Assignment Code: BBCCT-105/TMA/2023

Course Code: BBCCT-105

Assignment Name: Proteins

Year: 2023

Verification Status: Verified by Professor

Answer all the questions given below:

Q1) Describe the properties of amino acids.

Ans) Amino acids are the building blocks of proteins and are essential to life. There are twenty different amino acids that occur naturally in proteins, each with a unique side chain or "R" group that determines its properties. These properties include polarity, acidity, basicity, and size.

The structure of an amino acid is composed of a central carbon atom, known as the alpha carbon, bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and an R group. The amino group is basic, while the carboxyl group is acidic. The R group, which varies between different amino acids, determines their unique properties.

Amino acids can be classified into four groups based on the properties of their R groups. Nonpolar amino acids have hydrophobic R groups, which means they are not soluble in water. These amino acids tend to be found in the interior of proteins, away from water. Examples of nonpolar amino acids include alanine, glycine, and valine.

Polar amino acids have hydrophilic R groups, which means they are soluble in water. These amino acids tend to be found on the surface of proteins, where they can interact with water molecules. Examples of polar amino acids include serine, asparagine, and glutamine.

Acidic amino acids have negatively charged R groups, which means they are acidic. These amino acids can donate hydrogen ions (H+) and are often found on the surface of proteins, where they can interact with other charged molecules. Examples of acidic amino acids include aspartic acid and glutamic acid.

Basic amino acids have positively charged R groups, which means they are basic. These amino acids can accept hydrogen ions (H+) and are often found on the surface of proteins, where they can interact with negatively charged molecules. Examples of basic amino acids include lysine, arginine, and histidine.

Amino acids can also be categorized as essential, or nonessential based on whether they can be synthesized by the body. Essential amino acids cannot be synthesized by the body and must be obtained through the diet. Nonessential amino acids can be synthesized by the body and do not need to be obtained through the diet.

Q2) Describe mechanical methods of cell disruption with suitable examples.

Ans) Mechanical methods of cell disruption involve the use of physical force to break open cells and release their contents. These methods are often used in laboratory settings to extract proteins, DNA, or other cellular components from cells. Some examples of mechanical methods of cell disruption include sonication, grinding, and homogenization.

1. Sonication involves the use of high-frequency sound waves to disrupt cells. The sound waves create pressure waves that cause the cells to vibrate and eventually break open. This method is often used to extract DNA or proteins from cells.

2. Grinding involves the use of a mortar and pestle or a bead mill to physically grind cells and break open their walls. This method is often used to extract proteins from tough tissues, such as muscle or bone.

3. Homogenization involves the use of a mechanical homogenizer to break open cells. The cells are placed in a small chamber and subjected to high pressure or shear forces, which cause them to rupture. This method is often used to extract proteins or organelles from cells.

Q3) With the help of schematic diagram explain separation of proteins using ammonium sulphate precipitation method.

Ans) This whole method is based on a physical property called "solubility," which is interesting because it depends on "salinity," or how much salt is dissolved in the solution. Proteins are soluble at different salt concentrations, which makes it easier to separate (precipitate) at high salt concentrations. Ammonium sulphate [(NH4)2SO4] was chosen because it doesn't change the pH of the solution, so the structure of the protein doesn't change. It is also easy to dissolve and cheap.

Let's get a feel for how ammonium sulphate precipitation works by looking at how salting out is used to separate proteins. In general, a molecule's ability to dissolve in a medium depends on whether it is polar or non-polar (hydrophilic or phobic) and how strong the ions in the medium are (solvent). When there is a lot of salt, the ionic strength of the solvent is high, so it can't break up the molecules and they stick together.

Adding ammonium salt to a solution of protein makes it easier for the protein to settle out. This is the same idea behind ammonium sulphate precipitation (out of the solution). The name for this is "salting out." This is the best way to separate the DNA from the protein in a solution while concentrating the protein (cell extract). But dialysis can get rid of the salt that is stuck to the protein.

