Assignment Code: BBYET-141/TMA/2021-2022

Course Code: BBYET-141

Assignment Name: Cell and Molecular Biology

Year: 2021-2022 (1st July 2021 to 30th June 2022)

Verification Status: Verified by Professor

Note: Attempt all questions. The marks for each question are indicated against it.

Q1. a) State whether these statements are ‘True’ or ‘False’. (1×5=5)

i) In descending chromatography, the solvent travels down the paper and the movement of solvent is assisted by gravity.

Ans) True

ii) Gas chromatography is generally used for thermo-unstable and non-volatile samples.

Ans) False

iii) Diaphragm (Iris) regulates the amount of light entering the condenser in the microscope.

Ans) False

iv) The cells of prokaryotes are simpler than those of eukaryotes and lack internal compartmentalization and complexity.

Ans) True

v) The progression of a cell to the next stage in the cell cycle can be halted at specific points.

Ans) True

Q1. b) Define the following: (1×5=5)

i) Plasmodesmata

Ans) Plasmodesma is a singular form of plasmodesmata. The plasmodesmata definition states that it is a microscopic cytoplasmic canal, which can pass through the plant cell walls and allows the molecules to directly communicate with the adjacent plant cells. Plasmodesmata usually occur during the cell division process. Here, the traces of the endoplasmic reticulum caught by the new cell walls that can develop into daughter cells.

ii) Micelle

Ans) A micelle is an aggregate (or supramolecular assembly) of surfactant phospholipid molecules dispersed in a liquid, forming a colloidal suspension (also known as associated colloidal system). A typical micelle in water forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single-tail regions in the micelle centre.

iii) Retention factor

Ans) In chromatography, the retardation factor (R) is the fraction of an analyte in the mobile phase of a chromatographic system. In planar chromatography in particular, the retardation factor RF is defined as the ratio of the distance travelled by the centre of a spot to the distance travelled by the solvent front. Ideally, the values for RF are equivalent to the R values used in column chromatography.

iv) Microbodies

Ans) A microbody (or cytosome) is a type of organelle that is found in the cells of plants, protozoa, and animals. Organelles in the microbody family include peroxisomes, glyoxysomes, glycosomes and hydrogenosomes. In vertebrates, microbodies are especially prevalent in the liver and kidney.

v) Replicon

Ans) A replicon is a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication.

Q2. a) With the help of a well labelled diagram describe the major differences between prokaryotic and eukaryotic cells. (5×2=10)

Ans) The diagrams below depict the differences between prokaryotic and Eukaryotic cells.

Q2. b) Give an outline of polypeptide synthesis in bacteria. 

Ans) The synthesis of proteins in bacteria is essentially a two-stage process involving transcription (the synthesis of a messenger RNA (mRNA) intermediate using one strand of the duplex DNA as the template) and translation (the decoding of the information in the mRNA into an ordered arrangement of amino acids to form a polypeptide). The DNA strand that acts as the template for the mRNA (and to which it is complementary) is known as the anticoding or template strand, and the DNA strand that bears the same sequence (except for the replacement of thymine by uracil) is known as the coding strand. Transcription is the synthesis of RNA using DNA as a template. The process is carried out by the enzyme RNA polymerase. The same enzyme is responsible for the transcription of all the genes in a bacterial cell, including mRNA, rRNA and transfer RNA (tRNA). RNA polymerase initiates and terminates transcription at specific points in the DNA. Transcription is initiated downstream of specific sequences called promoters, sites that are recognized and bound by RNA polymerase. The process of transcription can be divided into a series of stages: template recognition, initiation, elongation, and termination. The linear sequence of nucleotides in mRNA is decoded and translated into a linear sequence of peptide bond-linked amino acids that make up the equivalent protein. The process of translation is carried out on large ribonuclear-protein complexes called ribosomes.

Q3. a) Explain the structure of DNA with the help of a well labelled diagram. (5×2=10)

Ans) DNA is a macromolecule consisting of two strands that twist around a common axis in a shape called a double helix. The double helix looks like a twisted ladder—the rungs of the ladder are composed of pairs of nitrogenous bases (base pairs), and the sides of the ladder are made up of alternating sugar molecules and phosphate groups.

A double helix model of DNA as proposed by Watson and Crick.

Q3. b) Enlist the major functions of Golgi bodies.

Ans) The Golgi Complex is also known as the Golgi Apparatus. It is a membrane-bound organelle made up primarily of cisternae, which are flattened, stacked pouches. This cell organelle oversees delivering, altering, and packing proteins and lipids to specific locations. The Golgi Apparatus is a structure found in the cytoplasm of both plant and animal cells.

