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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
H2N CH C N CH CO2H
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(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.
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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 ; 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 Waals 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 N H
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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
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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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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 +
C OH
+ H2O
PJC/2009/P2/Q5a,b 12.
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(a)(ii) At temperatures above 60oC, there is sufficient heat energy to break the hydrogen bonds maintaining the -helix structure. This causes the -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 -subunits and two -subunits) combined together to form a globular protein. There is considerable amount of R-group interactions between an -subunit and the neighbouring -subunit. Each subunit has a haem group bonded to it. The iron(II) in the haem group can bind to oxygen.
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(d)
Type of interaction Diagram illustrating the type of interaction Disulfide bridge/linkage
CH2
S S CH2
CH2
2$%2" $%32%5
COO-
NH3 CH2
Hydrogen bonding
+ CH2OH
Or
O CH2
H +
+ CH2OH
CCH2
CH2
6 PFIQ@DP@ H8 HAGBQ78GH@AR
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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)
(e)
ion-dipole interaction O
COO-
H +
H C CH2SH H3+N O
ion-dipole interaction
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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. COOAg+
OR Disulphide linkages are broken Ag+ will break the SS 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
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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TPJC/2009/P2/Q6a 16.
(i)
(ii)
Since the CO2H group is deprotonated to give CO2-, aminoethanoic acid will move towards the positive electrode.
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(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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+ 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.
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