Q4) List four important applications and principles of each of the following: thin layer chromatography, high performance chromatography, affinity chromatography, and ion exchange chromatography.

Ans)

Thin Layer Chromatography (TLC)

Thin layer chromatography is a separation technique that is based on the movement of components of a mixture over a thin layer of adsorbent material. The principles of TLC include adsorption, capillary action, and diffusion. Some of the important applications of TLC are:

1. Qualitative Analysis of Natural Products: TLC is commonly used to identify natural products, such as essential oils, terpenoids, and flavonoids.

2. Purity Testing of Drugs: TLC is used in the pharmaceutical industry for the quality control of drugs, including testing for purity and impurities.

3. Analysis of Food Dyes: TLC can be used to identify and analyse food dyes and additives.

4. Forensic Analysis: TLC is used in forensic science for the detection and analysis of drugs and other chemical compounds.

High Performance Chromatography (HPLC)

High Performance Chromatography (HPLC) is a separation technique that is widely used in analytical chemistry to separate and quantify components of a mixture. The principles of HPLC include adsorption, partition, ion exchange, and size exclusion. Some of the important applications of HPLC are:

1. Separation of Pharmaceutical Compounds: HPLC is used in the pharmaceutical industry to separate and quantify drug compounds.

2. Separation and Analysis of Biomolecules: HPLC is commonly used in the field of biochemistry to separate and analyse biomolecules, such as proteins, nucleic acids, and carbohydrates.

3. Environmental Analysis: HPLC is used to analyse environmental samples, such as water and soil, for pollutants and toxins.

4. Analysis of Food and Beverages: HPLC can be used to analyse food and beverages for contaminants, additives, and flavour compounds.

Affinity Chromatography

Affinity chromatography is a separation technique that is based on the selective binding of a target molecule to a specific ligand. The principles of affinity chromatography include molecular recognition, specificity, and reversible binding. Some of the important applications of affinity chromatography are:

1. Purification of Biomolecules: Affinity chromatography is widely used to purify biomolecules, such as enzymes, antibodies, and hormones.

2. Study of Protein-Protein Interactions: Affinity chromatography can be used to study protein-protein interactions by capturing a target protein and its binding partners.

3. Identification of Ligands: Affinity chromatography can be used to identify ligands that bind to a target molecule, such as a receptor or an enzyme.

4. Drug Discovery: Affinity chromatography can be used in drug discovery to identify potential drug targets and to screen for drug candidates.

Ion Exchange Chromatography

Ion exchange chromatography is a separation technique that is based on the charge of the components of a mixture. The principles of ion exchange chromatography include ion exchange, electrostatic interactions, and reversible binding. Some of the important applications of ion exchange chromatography are: 

1. Purification of Proteins: Ion exchange chromatography is used to purify proteins based on their charge and isoelectric point.

2. Analysis of Nucleic Acids: Ion exchange chromatography can be used to separate and analyse nucleic acids based on their charge and size.

3. Separation of Amino Acids: Ion exchange chromatography can be used to separate and analyse amino acids based on their charge and polarity.

4. Purification of Monoclonal Antibodies: Ion exchange chromatography is commonly used to purify monoclonal antibodies for research and therapeutic applications.

Q5) Write the principle of electrophoresis. Explain Isoelectric focusing using a neatly label diagram. List its advantages.

Ans) Electrophoresis is a separation technique that is based on the movement of charged molecules in an electric field. In electrophoresis, a sample is loaded onto a gel matrix, which is placed in an electric field. The charged molecules migrate through the gel matrix at different rates, based on their size, shape, and charge. The separated molecules can be visualized and quantified by staining or fluorescence detection.

Isoelectric Focusing

Isoelectric focusing is a type of electrophoresis that separates molecules based on their isoelectric points. The pI is the pH at which the molecule has no net charge. In IEF, a pH gradient is established across a gel matrix, and the sample is loaded at one end of the gel. As the electric field is applied, the charged molecules migrate through the gel matrix until they reach the region where the pH equals their pI. At this point, the molecule has no net charge and stops migrating. This results in the separation of molecules based on their pI values.