Functions

Listed below are the functions of Golgi complex

1. The vital function of the Golgi apparatus is packaging and secretion of proteins.

2. It receives proteins from Endoplasmic Reticulum.

3. It packages it into membrane-bound vesicles, which are then transported to various destinations, such as lysosomes, plasma membrane or secretion.

4. They also take part in the transport of lipids and the formation of lysosomes.

5. Post-translational modification and enzymatic processing occur near the membrane surface in Golgi bodies, e.g., phosphorylation, glycosylation, etc.

6. Golgi apparatus is the site for the synthesis of various glycolipids, sphingomyelin, etc.

7. Complex polysaccharides of the cell wall are synthesised in the Golgi apparatus in plant cells.

Q4. a) Chloroplast and mitochondria are the semi-autonomous organs. Justify the statement. (5×2=10)

Ans) Assertion: Mitochondria and chloroplast are semiautonomous organelles.

Semi-autonomous cell organelles, such as mitochondria and chloroplasts, have their own DNA and ribosomes. As a result, they can produce some of their own proteins. Other proteins rely on the nucleus to function.

Justification: Mitochondria are huge cell organelles that are present in large numbers.

They have their own DNA that can reproduce on its own, as well as their own ribosomes and the ability to synthesise proteins. Because the shape and functioning of mitochondria are controlled by the cell's nucleus and are dependent on the availability of materials from the cytoplasm, they are considered semi-autonomous rather than fully autonomous. Similarly, to mitochondria, chloroplasts have their own DNA and reproduce autonomously, but most of the protein and enzyme requirements are met by the nuclear genome. During cell division, they are passed down to the daughter cells. Mitochondria are recognised as the cell's powerhouse since they aid in the production of ATP molecules. Animal cells and algae are the only places where chloroplasts can be found. It contains chlorophyll, a green pigment that aids in the photosynthetic process. As a result, the Assertion is true.

Q4. b) Describe the major features of endosymbiont theory of origin of chloroplast and mitochondria.

Ans) Mitochondria are the "powerhouses" of the cell, breaking down fuel molecules and capturing energy in cellular respiration.

Chloroplasts are found in plants and algae. They're responsible for capturing light energy to make sugars in photosynthesis.

Mitochondria and chloroplasts likely began as bacteria that were engulfed by larger cells (the endosymbiont theory).

Features of Endosymbiont theory of origin

Both mitochondria and chloroplasts contain their own DNA and ribosomes. Why would these organelles need DNA and ribosomes, when there is DNA in the nucleus and ribosomes in the cytosol? Strong evidence points to endosymbiosis as the answer to the puzzle. Symbiosis is a relationship in which organisms from two separate species live in a close, dependent relationship. Endosymbiosis (endo- = “within”) is a specific type of symbiosis where one organism lives inside the other.

Bacteria, mitochondria, and chloroplasts are similar in size. Bacteria also have DNA and ribosomes like those of mitochondria and chloroplasts. Based on this and other evidence, scientists think host cells and bacteria formed endosymbiotic relationships long ago, when individual host cells took in aerobic (oxygen-using) and photosynthetic bacteria but did not destroy them. Through millions of years of evolution, the aerobic bacteria became mitochondria, and the photosynthetic bacteria became chloroplasts.

Q5. a) Explain various stages of cell cycle with the help of well labelled diagrams. (5×2=10)

Ans)

Cell Cycle depicting various checkpoints.

Q5. b) Describe the cloverleaf structure of tRNA with the help of labelled diagram.

Ans) The cloverleaf model of tRNA is a model that depicts the molecular structure of tRNA. The model revealed that the chain of tRNA consists of two ends—sometimes called "business ends"—and three arms. Two of the arms have a loop, D-loop (dihydro U loop) and Tψc-loop with a ribosome recognition site. The third arm known as "variable arm" has a stem with optional loop.

    A clover-leaf model of t RNA.

Q6. a) Describe in brief the various cell inclusions found in plants. (5×2=10)

Ans) Cell inclusions or ergastic compounds are metabolic results of a cell's life cycle. These are nutrients or pigments. Ergastic compounds can be found in cell walls, vacuoles, or organelles. They might be soluble or insoluble, organic, or inorganic. These include reserve foods, inorganic materials, secretory and excretory products.

