SEMESTER -IICORE PAPER III :CELL BIOLOGYUNIT – IUltrastructure of Eubacteria- Cell wall – Cell membrane- Extra mural layer - Slime –Capsule – Cytoplasmic inclusions – Mesosomes – Nuclear material – Reserve materials -Pigment – Cell appendages – Flagella – Pili.UNIT – IIUltrastructure and functions of Eukaryotic cell organelles – Cell wall – Cell membrane -Mitochondria – Chloroplast – Endoplasmic reticulum – Golgi complex – Nucleus –Ribosomes – Other cell inclusions and Flagella.UNIT IIICell division in Bacteria – Binary fission - Cell division of Eukaryotes – Mitosis andMeiosis.UNIT IVArchaebacterial cell wall and cell membranes of Methanogens - Halophiles -Thermoacdiphiles.UNIT VTransport mechanisms – Diffusion - Facilitated diffusion – Active transport – Grouptranslocation – Phagocytosis – Pinocytosis.References1. Prescott, L.M J.P. Harley and C.A. Klein 1995. Microbiology 2nd edition Wm, C.Brown publishers.2. Michael J. Pelczar, Jr. E.C.S. Chan, Moel : Microbiology Mc Graw Hill Book R. Krieg,1986 Company3. Stainer R.Y. Ingraham J.L. Wheolis H.H and Painter P.R. 1986 The Microbial world, 5thedition. Eagle Works Cliffs N.J. Prentica Hall.

PART I

1. What are the different shapes of bacteria?

There are many bacterial morphologies, each of them with a specific name.

Rod-shaped (Baccilus) i.e. Escherichia coli, Bacillus cereus Spherical (Coccus):  i.e. Staphylococcus epiderminis Curved (Vibrio, Spirochaete) i.e. Vibrio cholera, Rhodospirilium rubrum Square-shaped (Arcula) Star-shaped (Stella)

2. How do bacteria attach to surfaces?

Bacterial cells often attach to surfaces through specific structures. This is necessary for the overall survival of bacteria, especially pathogenic ones. This process is supported by glycocalyx, pili and fimbriae.

3. What helps bacteria synthesise protein ?

Protein synthesis is a very important process for both eukaryotes and prokaryotes. In this process, nucleotide sequence in a segment of  DNA is translated into the specific sequence of amino acids in a protein. Translation occurs at ribosomes; ribosomes consist of RNA and proteins. While eukaryotic cells have 80S ribosomes, bacterial cells contain 70S ribosomes.

4. Most eukaryotic cells also have other membrane-bound internal structures called organelles. 

5. Cell wall of eukaryotes are made of chitin.

6. What is Nucleoid ?

Region of the cytoplasm that contains naked DNA, which is the genetic information of the cell.

7. What is Mitosis?

Mitosis is a form of eukaryotic cell division that produces two daughter cells with the same genetic component as the parent cell. Chromosomes replicated during the S phase are divided in such a way as to ensure that each daughter cell receives a copy of every chromosome.

8. What is Meiosis?

Meiosis is the form of eukaryotic cell division that produces haploid sex cells or gametes (which contain a single copy of each chromosome) from diploid cells (which contain two copies of each chromosome). The process takes the form of one DNA replication followed by two successive nuclear and cellular divisions (Meiosis I and Meiosis II).

9. What is Zygotene?

Zygotene: homologous chromosomes become closely associated (synapsis) to form pairs of chromosomes (bivalents) consisting of four chromatids (tetrads).

10. What is Methanogen?

Methanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They are classified as archaea, a domain distinct from bacteria. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans.

11. What is Active transport?

Active transport is the movement of molecules across a cell membrane in the direction against their concentration gradient, i.e. moving from an area of lower concentration to an area of higher concentration.

12. What is Symport?

Symport uses the downhill movement of one solute species from high to low concentration to move another molecule uphill from low concentration to high concentration (against its electrochemical gradient). Both molecules are transported in the same direction.

13. What is Phagocytosis?

Phagocytosis is the process of engulfment of bacteria by cell.

14. What is Endocytosis?

Endocytosis is the process by which cells take in materials. The cellular membrane folds around the desired materials outside the cell. The ingested particle becomes trapped within a pouch, vacuole or inside the cytoplasm. Often enzymes from lysosomes are then used to digest the molecules absorbed by this process.

15. What is Pinocytosis?

Pinocytosis is the process of engulfment of liquid particles by a cell (in humans this process occurs in the small intestine, cells there engulf fat droplets)

PART II

Write about the cell wall of bacteria?

Cell wall

The cell wall of bacteria protects the cell from osmostic shock and physical damage. In addition, it also confers rigiditiy and shape of bacterial cells.

Although bacterial cell walls all consist of peptidoglycan, also known as murein or mucopeptide, they differ in certain properties in two groups of bacteria, namely gram-negative and gram-positive. The properties of peptidoglycan are discussed below.

Polysaccharide backbone - consists of 2 alternately repeating sugars such as NAG (N-acetylglucosamine) and NAM (N-acetylmuramic) .

Tetrapeptide - links the two polysaccharide backbones, forming a peptidoglycan subunit. Here, some unusual amino acids such as L-Alanine, D-Glutamaic acid, D-Lysin and D-Alanin are found. Note that D-type amino acids are very rare in all organisms.

