Sbc b10 assignment by brian juma
- 1. PWANI UNIVERSITY REG. NO: SB02/PU/40063/19 NAME: BRIAN JUMA NYONGESA SCHOOL: PURE AND APPLIED SCIENCES COURSE: BSc BIOCHEMISTRY UNIT CODE: SBC B102 UNIT NAME: STRUCTURES OF BIOMOLECULES DEPARTMENT: BIOLOGY LECTURER NAME: DR. GHRIS NGENY ASSIGNMENT: TAKE AWAY CAT 2 EXAM DATE SUBMITTED:
- 2. 1. Discuss protein denaturation highlighting five different denaturing agents. Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process.Denaturation disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape. Denaturation occurs becausethe bonding interactions responsible for the secondarystructure (hydrogen bonds to amides) and tertiary structure are disrupted. In tertiary structure there are four types of bonding interactions between "side chains" including: hydrogen bonding, salt bridges, disulfide bonds, and non- polar hydrophobic interactions. which may be disrupted. Therefore, a variety of reagents and conditions can cause denaturation. The most common observation in the denaturation process is the precipitation or coagulation of the protein. The agents include; Heat: Heat can be used to disrupt hydrogen bonds and non-polar hydrophobic interactions. This occurs because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and violently that the bonds are disrupted. The proteins in eggs denature and coagulate during cooking. Alcohol Disrupts Hydrogen Bonding: Hydrogen bonding occurs between amide groups in the secondary protein structure. Hydrogen bonding between "side chains" occurs in tertiary protein structure in a variety of amino acid combinations. All of these are disrupted by the addition of another alcohol. A 70% alcohol solution is used as a disinfectant on the skin. This concentration of alcohol is able
- 3. to penetrate the bacterial cell wall and denature the proteins and enzymes inside of the cell. Acids and Bases DisruptSalt Bridges: Salt bridges result from the neutralization of an acid and amine on side chains. As might be expected, acids and bases disrupt salt bridges held together by ionic charges. A type of double replacement reaction occurs where the positive and negative ions in the salt change partners with the positive and negative ions in the new acid or baseadded. This reaction occurs in the digestive system, when the acidic gastric juices cause the curdling (coagulating) of milk. Heavy Metal Salts: Heavy metal salts act to denature proteins in much the same manner as acids and bases. Heavy metal salts usually contain Hg+2 , Pb+2, Ag+, Tl+, Cd+2 and other metals with high atomic weights. Since salts are ionic they disrupt salt bridges in proteins. The reaction of a heavy metal salt with a protein usually leads to an insoluble metal protein salt. 2. Highlight the principle of two common methods applied in protein sequencing. Protein sequencing is the practical process ofdetermining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information (one or more sequence tags) to identify it with reference to databases of protein sequences derived from the conceptual translation of genes. The two common methods used are: 1. Protein sequencer. 2. Edman degradation
- 4. EDMAN DEGRADATION METHOD The Edman degradation is a very important reaction for protein sequencing, because it allows the ordered amino acid composition of a protein to be discovered. Automated Edman sequencers are now in widespread use, and are able to sequence peptides up to approximately 50 amino acids long. A reaction scheme for sequencing a protein by the Edman degradation follows; some of the steps are elaborated on subsequently. 1. Break any disulfide bridges in the protein with a reducing agent like 2- mercaptoethanol. A protecting group suchas iodo-acetic acid may be necessary to prevent the bonds from re-forming. 2. Separate and purify the individual chains of the protein complex, if there are more than one. 3. Determine the amino acid composition of each chain. 4. Determine the terminal amino acids of each chain. 5. Break each chain into fragments under 50 amino acids long. 6. Separate and purify the fragments. 7. Determine the sequence of each fragment. 8. Repeat with a different pattern of cleavage. 9. Constructthe sequence of the overall protein. PROTEIN SEQUENCER 3. Describe the Watsonand Crick secondarystructural model of DNA. Watson and Crick, (1953), proposed that DNA structure is made up of nucleotides, in which two nucleotide chains wind into a double helical structure. The backboneof the two nucleotide chains, which consist of alternating sugar and phosphategroups are separated from each by a regular distance, approximately 1.1nm across the center of the helix. This spaceis exactly filled
- 5. by base pairs consisting of one purine (Adenine & Guanine) and one pyrimidine (Thymine & cytosine) i.e. A to T and G to C. The base pairs lie in a flat plane roughly perpendicularly to the long axis of the molecule. Each complete turn of the double helix, which was proposed to twist in a right-handed direction includes ten base pairs. The packaging of atoms in the DNA double helix produces two conspicuous grooves that spiral around the surface of the molecule. The two grooves are of equivalent depth, but one, the major/ wide groove is significantly wider than the other. This led the atoms (base) to fit together properly. The base pairs form hydrogen bonds between them, i.e. A-T and G-T. This formation showed that, the hydrogen bonding of A-T was structurally similar to that of G-T. Hydrogen bonds stabilize the double stranded helical structure of DNA. The distinguishing feature of base pairing is its specificity. Adenine base in one strand forms two hydrogen bonds with a thymine base in the opposite strand, or guanine forms three hydrogen bonds with a cytosine base in the oppositestrand. This AT/GC arrangement, the base sequence of two DNA strands is complementary to each other. That is, you can predict the sequence in one DNA if you know the sequence in the oppositestrand. For example, if the one strand has the sequence of 5’ -GCGGATTT-3’ , the oppositestrand must be 3’ -CGCCTAAA-5’ . With regard to their 5’ and 3’ directionality, the two strands of a DNA double helix are antiparallel. 4. Draw the structure of the tripeptide: Cys-Pro-Metand label its peptide bonds.