1. Reserve foods

Starch, glycogen, lipid droplets, and aleurone grains are examples. Starch grains are present in seeds, fruits, tubers, and rhizomes. Endosperm and cotyledons contain a lot of fat. Aleurone grains are insoluble storage proteins found in aleuroplasts. They are found in wheat, rice, and maize outer endosperm cells.

2. Inorganic Materials

Anhydrous silicate salts are inorganic compounds present in plants. Prisma, needle, and rhomboidal (diamond) calcium oxalate deposits have been recorded in plants of several families. Raphides are bundled. Raphides are needle-shaped calcium oxalate crystals. They occur in over 200 plant families. Cystoliths are calcium carbonate crystals found in plants. A cystolith is an epidermal cell wall protrusion generated in a cellulose matrix by lithocysts. Plant leaves include these.

3. Secretory Products

Cell inclusions or ergastic compounds are substances released by glands and other organs of plants. Green pigments like chlorophyll a and b, orange, and yellow pigments like carotene, xanthophylls and anthocyanin pigments are examples. Anthocyanins are found in fruit vacuolar sap, flower petals, and some plant leaves. Other products are nectar released by plant nectaries and enzymatic proteins in protoplasm.

4. Excretory Products

Excretory products are chemicals created during metabolism but not utilised by plants. Alkaloids are nitrogenous substances composed of carbon, hydrogen, oxygen, and nitrogen. Plant storage organs including seeds, bark, and leaves contain them. They dissolve in booze. Quinine, reserpine, nicotine, caffeine, strychnine, morphine, and atropine are alkaloids that are not removed by plants. Glucosides, which are carbohydrate degradation products, are excretory products like alkaloids. digitoxin in addition to tannins, latex is a milky material released by latex glands in Hevea brasiliensis (rubber). Other excretory products include volatile oils produced by cells, resins from essential oils, gums from cellulose cell wall disintegration, and organic acids found in leaves and fruits.

Q6. b) Discuss the role of enzyme topoisomerases in DNA replication.

Ans) Topoisomerases cause transitory breaks in DNA that act as a swivel for DNA unwinding and keep DNA untangled. Enzyme topoisomerases give rotation axes for circular DNA molecules. The enzyme causes a brief break in DNA molecules that permits opposing DNA segments to break. Circular chromosomal replication in E. coli is bidirectional. Two replication forks consecutively migrate around the circular chromosome. Thus, the Cairns experiment suggested that E. coli chromosomal replication advances in both directions.

Enzyme Topoisomerases modify DNA supercoiling. Martin Gellert and James Wang discovered topoisomerases. They are classified as type I or II. Whereas Topoisomerase I cut just one strand of DNA, whereas Topoisomerase II cuts both strands, allowing the loop of the opposite helix segment to pass. DNA gyrase is a Type II Topoisomerase identified in E. coli. The enzyme relieves mechanical strain during E. coli replication. The enzyme removes supercoils before the replication fork. DNA gyrase performs this by cleaving both strands of the DNA duplex, then closing the cuts. The process is powered by ATP hydrolysis energy. The replication fork's motion creates positive supercoils in the copied DNA ahead of it.

Q7. Describe the various steps of DNA replication in prokaryotes. (10)

Ans) The following is a summary of the several processes involved in DNA replication in prokaryotes:

1. The DNA molecule's double helix structure is unzipped. This is accomplished with the assistance of an enzyme called helicase, which breaks the hydrogen bonds between the complimentary bases.

2. A 'Y' shaped replication 'fork' is formed when DNA strands are separated into two single strands. Two single strands of DNA serve as templates for creating new DNA strands.

3. One of the strands is orientated 3'-(5' in length (towards the replication fork). The leading strand is what it's called. The other strand is orientated 5'(3') in the other direction (away from the replication fork). This is referred to as the trailing strand. The two strands duplicate in distinct ways due to their differing orientations.

4. Primer, an RNA fragment, arrives and bonds to the leading strand. The primer kicks off the DNA synthesis process. DNA polymerase connects to the leading strand and proceeds forward in the 5' to 3' direction, adding new complementary nucleotide bases to the DNA strand. Continuous replication is the name for this sort of replication.

5. RNA primers (made by the enzyme primase) bind to the lagging strand at specific places. Okazaki fragments are subsequently inserted to the lagging strand in the same 5'(3' direction as the leading strand. Because the pieces will need to be put together later, this sort of replication is referred to as discontinuous replication.

6. With the help of an enzyme called exonuclease, the nucleotides are matched up (A with T, C with G) and the primer is removed (s). Complementary nucleotides fill in the gaps. The new strand is proofread to ensure that the new DNA sequence is error-free.