Peptide cross bridge - links peptidoglycan subunits together . Variations in cross bridges show the diversity of peptidoglycan subuints. In Gram-positive bacteria i.e. Staphylococcus aureus, the cross-linkage is a glycin pentapeptide. In Gram-negative bacteria i.e. E.coli, cross-linkage is formed by the direct link between diaminopimelic acid (DAP) of one chain to terminal D-alanine of another chain.

The table below shows the differences of cell wall structure in gram-positive and gram-negative bacteria.

 

What helps bacteria move?

Most bacteria can locomote to different parts of their environment, which helps them to find new resources to survive. This process is due to flagellum (plural, flagella) pushing or pulling the cell through a liquid medium.

Structure of flagella

Long filamentous appendages containing a filament, hook and basal body. Filament: consists of protein flagellin. Hook: single type of protein, connects filament to the basal body. Basal body: contains a rod and several rings in gram-negative bacteria. ( Gram-positive

bacteria only have the inner pair of rings). This contributes to rotation of flagella, using energy from the activity of proton pumps.

Types of Flagella distribution

Monotrichous flagella: one flagellum, if it originates from one end of the cell, it is called polar flagellum. Rapid swimming caused by the rotation of flagella.

Peritrichous flagella: flagella surround the cell. Bundled peritrichous flagella give rise to slower forward motion than polar flagella.

Many other types exist but not discussd here.

Function of flagella

Chemotaxis:   movement of bacteria toward or away from chemical stimuli Magnetotaxis: movement along the Earth's magnetic field.  Happen in magnetotatic

bacteria, which contain magnetosomes including iron. Phototaxis:     response to differences in light density. Bacteria swim to areas of particular

light intensities.

 

 

Write a short notes about eukaryotic cell?

A eukaryote is any organism whose cells contain a nucleus and other structures (organelles) enclosed within membranes. Eukaryotes are formally the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart fromprokaryotic cells is the nucleus, enclosed by the nuclear envelope, which contains the genetic material. The presence of a nucleus gives eukaryotes their name, which comes from the Greek . Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria or the Golgi apparatus. In addition, plants and algae contain chloroplasts. Many unicellular organisms are eukaryotes, such as protozoa. All multicellular organisms are eukaryotes, including animals, plants and fungi.

Cell division in eukaryotes is different from that in organisms without a nucleus (Prokaryote). There are two types of division processes. In mitosis, one cell divides to produce two genetically

identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.

The domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, areprokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things; even in a human body there are 10 times more microbes than human cells. However, due to their much larger size, their collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1.6–2.1 billion years ago.

Give me a detailed note on eukaryotic cell structure and function?

Eukaryotic Cell Structure and Function

A cell is defined as eukaryotic if it has a membrane-bound nucleus. Any organism composed of eukaryotic cells is also considered as eukaryotic organism. Case in point

All of the organisms we can see with the naked eye are composed of one or more eukaryotic cells, with most having many more than one. This means that most of the organisms we are familiar with are eukaryotic. However, most of the organisms on Earth, by number, are actually prokaryotic. 

Most plants, animals, and fungi are composed of many cells and are, for that reason, aptly classified as multicellular, while most protists consist of a single cell and are classified as unicellular. 

All eukaryotic cells have

1. A nucleus 

2. Genetic material 

3. A plasma membrane 

4. Ribosomes 

5. Cytoplasm, including the cytoskeleton 

Most eukaryotic cells also have other membrane-bound internal structures called organelles. 

Organelles include

Mitochondria 

Golgi bodies 

Lysosomes 

Endoplasmic reticulum 

Vesicles 

There are a few major differences between animal, plant, fungal, and protistan cells, and guess what? Here they are: 

All plant cells have

1. A cell wall made of cellulose 

2. A large central vacuole 

3. Chloroplasts 

Some animal and protistan cells have

1. Flagella 

2. Cilia 

All animal cells have

1. Centrioles

All fungal cells have

1. A cell wall made of chitin.

Structures Found in All Eukaryotic Cells

The Nucleus and Eukaryotic Genetic Material

Explain Binary fission?

Binary Fission

Most bacteria rely on binary fission for propagation. Conceptually this is a simple process; a cell just needs to grow to twice its starting size and then split in two. But, to remain viable and competitive, a bacterium must divide at the right time, in the right place, and must provide each offspring with a complete copy of its essential genetic material. Bacterial cell division is studied in many research laboratories throughout the world. These investigations are uncovering the genetic mechanisms that regulate and drive bacterial cell division. Understanding the mechanics of this process is of great interest because it may allow for the design of new chemicals or novel antibiotics that specifically target and interfere with cell division in bacteria.

Before binary fission occurs, the cell must copy its genetic material (DNA) and segregate these copies to opposite ends of the cell. Then the many types of proteins that comprise the cell division machinery assemble at the future division site. A key component of this machinery is the protein FtsZ. Protein monomers of FtsZ assemble into a ring-like structure at the center of a cell. Other components of the division apparatus then assemble at the FtsZ ring. This machinery is positioned so that division splits the cytoplasm and does not damage DNA in the process.  As division occurs, the cytoplasm is cleaved in two, and in many bacteria, new cell wall is synthesized. The order and timing of these processes (DNA replication, DNA segregation, division site selection, invagination of the cell envelope and synthesis of new cell wall) are tightly controlled.

