pair of geometric isomers and name the configuration of each of them

2.4. Sort compounds 2a, 2b, 2d, 2e, 2f, 2h, 2k, 2n and 2m in order of increasing boiling point

2.5. Sort compounds 2o, 2h and 2l in order of increasing solubility in water, explaining briefly your choice.

3. Within the designated spaces in the Answer Book, answer 3.1 through 3.3 for up to 25 marks, total.

3.1. Considering compounds 3a through 3l, identify: ONE PAIR of geometric isomers; TWO PAIRS of

enantiomers and THREE PAIRS of identical molecules. [6 marks]

3.2. State the configurations of each of the geometric isomers and of each of the enantiomers.

Draw the relevant structures in the space provided in the Answer Book and show the workings

that allow you to determine the configuration. [9 marks]

3.3. Sort compounds 3a,3b, 3c, 3f and 3k in order of increasing solubility in water and briefly justify

your ordering. [10 marks]

4. Within the designated spaces in the Answer Book, answer 4.1 through 4.3 for up to 25 marks, total.

Refer to the Figure on page 7 throughout.

4.1. Sort compounds 4a to 4c in order of increasing melting point and briefly justify your ordering.

[7 marks]

4.2. Chemically classify each named compound seen in the Table below, 4a through 4k, by writing

its name in the appropriately labelled box in the Answer Book. Bear in mind that some boxes

may correctly identify more than one compound. [4 marks]

4.3 Which amino-alcohol, incorporated within a lipid structure, will lead to neutral lipid at pH 7?

Which will lead to a negatively-charged lipid? [Bear in mind that the pKa of an ammonium

cation is between 9 and 10 and that of carboxylic acid between 2 and 5.] [4 marks]

4.4. Sketch a suitable sequence of synthetic reactions to obtain 4f from 4d. State what reagents,

other than 4f and 4d will be needed, and what type of reaction (addition, elimination,

substitution, redox, hydrolysis or condensation) describes every step. [10 marks]

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5. Within the designated spaces in the Answer Book, answer 5.1 through 5.5 for up to 25 marks, total.

5.1. Identify the chemical type of each

compound, according to the

options given in the Answer Book.

[3 marks]

5.2. On the diagram as seen in the

Answer Book, CIRCLE all the chiral

centres in each structure.

[6 marks]

5.3. On the diagram as seen in the

Answer Book, label acetal and

hemiketal moieties, and peptide

bonds. Name the bond that links

the two saccharides in the

disaccharide. [4 marks]

5.4. Sketch the reaction of hydrolysis of

the peptide, clearly drawing the

reactants and products. [5 marks]

5.5. Identify the dinucleotide sequence

and state whether this is a DNA or

RNA dinucleotide. Sketch the

reaction of formation of the

dinucleotide from its constituent

nucleotides, clearly drawing

reactants and products, and state

which kind of reaction it is.

[7 marks]

(OBC) Page 9 of 24

6. Within the designated spaces in the Answer Book, answer 6.1 through 6.5 for up to 25 marks, total.

6.1. On the diagram provided in the Answer Book, draw a line across each peptide bond in

oligopeptide 6a. Write the single-letter sequence in the space provided. [6 marks]

6.2. On the diagram provided in the Answer Book, CIRCLE all the chiral centres in oligopeptide 6a. [4

marks]

6.3. Complete the Table in the Answer Book to indicate, for oligopeptide 6a, the charges on

ionisable groups and the net charge at pH 11 and at pH 7. What will be the net charge at its

isoelectric point? [5 marks]

As required, make use of the information provided in the amino acid table in the Supplement.

6.4. What moieties within oligopeptide 6a are those mainly responsible for the formation of an

alpha-helix? Name the process that leads to the unfolding of the alpha helix to yield a random

coil. [2 marks]

6.5. Complete the Table in the Answer Book to indicate, for oligopeptide 6a, which amino acid side

chains will be involved in: hydrophilic interactions, hydrophobic interactions, disulphide bridges

and salt bridges. In each case, briefly justify your choice. For which level(s) of structure are the

side chain interactions mainly responsible? [8 marks]

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Question 1

1.1. Draw the line-bond formula of each compound: 1a, 1c, 1g, 1h, 1i, 1j, 1k and 1m. [17 marks]

1d 1i

1l 1m

1.2. Classify reactions R1, R2, R4, R5, R6, R7, R9 and R10 by their type. [8 marks]

R1 R2

R4 R5

R6 R7

R9 R10

(OBC) Page 11 of 24

Question 2

2.1. Write the name (e.g. 2a, 2b, etc. through 2o) of the compounds seen in the Question Paper into the box corresponding to the compound’s chemical type. [4 marks] Alkanes

Alkenes Alkynes Primary alcohols

Secondary alcohols

Tertiary alcohols

Ethers

Primary amines Secondary amines

Tertiary amines Esters Ketones

Aldehydes

Acids Primary amides Secondary amides

Tertiary amides

2.2. Enter the names of all isomers of the respective compounds. [5 marks]

Isomers of 2a

Isomers of 2b

Isomers of 2c

Isomers of 2d Isomers of 2e

2.3. Write the compound names 2a, 2b, 2d, 2e, 2f, 2h, 2k, 2n and 2m in order of increasing boiling point. [9 marks]

Lowest boiling point

Highest boiling point

(OBC) Page 12 of 24

Question 2 (continued)

2.4. Sort compounds 2o, 2h and 2l in order of increasing water solubility[7 marks]

Least soluble Most soluble

Justification

(OBC) Page 13 of 24

Question 3

3.1. Considering compounds 3a through 3l, Identify: ONE PAIR of geometric isomers; TWO PAIRS of enantiomers and THREE PAIRS of identical molecules. [6 marks]