Isoelectric Focusing

Advantages of Isoelectric Focusing

1. High Resolution: Isoelectric focusing provides high resolution separation of molecules based on their pI values, which allows for the detection and quantification of closely related species.

2. Versatile: Isoelectric focusing can be used to separate a wide range of molecules, including proteins, peptides, and nucleic acids.

3. Automation: Isoelectric focusing can be easily automated, which reduces the variability and increases the reproducibility of the results.

4. Quantitative Analysis: Isoelectric focusing allows for quantitative analysis of molecules, which is important for studying changes in protein expression and modification.

5. Compatibility with Other Techniques: Isoelectric focusing can be combined with other separation and analytical techniques, such as SDS-PAGE and mass spectrometry, to provide complementary information about the molecules being studied.

Q6) Give a detailed account on Sanger’s protein sequencing method.

Ans) Sanger's protein sequencing method is a classic technique used to determine the amino acid sequence of a protein. The method is named after its inventor, Frederick Sanger, who received the Nobel Prize in Chemistry in 1958 for its development. The protein sequencing method involves four main steps: cleavage of the protein into smaller fragments, determination of the amino acid sequence of each fragment, alignment of the fragments to determine the complete protein sequence, and verification of the sequence.

Cleavage of the Protein: The first step in Sanger's protein sequencing method is to cleave the protein into smaller fragments. This is typically done using specific enzymes, such as trypsin, chymotrypsin, or cyanogen bromide, which cleave the protein at specific amino acid residues. The resulting fragments are separated by chromatography and purified for further analysis.

Determination of the Amino Acid Sequence: The second step in Sanger's protein sequencing method is to determine the amino acid sequence of each fragment. This is done by labelling the N-terminus of the fragment with a fluorescent or radioactive tag and subjecting it to a process called Edman degradation. In Edman degradation, the N-terminus of the fragment is reacted with a reagent that selectively cleaves the first amino acid residue from the peptide chain. The resulting amino acid is then identified using chromatography or mass spectrometry.

Alignment of the Fragments: The third step in Sanger's protein sequencing method is to align the amino acid sequences of the fragments to determine the complete protein sequence. This is done by comparing the overlapping regions of the fragments and identifying the common amino acids. The alignment process is typically done manually, although computer programs are available to assist in the process.

Verification of the Sequence: The final step in Sanger's protein sequencing method is to verify the sequence of the complete protein. This is typically done using additional techniques, such as enzymatic cleavage or chemical modification, to confirm the amino acid sequence.

Advantages of Sanger's Protein Sequencing Method

1. High Accuracy: Sanger's protein sequencing method is highly accurate and can determine the sequence of even complex proteins.

2. Versatility: Sanger's protein sequencing method can be used to sequence a wide range of proteins, including those that are difficult to study using other techniques.

3. Quantitative Analysis: Sanger's protein sequencing method allows for quantitative analysis of protein fragments, which is important for studying protein modifications and interactions.

Limitations of Sanger's Protein Sequencing Method

1. Time-Consuming: Sanger's protein sequencing method is time-consuming, requiring several days to sequence a single protein.

2. Expensive: Sanger's protein sequencing method is relatively expensive, requiring specialized equipment and reagents.

3. Limited Information: Sanger's protein sequencing method provides information only about the linear sequence of amino acids and does not provide information about protein structure or function.

Q7) Describe the working principle of Tandem mass spectrometry and its applications.

Ans) Tandem mass spectrometry (MS/MS) is a powerful analytical technique that involves the use of two or more mass spectrometers to analyse a sample. The technique involves the fragmentation of the sample ions in the first mass spectrometer, followed by the separation and analysis of the resulting fragments in the second mass spectrometer.