What is the difference between Mitosis and meiosis? Explain.

Difference Between Mitosis and MeiosisMitosis and meiosis are two types of cell division processes that play the most crucial role in reproduction, and maintenance of the structural and functional integrity of tissues. Let us understand the various aspects that distinguish these two processes from each other.

A Brief OverviewMITOSIS MEIOSIS

One mother cell undergoes a single division, and gives rise to two daughter cells.

One mother cell undergoes two successive divisions, and gives rise to four daughter cells.

A haploid or diploid mother cell can undergo mitosis.

Only a diploid mother cell can undergo meiosis.

The ploidy of the daughter cell remains the same as that of the mother cell.

Ploidy reduction occurs giving rise to haploid daughter cells.

Synapsis and crossing over events do not occur during mitosis.

Synapsis and crossing over between homologous chromosomes occurs during meiosis I.

The genetic identity is retained after a mitotic division.

Genetic variation is introduced during meiotic divisions.

Centromeres spilt during anaphase, resulting in the separation of sister chromatids.

Centromeres and the sister chromatid pairs remain intact during meiosis I, but separate during meiosis II.

The major purpose is vegetative growth and asexual reproduction.

The major purpose is to facilitate sexual reproduction through gametogenesis.

It occurs in all cell types.Certain specialized cells called meiocytes, that are involved in sexual reproduction, undergo meiosis.

Give a diagrammatic representation on Meiosis in females?

Meiosis in females

 

 

Explain Methanogens?

Methanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They are classified as archaea, a domain distinct from bacteria. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. In marine sediments the biological production of methane, also termed methanogenesis, is generally confined to where sulfates are depleted, below the top layers.Moreover, the methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments.[ Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of the Earth's crust, kilometers below the surface. Not to be confused with methanotrophs which rather consume methane for their carbon and energy requirements.

Methanogens lack peptidoglycan, a polymer that is found in the cell walls of the Bacteria but not in those of Archaea. Some methanogens have a cell wall that is composed of pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.

Methanogens and extreme environments

Methanogens play the vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, ferriciron (Fe(III)), and sulfate) have been depleted. In deep basaltic rocks near the mid ocean ridges, they can obtain their hydrogen from the serpentinisation reaction of olivine as observed in the hydrothermal field of Lost City.

The thermal breakdown of water and water radiolysis are other possible sources of hydrogen.

Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates, which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.

Methanogens have been found in several extreme environments on Earth - buried under kilometres of ice in Greenland and living in hot, dry desert soil. They can reproduce at temperatures of 15 to 100 degrees Celsius. They are known to be the most common archaebacteria in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from three kilometres under Greenland by researchers from the University of California, Berkeley.

What is Endocytosis?

Endocytosis

Endocytosis is the process by which cells take in materials. The cellular membrane folds around the desired materials outside the cell. The ingested particle becomes trapped within a pouch, vacuole or inside the cytoplasm. Often enzymes from lysosomes are then used to digest the molecules absorbed by this process.

Biologists distinguish two main types of endocyctosis: pinocytosis and phagocytosis

In pinocytosis, cells engulf liquid particles (in humans this process occurs in the small intestine, cells there engulf fat droplets)

In phagocytosis, cells engulf solid particles.

PART III

Explain about bacterial cell structure and function?

Bacterial cell structure

 

Structures of cells

1. Cell wall2. Cytoplasmic membrane3. Chromosome4. Plasmid5. Ribosome6. Flagella7. Inclusion body8. Pili9. Endospore

Relative functions

1. Protect cells against osmotic shock (most important) and physical damage2. Regulation of substance transport into and out of cells.3. Contain genome.4. Contain supplemental genetic information such as resistance to antibiotics, production of

toxins and tolerance to toxic environment.5. Take part in protein synthesis.6. Movement of cells.7. Mineral storage of cells.8. Attachment to host, bacterial mating.9. Tough, heat resistance structure that help bacteria survive in adverse conditions.

How do bacteria attach to surfaces?

Bacterial cells often attach to surfaces through specific structures. This is necessary for the overall survival of bacteria, especially pathogenic ones. This process is supported by glycocalyx, pili and fimbriae.

Glycocalyx:

Structure: Polysaccharide layers; can be thick and stable like capsule or loosely attached to cell wall like slime layer.

Function:  Assist cells in adhesion to solid surface, and also protect pathogenic bacteria from the attack of the host's immune system.

Pili:

Structure:   Short, thin, straight, hairlike projections form surface of some bacteria. Composed of protein pilin, carbohydrate and phosphate. Pili are usually few.

Function:    Take part in adhesion of pathogen to specific host tissues. Sex pili are involved in genetic material exchange between mating bacterial cells.

Fimbriae:

Structure:   Similar to pili, but shorter and more abundant on the cell surface. Function:    Adhesion of cells to surface and formation of pellicles (biofilms)

containing thin sheets of cells on a liquid surface.

Cell wall

The cell wall of bacteria protects the cell from osmostic shock and physical damage. In addition, it also confers rigiditiy and shape of bacterial cells.

Although bacterial cell walls all consist of peptidoglycan, also known as murein or mucopeptide, they differ in certain properties in two groups of bacteria, namely gram-negative and gram-positive. The properties of peptidoglycan are discussed below.

