Topic 10.4 Amino Acids n Proteins Prelim Soln | Amino Acid | Cysteine

Amino Acids & Proteins – Suggested Solutions

Topic 10.4 : Amino Acids & Proteins AJC/2009/P2/Q4c 1. 1 – Arginine ; 2- alanine; 3- glutamic acid

VJC/2009/P3/Q5d 2. (i) Only one optical isomer is found naturally in silkworm and it rotates plane of polarised light due to presence of a chiral carbon. When alanine is synthesised from the reaction scheme, a racemic mixture containing equal amount of both enantiomers is formed. Thus net optical activity is zero. (ii) Heavy metal ions such as Cu2+ will attract negatively charged R groups such as — CO2-, hence disrupting the original ionic bonds holding the tertiary structure in egg white. This causes the protein chains to unfold and expose the hydrophobic R groups. Hence solubility decreases leading to precipitation and thus it turns white. HCI/2009/P3/Q5b,c (b) 3. (i) Quaternary structure refers to the arrangement of polypeptide chains (called sub-units) in a protein, which are held together by interactions between the side-chains of the polypeptides. (ii) Minimum Mr =
100 x 55.8 0.34

= 16 412

There are four sub-units in each haemoglobin molecule. (iii) (c) (i) (ii) 1: dative bond; 2: hydrogen bond; 3: ionic linkage Hydrolysis of the peptide linkage
N NH CH2 O H CH3 HC CH3 CH2

Hydrophobic interactions

{or zwitterion form}

H2N CH C N CH CO2H

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Amino Acids & Proteins – Suggested Solutions

(iii) IJC/2009/P2/Q5f (f) 4. (i)

Peptides are hydrolysed or broken down in gut or stomach by digestion.

(ii)

(iii)

Amino Acid

R group interactions

Cysteine

Proline

(iv)

JJC/2009/P2/Q7a,b 5. (a) (b) Ile-His-Cys-Pro-Gly-Val-Leu-Pro-Val-Lys-Val At low pH, −N / −NH becomes −NH+ / −NH2+. This disrupts the hydrogen bonds in the tertiary structure, and hence lead to denaturation.

246

Amino Acids & Proteins – Suggested Solutions

JJC/2009/P2/Q7c 6. (c) (i) (ii) Glu forms a peptide bond to cysteine, through the –COOH group of its side chain rather than its main carboxylic acid group. Zn2+ ions bind tightly to the –SH group of the cysteine residues. This disrupts the disulphide bridges in the tertiary structure, [1] This disruption results in the shape of the cartiliage protein being altered/ causes cartiliage protein to fold differently and hence, leads to denaturation of cartiliage protein. [1] MI/2009/P2/Q6a,b 7. B - at starting point C - nearest to +ve D - between C and B E - nearest to -ve above word polypeptide chain – tertiary below is secondary ; ά helix MJC/2009/P3/Q5a-c 8. Primary Structure – amide / peptide linkage ; Secondary Structure – hydrogen bonds between C=O & N-H groups ;Tertiary Structure – R group interactions (e.g. ionic, disulphide linkages, hydrogen bonding);Quaternary Structure – Van der Waal’s forces (bi)
H H N
+

peptide linkage
H C
+

O C N

H C H H H H

O C N H

H C

O C O
-

H H H H N H N
+

H H C H C H C
+

H

H N H

O

-

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Amino Acids & Proteins – Suggested Solutions

(ii) (ci) (ii)

H+ + +NH3CHCH3COO- → +NH3CHCH3COOH *similar format for the other Disulphide bonds The R groups are deprotonated which affect the electrostatic interactions causing unfolding of the protein chain hence denaturation occurs.

(iii) Pipette the 25.0 cm3 Fe2+ solution into a conical flask and add about 10 cm3 of sulphuric acid, including few drops of phosphoric acid. Titrate with the KMnO4 solution from a burette until the solution in conical flask turns from pale green to permanent pink. Repeat titration to get consistent results. 8H+ + MnO4– + 5Fe2+ → Mn2+ + 5Fe3+ + 4H2O SRJC/2009/P3/Q5d 9. (i) H2NCHCOOH Q: CH2OH H2NCHCOOH R: (ii) Q: Hydrogen bond R: Van der Waals forces of attraction NJC/2009/P2/Q2a-d 10. (a) It is a polypeptide chain joined by amino acid units through peptide bonds. IIe-Gly-Asp-Glu-Asn-Tyr (b) (i) -CH2SH + -CH2SH + [O] → -CH2S-SCH2- + H2O -CH2SH + -CH2SH → -CH2S-SCH2- + H2 -CH2SH + -CH2SH → -CH2S-SCH2- + 2[H] (ii) tdid : Valine – phenylalanine: ionic interaction : lysine- glutamic, lysine- aspartic acid H-bonding: Serine – Aspartic acid: (Serine- glutamic acid), (Aspartic – glutamic CH3

