Test: Proteins- 1 - NEET PG MCQ

Atypical Peptide Bond (Pseudopeptide Bond) (Isopeptide Bond) is a connection established between an amino group and a carboxyl group, with at least one not being an alpha group. This bond is observed in the side chains of proteins.
Characteristic Features

• Occurs post-translationally
• Can be formed either spontaneously or through enzymatic processes
• Can result in stably linked protein dimers, multimers, or complexes
• Provides resistance to proteolysis, as proteases are unable to hydrolyse the isopeptide bond

Examples

• Glutathione
• Thyrotropin Releasing Hormone
• Ubiquitin attached to protein
• Blood clots

Application of spontaneous Isopeptide Bond formation

• Development of a novel peptide tag called Isopeptag
• Utilised in:
  • In vivo Protein targeting
  • Fluorescence Microscopy
  • Imaging

Storage proteins are proteins that serve as reservoirs for amino acids and metal ions that can be readily mobilised.

• Casein from milk
• Vitellin from egg yolk
• Ovalbumin from egg white
• Glutelin from wheat
• Oryzenin from rice
• Gliadin from wheat
• Ferritin, which stores iron

Other examples include:

• Myoglobin, a transport protein for oxygen to skeletal muscle
• Ricin, an inhibitor of mammalian protein synthesis originating from castor beans, which inactivates eukaryotic 28S ribosomal RNA

Conservative [Homologous] Substitution refers to the process where one amino acid is substituted with another that shares similar properties. Examples of homologous substitution are illustrated in the diagram below:

Nonconservative (Nonhomologous) Substitution involves replacing one amino acid with another that has different characteristics.

Homologous substitution or conservative mutation does not lead to any alteration in the function of proteins. Examples of homologous substitution include:

Homologs, orthologs, and paralogs refer to relationships between genes:

• When two genes exhibit detectable sequence similarities (in nucleotide sequence within DNA and amino acid sequence in the proteins they encode), they are considered homologous, and the proteins they produce are termed homologs.
• Homologs originate from a common ancestor.
• Homologous genes within the same species are classified as paralogous, with their protein products referred to as paralogs.
• Paralogous genes arise from gene duplication.
• Paralogs share not only similarities in amino acid sequence but also in their three-dimensional structures.
• In contrast, homologous genes across different species are labelled as orthologous, and their corresponding proteins are called orthologs.
• The sequence variations in homologous genes can serve as a rough indicator of the extent of divergence between two species throughout evolution.

• Proteins at the isoelectric pH exhibit no net charge.
• They lack electrophoretic mobility.
• They show maximum precipitability.
• They have minimum solubility.
• They provide minimal buffering action.

• Hydrogen Bonds (the most significant bond)
• Hydrophobic Bonds
• Electrostatic Bonds (Ionic Bonds, Salt Bridges)
• van der Waals forces

• Hydrophobic Interactions
• Hydrogen Bonds
• Electrostatic Bonds
• van der Waals Forces

In recent years, the significance of renewable energy has become increasingly evident, as nations strive to reduce their reliance on fossil fuels. This transition is crucial for addressing climate change and achieving sustainable development goals.

• Countries around the globe are investing in technologies that harness solar, wind, and hydroelectric power.
• These efforts not only contribute to energy security but also create job opportunities in emerging industries.
• Furthermore, transitioning to clean energy sources can lead to improved air quality and public health.

However, challenges remain in the form of energy storage and grid integration. As the demand for renewable sources increases, it is essential to develop efficient systems to manage energy supply and demand.

Ultimately, the shift towards renewable energy represents a vital step in building a sustainable future for generations to come.

Myoglobin consists of a single polypeptide chain, whereas hemoglobin is composed of four polypeptide chains.

Denaturation of proteins does not result in the loss of the primary structure, meaning that the peptide bonds remain intact.

• However, the secondary and tertiary structures are disrupted.
• This leads to a loss of folding.

The primary structure refers to the linear arrangement of amino acids connected by peptide bonds within their peptide chains. The bond that characterises the primary structure is the peptide bond, a specific type of covalent bond.

The secondary structure involves the configurational relationships between residues that are approximately 3 to 4 amino acids apart in the linear sequence. This results in the folding of short segments (ranging from 3 to 30 residues) of the polypeptide into geometrically organised units.

Tertiary structure describes the complete three-dimensional conformation of a polypeptide. Quaternary structure refers to the spatial arrangement between polypeptide subunits when more than one polypeptide aggregates to create a single functional protein.