Polysaccharide backbone - consists of 2 alternately repeating sugars such as NAG (N-acetylglucosamine) and NAM (N-acetylmuramic) .

Tetrapeptide - links the two polysaccharide backbones, forming a peptidoglycan subunit. Here, some unusual amino acids such as L-Alanine, D-Glutamaic acid, D-Lysin and D-Alanin are found. Note that D-type amino acids are very rare in all organisms.

Peptide cross bridge - links peptidoglycan subunits together . Variations in cross bridges show the diversity of peptidoglycan subuints. In Gram-positive bacteria i.e. Staphylococcus aureus, the cross-linkage is a glycin pentapeptide. In Gram-negative bacteria i.e. E.coli, cross-linkage is formed by the direct link between diaminopimelic acid (DAP) of one chain to terminal D-alanine of another chain.

The table below shows the differences of cell wall structure in gram-positive and gram-negative bacteria.

 

Cytoplasmic membrane

The cytoplasmic membrane encloses the cytoplasm. It regulates the specific transport of substance between the cell and the environment. The cytoplasmic membrane contains 2 main components: lipid and protein.

The lipid component of the bacterial cell is phospholipid bilayer.

Thickness: 6-8nm. Unit: amphipathic phospholipid, consisting of 1 phosphate group (hydrophilic ) and

unbranched fatty acid chains (hydrophobic). Distribution of 2 portions: hydrophilic heads are exposed to the external environment or

the cytoplasm. The fatty acid chains point inward, facing each other due to hydrophobic effects (staying away from water).

Membrane proteins are located in various positions within the membrane, through specific interactions with phospholipid molecules. These proteins consist of 3 main groups: integral proteins, outer-surface proteins and inner-surface proteins. They play distinctive roles in cellular activities.

Integral proteins: firmly embedded in the membrane, transport substance across the cytoplasmic membrane in 3 main mechanisms known as uniport, symport and antiport.

Outer-surface proteins: usually in Gram-negative bacteria, interact with periplasmic proteins in the transport of large molecules into the cells.

Inner-surface proteins: cooperate with other proteins in enery yeilding reactions and also other important cellular functions.

How do bacteria store genetic information?

Genetic information in bacteria is stored in the sequence of DNA in two forms, that is bacterial chromosome and plasmid.

The following are the properties of a bacterial chromosome.

Location: Within nucleoid region , not surrounded by nuclear envelope. Number: 1 chromosome each cell. Size: E.coli 4640 kbp. Component: Single, double stranded, circular DNA.  Also contains RNA and proteins

that take part in DNA replication, transcription and regulation of gene expression. DNA does not interact with protein histone.

Information: Contain genes essential for cellular functions.

In addition to chromosome, bacterial cells may also contain another genetic element, plasmid.  Features of plasmid are analysed below.

Location:  In cytosol of bacterial cells. Number: From 1 to several. Size: Much smaller than chromosomes. Components: Single, double stranded, circular DNA. Information: Contains drug resistant genes as well as heavy metal resistant genes. Not

essential for growth and metabolism of bacteria.

 

What helps bacteria synthesise protein ?

Protein synthesis is a very important process for both eukaryotes and prokaryotes. In this process, nucleotide sequence in a segment of  DNA is translated into the specific sequence of amino acids in a protein. Translation occurs at ribosomes; ribosomes consist of RNA and proteins. While eukaryotic cells have 80S ribosomes, bacterial cells contain 70S ribosomes, which have the folllowing components.

70S ribosome

30S subunit: 21 proteins and 16S rRNA. 50S subunit: 34 proteins, a 23S rRNA and a 5S rRNA Combination of 2 subunits to form functional ribosome requires magnesium ions and

chemical energy. Activity of 70S ribosomes is blocked by antibiotics like erythromycin and streptomycin.

Notes: S is Svedburg unit, which represents how rapidly particles or molecules sediment in an ultracentrifuge. The larger a substance, the greater its S value.

Explain about movement of bacteria?

Most bacteria can locomote to different parts of their environment, which helps them to find new resources to survive. This process is due to flagellum (plural, flagella) pushing or pulling the cell through a liquid medium.

Structure of flagella

Long filamentous appendages containing a filament, hook and basal body. Filament: consists of protein flagellin. Hook: single type of protein, connects filament to the basal body. Basal body: contains a rod and several rings in gram-negative bacteria. ( Gram-positive

bacteria only have the inner pair of rings). This contributes to rotation of flagella, using energy from the activity of proton pumps.

Types of Flagella distribution

Monotrichous flagella: one flagellum, if it originates from one end of the cell, it is called polar flagellum. Rapid swimming caused by the rotation of flagella.

Peritrichous flagella: flagella surround the cell. Bundled peritrichous flagella give rise to slower forward motion than polar flagella.

Many other types exist but not discussd here.

Function of flagella

Chemotaxis:   movement of bacteria toward or away from chemical stimuli Magnetotaxis: movement along the Earth's magnetic field.  Happen in magnetotatic

bacteria, which contain magnetosomes including iron. Phototaxis:     response to differences in light density. Bacteria swim to areas of particular

light intensities.

 

 

Give a detailed account on eukaryotic organisms?