7. DNA ligase is an enzyme that seals the DNA sequence into two continuous double strands. As a result, after DNA replication, the DNA molecule created is made up of one new and one old nucleotide chain. As a result, DNA replication is considered semi-conservative.

Q8. a) Describe lac operon of E.coli highlighting its major features. (5×2=10)

Ans) The idea that genes with metabolically related functions are clustered together so that their transcription can be regulated as a single unit is a crucial component of the operon paradigm.

Lactose metabolism and lac operon regulation: Lactose is a carbohydrate present in large amounts in milk. It is broken down by E. coli in the mammalian gut. Lactose does not readily diffuse through the membrane of the E. coli cell and is actively carried into the cell by the protein permease. Lactose cannot be used as a direct source of energy. Lactose transport into the cell is a dynamic process mediated by the enzyme permease. E. coli breaks it down into glucose and galactose first. The enzyme galactosidase catalyses this reaction. Furthermore, this enzyme converts lactose to allolactose, a molecule that plays a crucial role in lactose metabolism regulation. The lac operon also produces thiogalactoside transacetylase, a third enzyme whose role in lactose metabolism is still unknown.

An example of an inducible operon is the lac operon. The enzymes galactosidase, permease, and transacetylase are encoded by the neighbouring structural genes in the lac operon of E. coli, coupled with a shared promoter lac P. The lac Z gene codes for galactosidase, the lac Y gene for permease, and the lac A gene for thiogalactoside transacetylase. Lactose appears to be the inducer here, and allolactose is responsible for induction, as you have already learned about the negative inducible operon.

There are two situations in which lactose is metabolized by lac operon.

1. In the absence of lactose, transcription is inhibited because the regulator protein (repressor) binds to the operator which blocks the binding of RNA polymerase.

2. When lactose is present, the structural genes are transcribed and translated. This is because some of the lactose gets converted into allolactose which then binds to the regulator protein, making the protein inactive. Since the regulator protein cannot bind to the operator the structural genes get freely transcribed and translated.

Q8. b) Enlist the major features of Genetic code.

Ans)

The salient feature of genetic code are as follows:

1) Each codon thus has 3 bases producing 64 codons. Out of these 64 codons, only 61 can produce amino acids. The rest 3 are used as stop codons during the process of translation.

2) One codon is responsible to direct the reactions for producing an amino acid. Hence, the process is specific and focused.

3) Some of the amino acids can have multiple codons for production. This is called the degeneracy of genetic code. For example, Valine (Val) has four different sequential codons for production. They are GUA, GUC, GUU, and GUG.

4) Codons are responsible for the formation of mRNA. On the other hand, mRNA is responsible for the generation of genes.

5) Another prime feature of the genetic code is that it is universal. It means that one codon will lead to the formation of one amino acid. For instance, Phenylalanine (Phe) has the genetic code UUU. It is universal across all living beings. It means that the Phe of a bacterium will be like that of a human being.

6) Sometimes, codons have dual functions too. For instance, AUG is the genetic code for Methionine (Met). It also acts as an initiator or start codon.

7) The standard genetic code is universal virtually among all extant life forms.

Q9. Give a diagrammatic representation of transcription process in prokaryotes. Enlist the role of various enzymes involved in it. (10)

Ans)

An overview of transcription showing the four main stages. Note that RNA polymerase moves along the template strand of the DNA in the 3’à5’direction and the newly formed RNA molecule grows in 5’à3’ direction. NTPs- Nucleoside triphosphates

Role of Enzymes

Proteins that operate as biological catalysts are known as enzymes (biocatalysts). Catalysts help to speed up chemical reactions. Substrates are the molecules on which enzymes can function, and the enzyme changes the substrates into various molecules called products. Enzyme catalysis is required for almost all metabolic activities in the cell to occur at rates rapid enough to sustain life: 8.1 Individual steps in metabolic processes are catalysed by enzymes. Enzymology is the study of enzymes, and pseudoenzyme analysis acknowledges that some enzymes have lost their ability to carry out biological catalysis over time, as evidenced by their amino acid sequences and strange 'pseudocatalytic' features.

Enzymes are known to catalyse over 5,000 different biological reactions. Ribozymes, which are catalytic RNA molecules, are another type of biocatalyst. The specificity of enzymes stems from their three-dimensional architectures.

