Biotechnika Questions 2

1. Which amino acid forms disulphide bond & why?
2. Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond.What is meant by the term "residue" in this context?
3. What is Molten Globule?
4. How are the properties of an alpha helix different from a beta strand? How are they similar? How do each of these secondary structure affect theproperties of a protein, such as silk?

Answers :-

1-Cysteine amino acid can form disulphide bond because it contain –SH (sulphahydral) group. Disulphide bond form between two cysteine amino acid by removal of one H2 molecule by oxidation.


 2-In this context a ‘residue’ means an amino acid molecule that has lost a water molecule by becoming joined to a molecule of another amino acid. 

 3-A molten globule is a stable, partially folded protiene state found in mildly deaturing conditions such as low pH  mild denaturant, or high temperture. Molten globules are collapsed and generally have some native-like secodary sructure but a dynamic tertiary strcture as seen by far and near circular dichromism (CD) specroscopy, respectively. These traits are similar to those observed in the transient intermediate states found during the folding of certain proteins, especially globular protiens that undergo hydrophobic collapse, and therefore the term "molten globule" is also used to refer to certain  protien folding
intermediates corresponding to the narrowing region of the folding funnel higher in energy than the native state but lower than the denatured state. The molten globule ensembles sampled during protein folding and unfolding are thought to be roughly similar.
4-Alpha helix and beta-sheet conformations are the two main types of secondary structure of a protein molecule.
In the alpha-helix structure, the polypeptide curls longitudinally by the action of hydrogen bonds forming a spiral, or helix. In the beta-sheet conformation, the protein is more distended and the hydrogen bonds form a zig-zag-shaped protein structure called B-strand. Many assembled beta-strands make a beta-sheet.
Alpha helix and beta sheet both are secondary structure of protein and involve hydrogen bonds.
Silk is made up of the amino acids Gly-Ser-Gly-Ala and forms Beta pleated sheets. H-bonds form between chains, and side chains form above and below the plane of the H-bond network.
The high proportion (50%) of glycine, which is a small amino acid, allows tight packing and the fibers are strong and resistant to stretching. The tensile strength is due to the many interseeded hydrogen bonds. Since the protein forms a Beta sheet, when stretched the force is applied to these strong bonds and they do not break.

other answers for ques - 4 

Difference: (i) Alpha helix is formed by hydrogen bonds between carbonyl oxygen of first amino and amide N of fourth amino acid residues while beta sheet is formed when hydrogen bonds are formed between the carbonyl oxygens and amide hydrogens of two or more adjacent extended polypeptide chains.
(ii)alpha helix show intra chain hydrogen bonding and cross linking by disulphide bond is present while beta sheet show interchain hydrogen bonding.
(iii)alpha helix are tough, insoluble showing varying flexibility and hardness while beta sheets are soft, flexible filaments.
(iv)Alpha helix are right or left handed, while beta sheets are parallel or antiparallel.
(v)polar residues are found in beta sheet while is absent in former.
Proline occurs in beta-pleated sheet.
Similarity:Both are secondary structure of protein and are stabilized by hydrogen bond

The polypeptide chains of silk fibroin, a protein of silk worm are predominantly rich in the beta pleated conformation. Fibroin is rich in Ala and Gly residues, permitting a close packing of sheets and an interlocking arrangement of R groups. The overall structure is stabilized by extensive hydrogen bonding between all peptide linkages in the polypeptides of each sheet and by the optimization of van der Waals interactions between sheets. Silk does not stretch, because the conformation is already highly extended. However, the structure is flexible because the sheets are held together by numerous weak interactions rather than by covalent bonds in other proteins such as the disulfide bonds in alpha-keratins

Biotechnika Questions1

Name two nonpolar amno acids.

• 1a) Sickle cell anaemia results from a substitution of a valine for a glutamate. What do you expect the effect might be if mutation were to have placed a leucine at that site? Or an aspartate?

Which of the two photosystems operates at the most negative redox potential?

• 2a) Which among them generates the strongest reducing agent?
• 2b) Which among them must absorb 4 photons during each round of non cyclic photophosphorylation?
• 2c) Name some accessory pigments that surround each
  photosystem?

AnsWERS :-

1. There are eight amino acids with nonpolar side chains. Glycine, alanine, and proline have small, nonpolar side chains and are all weakly hydrophobic.
Phenylalanine, valine, leucine, isoleucine, and methionine have larger side chains and are more strongly hydrophobic.

1a. Sickle cell anemia results is caused due to substitution of charged amino acid i.e glutamate (at the 6th position ) by valine which is non polar in nature hence due to the charge variance in the molecule the structure of the hemoglobin molecule changes drastically making it sickle shaped.
Leucine also has a non polar nature hence it would also result in abnormality of haemoglobin molecule.
However when you have a charged counterpart like aspartic acid which has the same equivalent charge and polar nature present in the molecule, replacing glutamate, it would not cause any abnormality in the haemoglobin molecule but would decrease the chain length by one Ch2 group which is additional in glutamate

Q2. PSI generates the most negative redox potential because it involves NADP+-NADPH coupled reaction which has a standard redox potential of -0.32V as compared to PSII which involves o2-H20 coupled reaction having a standard redox potential of +0.82V

Q2. a *** very imp** The strongest reducing agent is generated by photosystem Iit produces NADPH from NADP+
(note by:strong oxidising is produced by Photosystem II since it produces oxygen from water)

Q2b.Both the photosystems must absorb four photons.
(Explanation: The production of one molecule of oxygen requires the removal of four electrons from two water molecules.The removal of electrons from water requires the absorption of four photons, one for each electron. At the same time the reduction of one molecule of NADP+ requires transfer of 2 electrons. Thus hypotectically if only one photosystem were able to transfer electrons from H2O to NADP+, four photons would be sufficient to produce two molecules of NADPH. Because two photosystems are utilized in the cell that number is doubled to eight four being utilised by PSII and four in PSI.)

2 H2O + 2 NADP ----4Photons---> 1 O2 + 2 NADPH (Overall light reaction)

Q2c. Accessory Pigments are chlorophyll b (also c, d, and e in algae and protistans), xanthophylls, and carotenoids or phycobiliproteins (beta carotenoids)