Eukaryote

A eukaryote is any organism whose cells contain a nucleus and other structures (organelles) enclosed within membranes. Eukaryotes are formally the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart fromprokaryotic cells is the nucleus, enclosed by the nuclear envelope, which contains the genetic material. The presence of a nucleus gives eukaryotes their name, which comes from the Greek . Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria or the Golgi apparatus. In addition, plants and algae contain chloroplasts. Many unicellular organisms are eukaryotes, such as protozoa. All multicellular organisms are eukaryotes, including animals, plants and fungi.

Cell division in eukaryotes is different from that in organisms without a nucleus (Prokaryote). There are two types of division processes. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.

The domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, areprokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things; even in a human body there are 10 times more microbes than human cells. However, due to their much larger size, their collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1.6–2.1 billion years ago.

Cell features

Eukaryotic cells are typically much larger than those of prokaryotes. They have a variety of internal membranes and structures, called organelles, and a cytoskeleton composed of microtubules, microfilaments, and intermediate filaments, which play an important role in defining the cell's organization and shape. Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.

Detail of the endomembrane system and its components

Internal membrane

Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles or vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. It is probable that most other membrane-bound organelles are ultimately derived from such vesicles.

The nucleus is surrounded by a double membrane (commonly referred to as a nuclear envelope), with pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form what is called the endoplasmic reticulum or ER, which is involved in protein transport and maturation. It includes the rough ER where ribosomes are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth ER. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles, called Golgi bodies or dictyosomes.

Vesicles may be specialized for various purposes. For instance, lysosomes contain enzymes that break down the contents of food vacuoles, and peroxisomes are used to break down peroxide, which is toxic otherwise. Many protozoa have contractile vacuoles, which collect and expel excess water, and extrusomes, which expel material used to deflect predators or capture prey. In higher plants, most of a cell's volume is taken up by a central vacuole, which primarily maintains its osmotic pressure.

Mitochondria and plastids

Mitochondria are organelles found in nearly all eukaryotes. They are surrounded by two membranes (each a phospholipid bi-layer), the inner of which is folded into invaginations called cristae, whereaerobic respiration takes place. Mitochondria contain their own DNA. They are now generally held to have developed fromendosymbiotic prokaryotes, probably proteobacteria. The few protozoa that lack mitochondria have been found to contain mitochondrion-derived organelles, such as hydrogenosomes and mitosomes; and thus probably lost the mitochondria secondarily.

Plants and various groups of algae also have plastids. Again, these have their own DNA and developed from endosymbiotes, in this case cyanobacteria. They usually take the form of chloroplasts, which like cyanobacteria containchlorophyll and produce organic compounds (such as glucose) through photosynthesis. Others are involved in storing food. Although plastids

likely had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion.

Endosymbiotic origins have also been proposed for the nucleus, for which see below, and for eukaryotic flagella, supposed to have developed from spirochaetes. This is not generally accepted, both from a lack of cytologicalevidence and difficulty in reconciling this with cellular reproduction.

Cytoskeletal structures

Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar structures called cilia. Flagella and cilia are sometimes referred to asundulipodia, and are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin. These are entirely distinct from prokaryotic flagellae. They are supported by a bundle of microtubules arising from a basal body, also called a kinetosome or centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella also may have hairs, or mastigonemes, and scales connecting membranes and internal rods. Their interior is continuous with the cell's cytoplasm.

Microfilamental structures composed of actin and actin binding proteins, e.g., α-actinin, fimbrin, filamin are present in submembraneous cortical layers and bundles, as well. Motor proteins of microtubules, e.g., dynein or kinesin and actin, e.g.,myosins provide dynamic character of the network.

Centrioles are often present even in cells and groups that do not have flagella, but conifers and flowering plants have neither. They generally occur in groups of one or two, called kinetids that give rise to various microtubular roots. These form a primary component of the cytoskeletal structure, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles may also be associated in the formation of a spindle during nuclear division.

The significance of cytoskeletal structures is underlined in the determination of shape of the cells, as well as their being essential components of migratory responses like chemotaxis and chemokinesis. Some protists have various other microtubule-supported organelles. These include the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the haptophytes, which have a peculiar flagellum-like organelle called the haptonema.

Cell wall

The cells of plants, fungi, and most chromalveolates have a cell wall, a layer outside the cell membrane, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell.

The major polysaccharides making up the primary cell wall of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.

Cell wall

Forms a protective outer layer that prevents damage from outside and also bursting if internal pressure is high.Plasma MembraneControls entry and exit of substances, pumping some of them in by active transport.CytoplasmContains enzymes that catalyse the chemical reactions of metabolism and contains DNA in a region called the nucleoid.PiliHair like structures projecting from the cell wall that can be used to pull cells together.FlagellaSolid protein structures, with a corkscrew shape, projecting from the cell wall, which rotate and cause locomotion.NucleoidRegion of the cytoplasm that contains naked DNA, which is the genetic information of the cell.RibosomesSmall granular structures that synthesise proteins by translating messenger RNA. Some proteins stay in the cell and others are secreted.

Explain Cell cycle and Mitosis?

The cell cycle

Actively dividing eukaryote cells pass through a series of stages known collectively as the cell cycle: two gap phases (G1 and G2); an S (for synthesis) phase, in which the genetic material is duplicated; and an M phase, in which mitosis partitions the genetic material and the cell divides.

G1 phase. Metabolic changes prepare the cell for division. At a certain point - the restriction point - the cell is committed to division and moves into the S phase.