248

Amino Acids & Proteins – Suggested Solutions

acid) (c) (i) Optimum working pH for this enzyme is 2.5. At pH lower or above 2.5, the existing ionic or H-bonding interactions are destroyed . changing the tertiary structure of protein rendering it inactive. (ii) Addition of heavy metal ions which will destroy the disulfide bonds by forming ppt with sulfur. Protein denatured therefore lost its activity. Supply of heat/ high temp also acceptable. (d) (i)
H CH3CONHC COOH (CH2)4NHCOCH3

(ii)

Both Lysine and compound A can react with alkali to form soluble salt. However, when compound A is formed, it loses its basic property as it forms the amide (not peptide) linkage. No reaction therefore insoluble in acid. However it is still soluble in alkaline medium as it still carries the COOH group that can react to form the soluble salt in alkaline solution.

NYJC/2009/P3/Q1d 11. d(i) For the amino acid residue to be found on the outer surface of a water soluble globular protein, the R group must be a hydrophilic group. • • Hence, Serine (ser) will be found on the outer surface Lysine (Lys) will also be found on the outer surface The OH group on serine can form hydrogen bonds with water hence soluble. The NH2 group on lysine can form hydrogen bonds with water hence making it soluble. (ii) For Phe, Pro, Leu : Hydrophobic or van der Waals forces For Lys, Ser: hydrogen bonding (iii) Denaturation of proteins. When heated, the weaker R group interactions such as hydrogen bond and hydrophobic interactions stabilising the tertiary structure will be disrupted. Hence the polypeptide chain will uncoil itself and lose its shape.

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Amino Acids & Proteins – Suggested Solutions

However, the primary structure will still be intact. (iv) (v) for Lys (the zwitterions for any other amino acid can also be drawn) When a small amount of acid (H+) is added,
O O H3N CH O(CH 2)4 NH 2
O O H2N CH O(CH 2)4 NH 2 C O
-

H +

+

H3N CH (CH 2)4 NH 2

+

C

+

C OH

When a small amount of base (OH−) is added,
OH- +
H3N CH (CH 2)4 NH 2
+

C

+ H2O

PJC/2009/P2/Q5a,b 12.

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Amino Acids & Proteins – Suggested Solutions

RI/2009/P2/Q5a-d 13. (a)(i)

• • • •

N–H ---------:O=C lone pair on O atom δ+ on H and δ– on N α-helix

(a)(ii) At temperatures above 60oC, there is sufficient heat energy to break the hydrogen bonds maintaining the α-helix structure. This causes the α-helix structure to lose its helical shape to become a random coil. (a)(iii) extreme acidic pH (b) Primary structure of gastrin: Glu-Gly-Pro-Gly-Trp-Leu-Glu-Glu-Glu-Glu-Ala-Ala-Tyr-Trp-Met-Asp-Phe (c) Haemoglobin is a transport protein with quaternary structure. It consists of four polypeptide chains/subunits (specifically, two α-subunits and two β-subunits) combined together to form a globular protein. There is considerable amount of R-group interactions between an α-subunit and the neighbouring β-subunit. Each subunit has a haem group bonded to it. The iron(II) in the haem group can bind to oxygen.

251

Amino Acids & Proteins – Suggested Solutions

(d)

Any three of the following:

Type of interaction Diagram illustrating the type of interaction ¨¨§  Disulfide bridge/linkage
CH2

 ¡¢£¤¥¦¡ § ¨©¡ §

¥¤¥§¥¡ § ¦¡

S S CH2

Ionic interaction/ Electrostatic forces of attraction between oppositely charged groups

CH2

!"# $%& $' ($)0(&(123& "4!2%

2$%2" $%32%5

COO- 

NH3 CH2

Hydrogen bonding

δ+ CH2OH δ−
Or

δ− O CH2
H δ+

δ+ CH2OH δ−

Ο

CCH2 Ο

van der Waals’ forces/ hydrophobic forces

–CH2CH2CH3 + any other group e.g.

