Proteins, Enzymes, and Disulfide Bonds: A Study of Protein Structure and Function, Exercises of Biochemistry

Exercises on Biochemistry from Unit 1 - 4

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Unit 4. Part II + III. Proteins - Enzymes
9. Disulfide Bonds Determine the Properties of Many Proteins.
Some natural proteins are rich in disulfide bonds, and their mechanical
properties (tensile strength, viscosity, hardness, etc.) are correlated
with the degree of disulfide bonding.
(a) Glutenin, a wheat protein rich in disulfide bonds, is responsible for the cohesive and
elastic character of dough made from wheat flour. Similarly, the hard, tough nature of
tortoise shell is due to the extensive disulfide bonding in its α-keratin. What is the
molecular basis for the correlation between disulfide-bond content and mechanical
properties of the protein?
Disulfide bonds are covalent bonds which are much stronger than the non-covalent
forces in protein (hydrogen bonds, weak van der Waal forces etc.). Being strong in
nature, the disulfide bonds have a strong effect on the stabilization of protein
conformation. Disulfide bonds have marked effects on the mechanical strength
(tortoise shell) and stiffness (wheat dough) of the proteins that contain them.
(b) Most globular proteins are denatured and lose their activity when
briefly heated to 65oC. However, globular proteins that contain multiple
disulfide bonds often must be heated longer at higher temperatures to
denature them. One such protein is bovine pancreatic trypsin inhibitor
(BPTI), which has 58 amino acid residues in a single chain and contains
three disulfide bonds. On cooling a solution of denatured BPTI, the
activity of the protein is restored. What is the molecular basis for this
property?
Disulfide bonds in the BPTI cysteines residues prevent protein from changing its
structure and form. The disulfide bonds with in the BPTI’s three adjacent cysteines,
prevents the protein from changing its structure to any stable form and hence
prevent it from folding and unfolding completely.
Heating of globular proteins leads to increased thermal motion of amino acid
residues and disruption of many non-covalent interactions. However, disulfide
bonds are not broken by heating. The presence of these bonds prevents the
polypeptide from becoming completely randomized and can facilitate the refolding
of the protein when the temperature is reduced.
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Unit 4. Part II + III. Proteins - Enzymes

9. Disulfide Bonds Determine the Properties of Many Proteins. Some natural proteins are rich in disulfide bonds, and their mechanical properties (tensile strength, viscosity, hardness, etc.) are correlated with the degree of disulfide bonding. (a) Glutenin, a wheat protein rich in disulfide bonds, is responsible for the cohesive and elastic character of dough made from wheat flour. Similarly, the hard, tough nature of tortoise shell is due to the extensive disulfide bonding in its α-keratin. What is the molecular basis for the correlation between disulfide-bond content and mechanical properties of the protein?  Disulfide bonds are covalent bonds which are much stronger than the non-covalent forces in protein (hydrogen bonds, weak van der Waal forces etc.). Being strong in nature, the disulfide bonds have a strong effect on the stabilization of protein conformation. Disulfide bonds have marked effects on the mechanical strength (tortoise shell) and stiffness (wheat dough) of the proteins that contain them. (b) Most globular proteins are denatured and lose their activity when briefly heated to 65oC. However, globular proteins that contain multiple disulfide bonds often must be heated longer at higher temperatures to denature them. One such protein is bovine pancreatic trypsin inhibitor (BPTI), which has 58 amino acid residues in a single chain and contains three disulfide bonds. On cooling a solution of denatured BPTI, the activity of the protein is restored. What is the molecular basis for this property?  Disulfide bonds in the BPTI cysteines residues prevent protein from changing its structure and form. The disulfide bonds with in the BPTI’s three adjacent cysteines, prevents the protein from changing its structure to any stable form and hence prevent it from folding and unfolding completely.  Heating of globular proteins leads to increased thermal motion of amino acid residues and disruption of many non-covalent interactions. However, disulfide bonds are not broken by heating. The presence of these bonds prevents the polypeptide from becoming completely randomized and can facilitate the refolding of the protein when the temperature is reduced.

10. Amino Acid Sequence and Protein Structure. Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence. (a) Where might bends or β turns occur?  Β turns commonly (but not always) occur where Gly and Pro residues are found in the polypeptide chain. Thus, β turns might occur at the residue 6-7 and 19- positions of the peptide shown. Note that Gly is found in β turns because peptide bonds involving the imino nitrogen of Pro readily assume the cis configuration. (b) Where might intrachain disulfide cross-linkages be formed?  An intrachain disulfide cross-linkage could occur between the Cys residues of the peptide located at positions 13 and 24. 11. Enzyme activity. Why does hydrogen peroxide foam when put on a cut?  When poured onto a cut or scrape, hydrogen peroxide encounters blood and damaged skin cells. These contain an enzyme called catalase, which breaks down the hydrogen peroxide into water and oxygen. The fizzing you see in the form of bubbles is the oxygen gas escaping. Catalase can cause up to 200,000 reactions per second. This powerful foaming action can help clean dirt, dried blood, and damaged cells out of a wound. 12. Enzyme inhibitor. How is ciprofloxacin used to treat the bacterial infections?  Ciprofloxacin – an antibiotic belongs to a group of antibiotics called fluoroquinolones. It is used to treat serious infections, or infections when other anitbiotics have not worked. It is used to treat bacterial infections (such as chest infections (including pneumonia); skin and bone infections; sexually transmitted infections (STIs); conjunctivitis; eye infections; ear infections). It can be used to help stop people getting meningitis if they have been really close to someone with the infection.  It inhibits DNA replication by inhibiting bacterial DNA topoisomerase and DNA- gyrase. Of the fluoroquinolone class, ciprofloxacin is the most potent against gram- negative bacilli bacteria (notably, the Enterobacteriaceae such as Escherichia coli , Salmonella spp., Shigella spp., and Neisseria ). Ciprofloxacin also has effectiveness against some gram-positive bacteria. Ciprofloxacin is the most active against Pseudomonas aeruginosa, among the quinolones. Ciprofloxacin is one of the few oral antibiotics able to treat P. aeruginosa infections.