S phase. DNA synthesis replicates the genetic material. Each chromosome now consists of two sister chromatids.

G2 phase. Metabolic changes assemble the cytoplasmic materials necessary for mitosis and cytokinesis.

M phase. A nuclear division (mitosis) followed by a cell division (cytokinesis).

The period between mitotic divisions - that is, G1, S and G2 - is known as interphase.

Mitosis

Mitosis is a form of eukaryotic cell division that produces two daughter cells with the same genetic component as the parent cell. Chromosomes replicated during the S phase are divided in such a way as to ensure that each daughter cell receives a copy of every chromosome. In actively dividing animal cells, the whole process takes about one hour.

The replicated chromosomes are attached to a 'mitotic apparatus' that aligns them and then separates the sister chromatids to produce an even partitioning of the genetic material. This separation of the genetic material in a mitotic nuclear division (or karyokinesis) is followed by a separation of the cell cytoplasm in a cellular division (or cytokinesis) to produce two daughter cells.

In some single-celled organisms mitosis forms the basis of asexual reproduction. In diploid multicellular organisms sexual reproduction involves the fusion of two haploid gametes to produce a diploid zygote. Mitotic divisions of the zygote and daughter cells are then responsible for the subsequent growth and development of the organism. In the adult organism, mitosis plays a role in cell replacement, wound healing and tumour formation.

Mitosis, although a continuous process, is conventionally divided into five stages: prophase, prometaphase, metaphase, anaphase and telophase.

 

The phases of mitosis

Prophase

Prophase occupies over half of mitosis. The nuclear membrane breaks down to form a number of small vesicles and the nucleolus disintegrates. A structure known as the centrosome duplicates itself to form two daughter centrosomes that migrate to opposite ends of the cell. The centrosomes organise the production of microtubules that form the spindle fibres that constitute the mitotic spindle. The chromosomes condense into compact structures. Each replicated chromosome can now be seen to consist of two identical chromatids (or sister chromatids) held together by a structure known as the centromere.

Prometaphase

The chromosomes, led by their centromeres, migrate to the equatorial plane in the mid-line of the cell - at right-angles to the axis formed by the centrosomes. This region of the mitotic spindle is

known as the metaphase plate. The spindle fibres bind to a structure associated with the centromere of each chromosome called a kinetochore. Individual spindle fibres bind to a kinetochore structure on each side of the centromere. The chromosomes continue to condense.

Metaphase

The chromosomes align themselves along the metaphase plate of the spindle apparatus.

Anaphase

The shortest stage of mitosis. The centromeres divide, and the sister chromatids of each chromosome are pulled apart - or 'disjoin' - and move to the opposite ends of the cell, pulled by spindle fibres attached to the kinetochore regions. The separated sister chromatids are now referred to as daughter chromosomes. (It is the alignment and separation in metaphase and anaphase that is important in ensuring that each daughter cell receives a copy of every chromosome.)

Telophase

The final stage of mitosis, and a reversal of many of the processes observed during prophase. The nuclear membrane reforms around the chromosomes grouped at either pole of the cell, the chromosomes uncoil and become diffuse, and the spindle fibres disappear.

Cytokinesis

The final cellular division to form two new cells. In plants a cell plate forms along the line of the metaphase plate; in animals there is a constriction of the cytoplasm. The cell then enters interphase - the interval between mitotic divisions.

Explain Meiosis.

Meiosis

Meiosis is the form of eukaryotic cell division that produces haploid sex cells or gametes (which contain a single copy of each chromosome) from diploid cells (which contain two copies of each chromosome). The process takes the form of one DNA replication followed by two successive nuclear and cellular divisions (Meiosis I and Meiosis II). As in mitosis, meiosis is preceded by a process of DNA replication that converts each chromosome into two sister chromatids.

Meiosis I

Meiosis I separates the pairs of homologous chromosomes.

 

 

In Meiosis I a special cell division reduces the cell from diploid to haploid.

Prophase I

The homologous chromosomes pair and exchange DNA to form recombinant chromosomes. Prophase I is divided into five phases:

Leptotene: chromosomes start to condense. Zygotene: homologous chromosomes become closely associated (synapsis) to form pairs

of chromosomes (bivalents) consisting of four chromatids (tetrads). Pachytene: crossing over between pairs of homologous chromosomes to form chiasmata

(sing. chiasma). Diplotene: homologous chromosomes start to separate but remain attached by chiasmata. Diakinesis: homologous chromosomes continue to separate, and chiasmata move to the

ends of the chromosomes.

Prometaphase I

Spindle apparatus formed, and chromosomes attached to spindle fibres by kinetochores.

Metaphase I

Homologous pairs of chromosomes (bivalents) arranged as a double row along the metaphase plate. The arrangement of the paired chromosomes with respect to the poles of the spindle apparatus is random along the metaphase plate. (This is a source of genetic variation through random assortment, as the paternal and maternal chromosomes in a homologous pair are similar but not identical. The number of possible arrangements is 2n, where n is the number of chromosomes in a haploid set. Human beings have 23 different chromosomes, so the number of possible combinations is 223, which is over 8 million.)

Anaphase I

The homologous chromosomes in each bivalent are separated and move to the opposite poles of the cell

Telophase I

The chromosomes become diffuse and the nuclear membrane reforms.