CH2

6 6 789 @AB @C D@EFDBDGHIB 8P7 HA

6 PFIQ@DP@ H8 HAGBQ78GH@AR

CH2CH3 CH2CH3 CH2

252

Amino Acids & Proteins – Suggested Solutions

SAJC/2009/P2/Q9a-e 14.

(a) (b)

VAL-CYS-ASP-LYS-GLY-CYS-LYS-VAL-ARG The cool environment prevent the denaturation of protein insulin by heat which will disrupt side chain interactions in the tertiary structure of protein causing the protein to lose its native conformation/3D structure/coagulation.

(c)

(d)

COOH H C CH2S H2N

H2N SCH2 C H COOH disulfide linkage [1]

(e)

ion-dipole interaction O

COO-

H δ+

H

H C CH2SH H3+N δ− O

H

H

ion-dipole interaction

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Amino Acids & Proteins – Suggested Solutions

TJC/2009/P2/Q4a,b 15.

(a)

• Anti-parallel, three strands, correct repeat unit, correct orientation of bonds to score 1 mark • If above is met, then 1 mark awarded for hydrogen bonds between strands between C=O to N-H Hydrogen bond
O N H O N H O N C R C R R C O H N C O H N C O H N R R R

(b)

(i)

In the presence of metal ions, e.g. Ag+. Ionic bonds are broken

● Negatively charged R groups form salts or complex ions with the metal ions,
e.g. –COO−Ag+

OR ● Disulphide linkages are broken ● Ag+ will break the S—S bond (e.g. –CH2 – S – Ag) OR ● hydrogen bonds / permanent-dipole-permanent dipole interactions are broken ● Ag+ will interrupt electrostatic forces between polar R-groups
(ii) At pH 2. Ionic bonds are broken

● Addition of H+ neutralizes/protonates basic/alkaline groups,
e.g. –COO− + H+ → –COOH

OR ● hydrogen bonds / permanent-dipole-permanent dipole interactions are broken ● Addition of H+ neutralizes/protonates basic/alkaline groups,
e.g. –NH2 + H+ → –NH3+

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Amino Acids & Proteins – Suggested Solutions

TPJC/2009/P2/Q6a 16.

VJC/2009/P2/Q4a-e 17. (a)

(i)

H3N+CH2COO- + H+ H3N+CH2COO- + OH-

H3N+CH2COOH H2NCH2COO- + H2O

(ii)

Since the –CO2H group is deprotonated to give –CO2-, aminoethanoic acid will move towards the positive electrode.

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Amino Acids & Proteins – Suggested Solutions

(b) (i) H O H H O H H O H H O H H O H H | || | | || | | || | | || | | || | | + H3N - C – C – N – C – C – N – C – C – N – C – C – N – C – C – N – C – CO2H | | | | | | + CH2CO2H CH2OH CH2SH CH3 (CH2)4N H3 CH3 (ii) Any 2 of the following: Ionic bond between charged –CH2COO- and –(CH2)4NH3+ groups. Hydrogen bond between –OH of –CH2COOH group and –CH2OH group. Disulfide bond bween –CH2SH group of cysteine residues. Van der waals’ forces between non-polar –CH3 groups. (iii) Add acidified MnO4- (OR acidified Cr2O72-) to each solution and heat. Serine will decolorize the purple MnO4- (OR turns orange Cr2O72- green) but alanine will not. [N.B: Na and PCl5 NOT accepted as aqueous solutions are used.] c(i)

c(ii) -CH2OH, -CH2COOH, -CH2SH and -(CH2)4NH2 groups which are polar and hence hydrophilic will be located on the surface of the globular protein. -CH3 groups which are non-polar and hence hydrophobic will be located inside the protein away from the aqueous surroundings.

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Amino Acids & Proteins – Suggested Solutions

(d) R H R | | | -C–N–C–C– | || | H O H (e)

+ H2O

-CHRNH2 +

-CHRCOOH

The primary structure of the pentapeptide is cys-ala-cys-ala-cys. Cysteine is before Alanine since enzyme X cleaved the cys-ala peptide bond to give cys and two ala-cys. Alanine is also before Cysteine since enzyme Y cleaved the ala-cys peptide bond to give two cys-ala and cys.

257

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