Enzymes, like other catalysts, lower the activation energy of a reaction to speed it up. Some enzymes can speed up the conversion of substrate to product by millions of times. Orotidine 5'-phosphate decarboxylase is an extreme example, allowing a reaction that would otherwise take millions of years to happen in milliseconds. Enzymes, like any other catalyst, are not consumed in chemical reactions and do not change the reaction's equilibrium. Enzymes are distinct from other catalysts in that they are considerably more specific. Other chemicals can alter enzyme activity, such as inhibitors and activators. Inhibitors reduce enzyme activity, while activators boost it. Enzyme inhibitors are found in many medicinal medications and toxins. When an enzyme is exposed to extreme heat, its activity falls dramatically, and many enzymes are (permanently) denatured, losing their structure and catalytic characteristics.

Q10. Write short notes on: (2×5 =10)

Q10. a) Kinetochore

Ans) In eukaryotic cells, a kinetochore is a disc-shaped protein structure that is linked with duplicated chromatids and where spindle fibres bind during cell division to pull sister chromatids apart. During mitosis and meiosis, the kinetochore forms on the centromere and connects the chromosome to microtubule polymers from the mitotic spindle.

During cell division, kinetochores initiate, control, and supervise the striking movements of chromosomes. Two sister chromatids are held together by a centromere during mitosis, which happens after the quantity of DNA in each chromosome is doubled (while preserving the same number of chromosomes) in S phase. Each chromatid contains its own kinetochore, which face in opposing directions and attach to the mitotic spindle apparatus's opposite poles. The sister chromatids separate after the transition from metaphase to anaphase, and the individual kinetochores on each chromatid drive their travel to the spindle poles that will define the two new daughter cells. The kinetochore is thus required for chromosomal segregation during mitosis and meiosis, which is traditionally connected with mitosis and meiosis.

Q10. b) Synaptonemal complex

Ans) In eukaryotes, the synaptonemal complex (SC) is a protein structure that forms during meiosis between homologous chromosomes (two pairs of sister chromatids) and is hypothesised to mediate synapsis and recombination. The SC is assumed to serve primarily as a scaffold that allows interacting chromatids to finish their crossing actions.

The synaptonemal complex is made up of three parts: two parallel lateral areas and a centre piece. At gametogenesis, this "tripartite structure" can be detected in both men and females during the pachytene stage of the first meiotic prophase. The lateral elements begin to develop during leptonema, prior to the pachytene stage, and they initiate and complete their coupling during the zygotene stage. When pachynema is over, the SC is usually dismantled and no longer identifiable.

Q10. c) Biological significance of meiosis

Ans) Biological Significance of Meiosis:

1. Meiosis is responsible for the formation of sex cells or gametes that are responsible for sexual reproduction.

2. It activates the genetic information for the development of sex cells and deactivates the sporophytic information.

3. It maintains the constant number of chromosomes by halving the same. This is important because the chromosome number doubles after fertilization.

4. In this process independent assortment of maternal and paternal chromosomes takes place. Thus, the chromosomes and the traits controlled by them are reshuffled.

5. The genetic mutation occurs due to irregularities in cell division by meiosis. The mutations that are beneficial are carried on by natural selection.

6. Crossing over produces a new combination of traits and variations.

Q10. d) Gene silencing

Ans) The regulation of gene expression in a cell to prohibit the expression of a specific gene is known as gene silence. Silencing of genes can happen during transcription or translation, and it's commonly employed in research. Methods for silencing genes are rapidly being exploited to develop therapies for cancer and other diseases such as infectious diseases and neurological disorders.

Gene silencing is frequently confused with gene knockdown. The expression of genes is lowered when they are silenced. Genes that have been knocked out, on the other hand, are fully removed from the organism's genome and hence have no expression. Because the methods used to silence genes, like as RNAi, CRISPR, or siRNA, often reduce the expression of a gene by at least 70% but do not eradicate it, gene silencing is considered a gene knockdown mechanism. Gene silencing methods are typically thought to be superior to gene knockouts because they allow researchers to study key genes that are required for the survival of animal models and cannot be eliminated. Furthermore, they provide a more comprehensive picture of disease progression, as disorders are frequently linked to genes with low expression.

Q10. e) Cell theory

Ans) In biology, cell theory is a scientific theory first formulated in the mid-nineteenth century, that living organisms are made up of cells, that they are the basic structural/organizational unit of all organisms, and that all cells come from pre-existing cells. Cells are the basic unit of structure in all organisms and the basic unit of reproduction.

The three tenets to the cell theory are as described below:

1. All living organisms are composed of one or more cells.

2. The cell is the basic unit of structure and organization in organisms.

3. Cells arise from pre-existing cells.