Geometric isomer pair

Enantiomer pair 1 of 2

Enantiomer pair 2 of 2

Identical pair 1 of 3

Identical pair 2 of 3

Identical pair 3of 3

3.2. State the configurations of each of the geometric isomers and of each of the enan- tiomers. Draw the relevant structures in the space provided in the answer booklet and show the workings that allow you to determine the configuration. [9 marks]

Geometric Isomer Pair 1

Compound name Isomer Compound name Isomer

Use the space below for your workings on the geometric isomer pair 1

Enantiomer Pair 1

Compound name Isomer Compound name Isomer

Use the space below for your workings on the enantiomer pair 1

(OBC) Page 14 of 24

Question 3 (continued)

Enantiomer Pair 2

Compound name Absolute configuration Compound name Absolute configuration

Use the space below for your workings on the enantiomer pair 2

3.3. Sort compounds 3a,3b, 3c, 3f and 3k in order of increasing solubility in water and briefly justify your ordering. [10 marks]

Least soluble Most soluble

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(OBC) Page 16 of 24

Question 4

4.1. Sort compounds 4a to 4c in order of increasing melting point in the spaces below. Briefly justify your ordering. [7 marks]

Lowest melting point Highest melting point

Question 4 (continued)

(OBC) Page 17 of 24

4.2. Write the name (e.g. 4a, 4b, etc. through 4k) of the compounds seen in the Question Paper into the box corresponding to the compound’s chemical type. [4 marks]

Saturated fatty acids

Unsaturated fatty acids Triacylglycerides Phosphoglycerides

Sterols

Amino alcohols Glycerol Dihydrogenphosphate

4.3. Which amino-alcohol, incorporated within a lipid structure, will lead to neutral lipid at pH 7? Which will lead to a negatively-charged lipid? [4 marks]

Neutral lipid

Negatively charged lipid

4.4. Sketch here the sequence of reactions to obtain 4f from 4d, noting the type of reaction for each step (more space on next page, if needed). State what reagents, other than 4f and 4d will be needed and what type of reaction (addition, elimination, substitution, redox, hydrolysis or condensation) describes every step. [10 marks]

(OBC) Page 18 of 24

Question 4 (continued)

Continue with sketch, as needed.

Question 5

5.1. Write 5a, 5b, or 5c into the box that correctly identifies the compound. [3 marks]

Peptide

Nucleotide Saccharide

5.2. CIRCLE all chiral centres in each structure: 5a, 5b, 5c. [6 marks]

5.3. Write an “A” over an acetal moiety; write an “H” over a hemiketal moiety; to the RIGHT of the disaccharide, state the type of the glycosidic bond. For the peptide, label the peptide bonds by drawing a line across them [4 marks]

(OBC) Page 20 of 24

Question 5 (continued)

5.4. Sketch the reaction of hydrolysis of the peptide, clearly drawing the reactants and products. [5 marks]

(OBC) Page 21 of 24

Question 5 (continued)

5.5. [7 marks, total]

The dinucleotide sequence is:

The dinucleotide is: DNA RNA (circle the correct answer)

Sketch the reaction of formation of the dinucleotide from its constituting nucleotides, clearly drawing reactants and products and state which kind of reaction it is.

1 (OBC) Page 22 of 24

Question 6

6.1. Draw a line across each peptide bond in oligopeptide 6a. Write the oligopeptide 6a acronym in single-letter code. [6 marks]

6a single-letter acronym:

6.2. Circle all of the chiral centres in 6a. [4 marks]

6.3. [5 marks total] Indicate below for each indicated ionisable group the charge on that group at pH 7 and the overall charge for oligopeptide 6a at the same pH.

N-terminus charge Side chain 1 charge Side chain 2 charge C-terminus charge Overall charge

Indicate below for each indicated ionisable group the charge on that group at pH 11 and the overall charge for oligopeptide 6a at the same pH.

N-terminus charge Side chain 1 charge Side chain 2 charge C-terminus charge Overall charge

6.4. What moieties within oligopeptide 6a are those mainly responsible for the formation of an alpha-helix? Name the process that leads to the unfolding of the alpha helix to yield a random coil. [2 marks]

(OBC) Page 23 of 24

6.5. Complete the Table, with reference to oligopeptide 6a. [8 marks]

Name the amino acids whose side chains will be involved in…

…hydrophilic interactions Justification: ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------------------------------- -------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------ --------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- -------------------------------------------------------------------------------------------------------------------------------------- ------------- ---------------------------------------------------------------------------------------------------------------------- ----------------------------- -----------------------------------------------------------------------------------------------

…hydrophobic interactions Justification: --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------- ---------- ------------------------------------------------------------------------------------------------------------------------- -------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------------------ --------------------------------------------------- ------------------------------------------------------------------------------------------------------------ ----------------------------------------------------------------------------------------------------------------------------- ---------

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…disulfide bridges Justification: --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------------------------------------------------- ---------- ----------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------------------------------- -------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------ --------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- -----------------------------------------------------------------------------------------------

…salt bridges Justification: ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------------------------------- -------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ------------------------------------------------------------------------------------ --------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- --------------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- ----------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------- ---------------------- -------------------------------------------------------------------------------------------------------------------------------------- ------------- ---------------------------------------------------------------------------------------------------------------------- ----------------------------- -----------------------------------------------------------------------------------------------

For which level(s) of structure are the side chain interactions mainly responsible?