Cytokinesis

The final cellular division to form two new cells, followed by Meiosis II. Meiosis I is a reduction division: the original diploid cell had two copies of each chromosome; the newly formed haploid cells have one copy of each chromosome.

Meiosis II

Meiosis II separates each chromosome into two chromatids.

 

 

The events of Meiosis II are analogous to those of a mitotic division, although the number of chromosomes involved has been halved.

Meiosis generates genetic diversity through:

the exchange of genetic material between homologous chromosomes during Meiosis I the random alignment of maternal and paternal chromosomes in Meiosis I

the random alignment of the sister chromatids at Meiosis II

 

Meiosis in females

 

 

Explain cell wall of Methanogen?

Methanogen

Methanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They are classified as archaea, a domain distinct from bacteria. They are common in

wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. In marine sediments the biological production of methane, also termed methanogenesis, is generally confined to where sulfates are depleted, below the top layers.Moreover, the methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments.[ Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of the Earth's crust, kilometers below the surface. Not to be confused with methanotrophs which rather consume methane for their carbon and energy requirements.

Physical description

Methanogens are coccoid (spherical) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all methanogens belong to Archaea. They are anaerobic organisms and cannot function under aerobic conditions. They are very sensitive to the presence of oxygen even at trace level. Usually, they cannot sustain oxygen stress for a prolonged time. However, Methanosarcina barkeri is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O2. Some methanogens, called hydrogenotrophic, use carbon dioxide (CO2) as a source of carbon, and hydrogen as a reducing agent.

The reduction of carbon dioxide into methane in the presence of hydrogen can be expressed as follows:

CO2 + 4 H2 → CH4 + 2 H2O

Some of the CO2 is reacted with the hydrogen to produce methane, which creates an electrochemical gradient across cell membrane, used to generate ATP through chemiosmosis. In contrast, plants and algae use water as their reducing agent.

Methanogens lack peptidoglycan, a polymer that is found in the cell walls of the Bacteria but not in those of Archaea. Some methanogens have a cell wall that is composed of pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.

Methanogens and extreme environments

Methanogens play the vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, ferriciron (Fe(III)), and sulfate) have been depleted. In deep basaltic rocks near the mid ocean ridges, they can obtain their hydrogen from the serpentinisation reaction of olivine as observed in the hydrothermal field of Lost City.

The thermal breakdown of water and water radiolysis are other possible sources of hydrogen.

Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates, which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.

Methanogens have been found in several extreme environments on Earth - buried under kilometres of ice in Greenland and living in hot, dry desert soil. They can reproduce at temperatures of 15 to 100 degrees Celsius. They are known to be the most common archaebacteria in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from three kilometres under Greenland by researchers from the University of California, Berkeley.

Another study has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in Utah, Idaho and California in the United States, and in Canada and Chile. Of these, five soil samples and three vapour samples from the vicinity of the Mars Desert Research Station in Utah were found to have signs of viable methanogens.

Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet.

Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate. Most methanogens are autotrophic producers, but those that oxidize CH3COO- are classed as chemotroph instead.

Comparative genomics and molecular signatures

Comparative genomic analysis has led to the identification of 31 signature proteins which are specific for the methanogens (also known as Methanoarchaeota). Most of these proteins are related to methanogenesis, and they could serve as potential molecular markers for the methanogens. Additionally, 10 proteins found in all methanogens which are shared by Archaeoglobus, suggest that these two groups are related. In phylogenetic trees, the methanogens are not monophyletic and they are generally split into three clades., Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.

Fermentative metabolism

Although most marine biogenic methane is the result of carbon dioxide (CO2) reduction, a small amount is derived from acetate (CH3COO-) fermentation.

In the fermentation pathway, acetic acid undergoes a dismutation reaction to produce methane and carbon dioxide:

CH3COO– + H+ → CH4 + CO2       ΔG° = -36 kJ/reaction

This disproportionation reaction is enzymatically catalysed. One electron is transferred from the carbonyl function (e– donor) of the carboxylic group to the methyl group (e– acceptor) of acetic acid to respectively produce CO2 and methane gas.

Archaea that catabolize acetate for energy are referred to as acetotrophic or aceticlastic. Methylotrophic archaea utilize methylated compounds such as methylamines, methanol, and methanethiol as well.

Briefly explain transport mechanism.

Active transport

Active transport is the movement of molecules across a cell membrane in the direction against their concentration gradient, i.e. moving from an area of lower concentration to an area of higher concentration. Active transport is usually associated with accumulating high concentrations of molecules that the cell needs, such as ions, glucose and amino acids. If the process uses chemical energy, such as from adenosine triphosphate (ATP), it is termed primary active transport. Secondary active transport involves the use of an electrochemical gradient. Active transport uses cellular energy, unlike passive transport, which does not use cellular energy. Active transport is a good example of a process for which cells require energy. Examples of active transport include the uptake of glucose in the intestines in humans and the uptake of mineral ions into root hair cells of plants.

Details

Specialized transmembrane proteins recognize the substance and allow it access[2] (or, in the case of secondary transport, expend energy on forcing it) to cross the membrane when it otherwise would not, either because it is one to which the phospholipid bilayer of the membrane is impermeable or because it is moved against the direction of the concentration gradient. The last case, known as primary active transport, and the proteins involved in it as pumps, normally uses the chemical energy of ATP. The other cases, which usually derive their energy through exploitation of an electrochemical gradient, are known as secondary active transport and involve pore-forming proteins that form channels through the cell membrane.