The working principle of tandem mass spectrometry involves three main steps: ionization, fragmentation, and analysis. In the first step, the sample is ionized using techniques such as electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI). The resulting ions are then introduced into the first mass spectrometer, where they are separated based on their mass-to-charge ratio (m/z).

In the second step, the selected ions are fragmented by collision-induced dissociation (CID) or other methods, which breaks them into smaller fragments. The resulting fragments are then introduced into the second mass spectrometer, where they are separated and analysed based on their m/z values. By analysing the fragments, the identity and structure of the original sample can be determined.

Tandem mass spectrometry has a wide range of applications in areas such as proteomics, metabolomics, and environmental analysis. In proteomics, it is used to identify and quantify proteins and peptides, and to study post-translational modifications. In metabolomics, it is used to study metabolic pathways and identify biomarkers for diseases. In environmental analysis, it is used to identify and quantify pollutants and their degradation products.

Q8) Illustrate the secondary structure of proteins.

Ans) The secondary structure of proteins refers to the local folding patterns that result from the interactions between amino acid residues in a polypeptide chain. The two most common types of secondary structure are alpha helices and beta sheets.

An alpha helix is a spiral structure formed by hydrogen bonds between amino acid residues that are located close to each other along the polypeptide chain. In an alpha helix, the backbone of the polypeptide chain forms the central axis of the helix, while the side chains of the amino acids extend outward from the helix. Alpha helices are often found in membrane proteins and structural proteins, such as keratin.

Beta sheets, on the other hand, are formed by hydrogen bonds between amino acid residues that are located far apart along the polypeptide chain. Beta sheets can be either parallel or anti-parallel, depending on the orientation of the polypeptide chains. In a parallel beta sheet, the polypeptide chains run in the same direction, while in an anti-parallel beta sheet, the polypeptide chains run in opposite directions. Beta sheets are often found in enzymes and other globular proteins.

The secondary structure of a protein is important because it helps to determine the overall shape and function of the protein. By folding into specific structures, proteins can interact with other molecules and perform their biological roles in cells and organisms.

Q9) Write a short note on protein mis-folding diseases.

Ans) Protein misfolding diseases are a group of disorders that are caused by the accumulation of misfolded proteins in the body. Misfolding of proteins can occur due to genetic mutations, environmental factors, or age-related changes. The misfolded proteins can form aggregates or plaques that interfere with normal cellular function and cause tissue damage.

Examples of protein misfolding diseases include Alzheimer's disease, Parkinson's disease, Huntington's disease, and prion diseases. These diseases can lead to a range of symptoms, including cognitive impairment, motor dysfunction, and neurological deficits. Protein misfolding diseases are an active area of research, and developing effective treatments for these disorders is a major goal of biomedical research.

Q10) What is bioinformatics? Give a detailed account on importance of biological databases.

Ans) Bioinformatics is a field of study that combines biological and computational sciences to analyse and interpret biological data, particularly data derived from high-throughput experimental technologies such as DNA sequencing, proteomics, and metabolomics. The goal of bioinformatics is to develop and apply computational algorithms and tools to analyse, manage, and interpret complex biological data sets.

Biological databases are an important component of bioinformatics, as they provide a centralized repository of data and information about genes, proteins, and other biological molecules. These databases contain a vast amount of data on gene sequences, protein structures and functions, and other biological information that can be used for a wide range of applications, including drug discovery, gene therapy, and personalized medicine.

The importance of biological databases lies in their ability to provide researchers with access to vast amounts of data and information that would be difficult or impossible to collect and analyse on their own. By accessing these databases, researchers can perform complex analyses and comparisons of biological data, identify patterns and correlations, and develop new hypotheses and research directions.

Q11) Describe specified functions of proteins.

Ans) Proteins are macromolecules that perform a wide range of functions in living organisms. Some of the most important functions of proteins include:

1. Enzymatic Catalysis: Many proteins act as enzymes that catalyse biochemical reactions in the body, including digestion, energy production, and DNA replication.