• Lactate dehydrogenase
• Alcohol dehydrogenase
• Glyceraldehyde-3-phosphate dehydrogenase
• Malate dehydrogenase
• Quinone oxidoreductase
• 6-phosphogluconate dehydrogenase
• D-glycerate dehydrogenase
• Formate dehydrogenase
• 3 a, 20 Ł -hydroxysteroid dehydrogenase

• Side chains contribute to the formation of bonds that are essential for the tertiary structure of proteins.
• The interactions between polypeptides also aid in establishing the three-dimensional configuration of proteins.
• Chaperones assist in protein folding, thus playing a crucial role in the three-dimensional structure.

Western blot, ELISA, chip assay, and dot blot rely on the interaction between antigens and antibodies. Therefore, they serve as confirmatory tests for proteins.

• A chip is another term for a microarray.
• Similar to a DNA chip, which involves DNA-DA hybridisation, there is a protein microarray or protein chip that focuses on antigen-antibody interactions.
• Dot blot or slot blot is a blotting technique where the step of transferring to a nitrocellulose membrane is omitted.
• This method can also be applied to proteins.

Two significant phosphoproteins are:

• Casein, which is present in milk
• Ovovitellin, located in egg yolk

Plasma Proteins in Transport Function

A peptide bond is created between the amino group of one amino acid and the carboxyl group of another amino acid.

• The cysteine residues do not have to be next to each other for a disulfide bond to form.
• The stability of the quaternary structure is maintained by noncovalent bonds.
• Denaturation can also be reversible.

• Separatory techniques of proteins
• Study of protein structure
• Precipitation of proteins

Precipitability is highest at isoelectric pH, thus the medium's pH should be adjusted to this level.

Precipitation reactions of proteins:

• Methods to precipitate proteins by neutralising their charge include:
  • Precipitation by heavy metallic salts: The reagents used are mercuric nitrate, zinc sulfate, lead acetate, and ferric chloride.
  • Precipitation by acids: Acids lower the pH of the medium to isoelectric pH, where precipitatability peaks. At isoelectric pH, proteins possess no net charge, resulting in the absence of a hydration shell. The reagents used are phosphotungstic acid, sulphosalicylic acid, phosphomolybdic acid, and trichloroacetic acid.

Methods to precipitate proteins by eliminating the hydration shell:

• Precipitation by neutral salts: Concentrated salt solutions can remove the hydration shell. The reagent used is ammonium sulfate, a process known as salting out.
• Precipitation by organic solvents: The reagents used include ether, alcohol, acetone, and others.

In Hb S, Glutamic acid is replaced by Valine. Hence the negative charge is decreased. So Hb S moves slower than
HbA₁.
The relative mobility of various Hb fractions in Hb electrophoresis.

Relative mobility of common Hb fractions from origin or point of application is
1 HbA₂, 2. HbS, 3. HbF, 4. HbA₁

SOS-PAGE combined with 2-mercaptoethanol or dithiothreitol can oxidatively cleave disulfide bonds, thereby separating the components of multimeric proteins.

• Option A: The protein is undergoing oxidative cleavage of the S-S bond rather than hydrolysis.
• Option B: The protein has a mass of 100 KDa. Two subunits of 20 KDa and 30 KDa do not constitute a 100 KDa protein.
• Option D: A disulphide bond is a covalent bond, not a non-covalent bond.

Methods for Separating and Purifying Biomolecules

• Salt fractionation (e.g. precipitation of proteins with ammonium sulfate)
• Chromatography: Paper, ion exchange, affinity, thin-layer, gas-liquid, high-pressure, gel filtration
• Electrophoresis: Paper, high-voltage, agarose, cellulose acetate, starch gel, polyacrylamide gel, SDS-polyacrylamide gel
• Ultracentrifugation

Methods for Determining Biomolecular Structures

• Elemental analysis
• UV, visible, infrared, and NMR spectroscopy
• Use of acid or alkaline hydrolysis to degrade the biomolecule understudy into its basic constituents
• Use of a battery of enzymes of known specificity to degrade the biomolecule under study (e.g. proteases, nucleases, glycosidases)
• Mass spectrometry
• Amino acid sequencing methods (e.g. for proteins and nucleic acids)
• X-ray crystallography

Edman's reaction is utilised to identify the sequence of amino acids in a polypeptide.