Sometimes the system transports one substance in one direction at the same time as cotransporting another substance in the other direction. This is called antiport. Symport is the name if two substrates are being transported in the same direction across the membrane. Antiport and symport are associated with secondary active transport, meaning that one of the two substances is transported in the direction of its concentration gradient utilizing the energy derived from the transport of second substance (mostly Na+, K+ or H+) down its concentration gradient.

Particles moving from areas of lower concentration to areas of higher concentration (i.e., in the opposite direction as, or against, the concentration gradient) require specific trans-membrane carrier proteins. These proteins have receptors that bind to specific molecules (e.g., glucose) and

thus transport them into the cell. Because energy is required for this process, it is known as 'active' transport. Examples of active transport include the transportation of sodium out of the cell and potassium into the cell by the sodium-potassium pump. Active transport often takes place in the internal lining of the small intestine.

Plants need to absorb mineral salts from the soil or other sources, but these salts exist in very dilute solution. Active transport enables these cells to take up salts from this dilute solution against the direction of the concentration gradient.

Primary active transport

The action of the sodium-potassium pump is an example of primary active transport.

Primary active transport, also called direct active transport, directly uses metabolic energy to transport molecules across a membrane.

Most of the enzymes that perform this type of transport are transmembrane ATPases. A primary ATPase universal to all animal life is the sodium-potassium pump, which helps to maintain the cell potential. Other sources of energy for Primary active transport are redox energy and photon energy (light). An example of primary active transport using Redox energy is the mitochondrial electron transport chain that uses the reduction energy of NADH to move protons across the inner mitochondrial membrane against their concentration gradient. An example of primary active transport using light energy are the proteins involved in photosynthesis that use the energy of photons to create a proton gradient across the thylakoid membrane and also to create reduction power in the form of NADPH.

Model of active transport

ATP hydrolysis is used to transport hydrogen ions against the electrochemical gradient (from low to high hydrogen ion concentration). Phosphorylation of the carrier protein and the binding of a hydrogen ion induce a conformational (shape) change that drives the hydrogen ions to transport against the electrochemical gradient. Hydrolysis of the bound phosphate group and release of hydrogen ion then restores the carrier to its original conformation.[5]

ATP using primary active transport types

1. P-type ATPase: sodium potassium pump, calcium pump, proton pump2. F-ATPase: mitochondrial ATP synthase, chloroplast ATP synthase3. V-ATPase: vacuolar ATPase4. ABC (ATP binding cassette) transporter: MDR, CFTR, etc.

Secondary active transport

Secondary active transport

In secondary active transport, also known as coupled transport or co-transport, energy is used to transport molecules across a membrane; however, in contrast to primary active transport, there is no direct coupling of ATP; instead it relies upon the electrochemical potential difference created by pumping ions in/out of the cell. Permitting one ion or molecule to move down an electrochemical gradient, but possibly against the concentration gradient where it is more concentrated to that where it is less concentrated increases entropy and can serve as a source of energy for metabolism (e.g. in ATP synthase).

In August 1960, in Prague, Robert K. Crane presented for the first time his discovery of the sodium-glucose cotransport as the mechanism for intestinal glucose absorption. Crane's discovery of cotransport was the first ever proposal of flux coupling in biology.

Cotransporters can be classified as symporters and antiporters depending on whether the substances move in the same or opposite directions.

Antiport

Function of Symports and Antiports

In an antiport two species of ion or other solutes are pumped in opposite directions across a membrane. One of these species is allowed to flow from high to low concentration which yields the entropic energy to drive the transport of the other solute from a low concentration region to a high one. An example is the sodium-calcium exchanger or antiporter, which allows three sodium ions into the cell to transport one calcium out.

Many cells also possess a calcium ATPase, which can operate at lower intracellular concentrations of calcium and sets the normal or resting concentration of this important second messenger. But the ATPase exports calcium ions more slowly: only 30 per second versus 2000

per second by the exchanger. The exchanger comes into service when the calcium concentration rises steeply or "spikes" and enables rapid recovery. This shows that a single type of ion can be transported by several enzymes, which need not be active all the time (constitutively), but may exist to meet specific, intermittent needs.

Symport

Symport uses the downhill movement of one solute species from high to low concentration to move another molecule uphill from low concentration to high concentration (against its electrochemical gradient). Both molecules are transported in the same direction.

An example is the glucose symporter SGLT1, which co-transports one glucose (or galactose) molecule into the cell for every two sodium ions it imports into the cell. This symporter is located in the small intestines, trachea, heart, brain, testis, and prostate. It is also located in the S3 segment of the proximal tubule in each nephron in the kidneys. Its mechanism is exploited in glucose rehydration therapy and defects in SGLT1 prevent effective reabsorption of glucose, causing familial renal glucosuria.Examples

Metal ions, such as Na+, K+, Mg2+, or Ca2+, require ion pumps or ion channels to cross membranes and distribute through the body

The pump for sodium and potassium is called sodium-potassium pump or Na +/K+-ATPase

In the epithelial cells of the stomach, gastric acid is produced by hydrogen potassium ATPase, an electrogenic pump

Water, ethanol, and chloroform exemplify simple molecules that do NOT require active transport to cross a membrane.