2. Structural Support: Some proteins provide structural support to cells and tissues, such as collagen in skin and bone, and actin and myosin in muscle.

3. Transport: Some proteins act as transporters, moving molecules and ions across cell membranes and through the bloodstream, such as haemoglobin, which transports oxygen in the blood.

4. Hormonal Regulation: Some proteins act as hormones, such as insulin, which regulates blood glucose levels.

5. Defence and Protection: Some proteins play a role in the immune system, such as antibodies, which bind to and neutralize pathogens and toxins.

6. Storage: Some proteins act as storage molecules, such as ferritin, which stores iron in cells.

7. Signalling and Communication: Some proteins act as signalling molecules, transmitting information between cells, and coordinating cellular responses.

Q12) Explain NMR principle.

Ans) Nuclear magnetic resonance (NMR) is a technique used to study the properties of atomic nuclei in a magnetic field. It is based on the principle that certain atomic nuclei possess a magnetic moment, which can interact with an external magnetic field.

When a sample is placed in a strong magnetic field, the atomic nuclei align with the magnetic field, and a radiofrequency pulse is applied to excite the nuclei. The nuclei then emit a signal that can be detected and analysed to provide information about the chemical structure and properties of the sample. NMR is widely used in chemistry, biochemistry, and other fields to determine the molecular structure and dynamics of molecules, such as proteins and DNA.

Q13) What is immunity? Describe the structure of immunoglobulins Ig E and Ig M using.

Ans) Immunity is the ability of the body to defend itself against foreign substances, such as pathogens, toxins, and cancer cells. The immune system is composed of various cells, tissues, and molecules that work together to recognize and eliminate foreign invaders.

One important component of the immune system is antibodies, which are produced by B cells in response to a specific antigen. There are several types of antibodies, also known as immunoglobulins, including IgE and IgM.

IgE is an immunoglobulin that is involved in allergic responses and parasitic infections. It is a relatively small protein, consisting of two heavy chains and two light chains. The heavy chains have a constant region and a variable region, which allows for binding to different antigens. The light chains also have a variable region that contributes to antigen binding. IgE has a unique structure in that it has an extra domain at the C-terminal end of the heavy chain, which allows it to bind to high-affinity receptors on the surface of mast cells and basophils. When IgE binds to its receptor and encounters the antigen, it triggers the release of inflammatory mediators, leading to the symptoms of an allergic reaction.

IgM is the largest of the immunoglobulins, consisting of five subunits arranged in a pentameric structure. Each subunit has a heavy chain and a light chain, with both chains contributing to antigen binding. IgM is produced during the early stages of an immune response and serves as a first-line defense against pathogens. It can bind to multiple antigens at once due to its pentameric structure, which allows for efficient neutralization and elimination of pathogens.

Both IgE and IgM are important components of the immune system and play critical roles in defending the body against foreign invaders. The unique structures of these immunoglobulins allow them to bind to specific antigens and trigger immune responses, leading to the elimination of pathogens and the maintenance of health and homeostasis.

Q14) Draw the structure of sarcomere. Explain sliding filament model of muscle contraction.

Ans)

The sliding filament model is a widely accepted theory that explains how muscle contraction occurs at the molecular level. It proposes that muscle contraction is the result of the interaction between the thick filaments (made up of myosin protein) and thin filaments (made up of actin protein) in the muscle fibres. According to the sliding filament model, during muscle contraction, the thick and thin filaments slide past each other, resulting in the shortening of the sarcomere, the basic unit of muscle contraction. The interaction between the thick and thin filaments is mediated by the cross-bridge cycle, where myosin heads on the thick filament bind to actin molecules on the thin filament, and then pull the thin filament towards the center of the sarcomere. This results in the contraction of the muscle fibre. The sliding filament model also proposes that the degree of muscle contraction is controlled by the amount of Ca2+ ions released from the sarcoplasmic reticulum in response to a nerve impulse. The Ca2+ ions bind to regulatory proteins on the thin filament, allowing for the cross-bridge cycle to occur.