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Bacteria and Viruses

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Welcome to MOOC-NPTEL course on bioengineering an interface with biology and medicine todaywere going to talk about bacteria and viruses.There is a brief outline of the lecture.We will talk about the diversity in bacteria gram positive and gram negative type of bacteriaand different type of harmful as well as useful applications from bacteria.We will also talk about viruses their structure reproduction how they mutate and how thatis relevant for the evolutionary context.Previously we have discussed about the tree of life.Let us look at phylogeny of prokaryotes and try to compare archaea Eukarya and bacteria.So, if you think about nuclear envelope bacteria and archaea, they do not have nuclear envelopewhereas Eukarya they have the nuclear envelope intact.If you look at membrane enclosed organelles again in bacteria and archaea it is absent.Whereas in new carrier it is present if you look at what are the specific component ofcell wall.Which is peptidoglycan it just present in bacteria, but it is absent in archaea andEukarya if you look at membrane lipids it is very uniquely present in archaea wherethere is some sort of branched hydrocarbons are present.Whereas in bacteria and Eukarya it is mainly unbranched hydrocarbons.So, this kind of you know gives you a little bit comparison and a uniqueness of each groupon one hand and a lot of commonalities between bacteria and archaea.And sometime the common features shared between archaea and the Eukarya.Let us first talk about bacteria what are bacteria that single cell organism very smallyou in fact need a microscope to visualize bacteria they can be found on any materialor surfaces.And even now billions of bacteria are on are in your body.Even right now there are different types of bacteria shown on the screen.E coli, Streptococcus there are many bacteria which are harmful there are many bacteriawhich are also useful how do they look like?So bacteria can be present in three basic shapes.Its sphere or Coci rods or Boselli and spiral shape.Most prokaryotic cells are which is 0.5 to 5 micron they are much smaller than the 10to 100 microns of many eukaryotic cells.Are bacteria alive?So, what does it mean to be alive? it means they can reproduce they can make their owncopies themselves do they need to eat?yes, they also eat but then the question comes how do bacteria eat.Many bacteria they make their own food from the sunlight like a plant some bacteria arescavengers they share the environment around them for example bacteria in your stomachare now eating what you eat today in the breakfast or the lunch.Some bacteria are pathogens the attack another living organism or other living things forexample even this bacteria on your face which can attack the skin.And some of them causes infection and even acne.How do bacteria move? so most of the mortal bacteria they propel themselves by the flagellawhich is a scattered on the surface at one or both ends.So, many bacteria the exhibit taxis or that is the ability for bacteria to move towardsor away from the stimulus for example chemotaxis.If we talk about chemotaxis that is a moment to worse or away from the chemical stimulus.How do bacteria reproduce? so bacteria mainly rely on binary fission for their propagation.And in this process the cell grows in number it also needs to grow to twice its startingsize and then it splits into the two bacteria.In binary fission bacteria makes copies by dividing is actually some of the process shownon the screen here for Escherichia coli as well as salmonella showing binary fission.What is the internal organization and DNA component inside bacteria?bacteria cells usually lack very complex architecture which is present in the eukaryotes the prokaryoticgenome it is circular it has this DNA as compared to the eukaryotic genome.The chromosome is located in the nuclear region and some species of bacteria they also havea small ring shape DNA which is extra chromosomal DNA called plasmids.So, what are the genetic diversity in the prokaryotes?Prokaryotes have considerable genetic variation and they are mainly three factors which areactually contributing to the genetic diversity of prokaryotes.It is rapid reproduction, Mutation and genetic recombination.The high diversity arises from the mutation allows for their rapid evolution.Now let us discuss specifically the genetic diversity of bacteria.So, bacteria allow researchers to investigate the molecular genetics in simplest true organisms.Bacterial chromosomes it is a circular DNA molecule with very few associated proteins.Bacteria also have the plasmids which are the small circular DNA molecules which canreplicate independently of their bacterial chromosomes.What are the sources of genetic variability in bacteria?Bacteria reproduce rapidly therefore the new mutation can very quickly increase a populationsgenetic diversity.Further the genetic diversity can also arise by the recombination of the DNA from two differentbacterial cells.Let us now look at the cell surface structures of bacteria.Bacterial cell wall contain peptidoglycan a network of sugar polymers cross linked bythe polypeptides.The eukaryotic cell walls they are made of cellulose or chitin.Gram stain can be used to classify based on their cell wall compositions.There two type of a broader group we can make based on the gram staining.One is gram positive which is much more simple it is a surface structure having more popularpeptidoglycan.Whereas gram negative is having less peptidoglycan and also contained an outer membrane.Let us look at the structure of bacterium cell wall and how the gram staining worksin a little bit more detail.First shown on the left side of the screen the gram positive bacteria they have thisthick cell wall which is made of peptidoglycan it traps a crystal violet testing and thenafter rinsing with alcohol it does not remove the crystal violet testing.So, therefore these bacteria if you look at it under microscope they look like purpleor violet colored bacteria which is known as gram positive bacteria.Now on the right side you can see the structure of gram negative bacteria where there is avery thin layer of peptidoglycan present.So, crystal violet stain can be very easy rinsed off from the cytoplasm and after furtherre staining the cell appears pink or red in color.So, now if you look at under the microscope these gram negative bacteria looks like pinkcolor notice.Let us have a lab session specifically for gram staining.Because you can easily do this kind of experiment where several washing and rinsing steps areinvolved and just by doing this straining you can broadly classify the bacteria intogram positive or gram negative.So, let us have a lab demonstration session on gram staining.Let us get started with gram staining this is the bacterial culture that were going touse for making the smear.This is clean glass this is a nichrome loop which is going to be used to make the smearon the . This is a spirit lamp which we are going to use for heat fixation step.First, we will sterilize this loop so that there is no contamination in the bacterialculture.We will let it cool so that the cells do not die.In case if we dip the hot loop, we really take a loop full of culture and make thissmear on the . We will first let it air dry once the smear air dries, we will use to heatfix the smear the heat fixation step is done so that the cells get stuck onto this anddo not get washed up and we wash the .After the heat fixation step, we will add crystal violet for one minute.After one minute we will wash off the stain.And then add grams iodine the grams iodine forms a complex with crystal violet and getstuck to the bacterial cell walls.So, when we wash the smear with de colorizer the gram positive bacteria cells stay violetand the gram negative cells lose the primary stain that is the crystal violet and thenget stained with the second counter stain which is the safranin.We will now add de colorizer which is acetone alcohol.After a few seconds we will wash off the de colorizer.We will now add safranin after two minutes we will wash up the safranin we will let thesmear get air dried.Once the smear has dried, we will add emotion oil and observe the smear.Under the oil emotional lens of the microscope.For gram positive bacteria we will see coci in clusters in purple and if we have gramnegative bacteria cells then we will absorb red cells that was all for gram staining.Thank you.Alright so let us say the patient comes to a clinician and doctor have no clue aboutyou know what type of bacterial diseases affecting this that individual.So, in that case the gram staining can immediately give the first level of information.Whether these bacteria belong to gram positive or gram negative.Now looking at the cell surface composition of bacteria.There are many antibiotic targets have been made.So, many antibiotics they target peptidoglycan and they damage bacterial cell wall.The gram negative bacteria they are more likely to be antibiotic resistant a polysaccharideor the protein layer which is called capsule that covers many prokaryotes.For the here I have shown many targets for the antibiotics for example the inhibitionof cell wall synthesis that can be governed and that can be controlled by antibioticslike penicillin cephalosporin and vancomycin.If we look at a deception of cell membrane function of that is what is being directedby antibiotic polymyxin.Inhibition of translation process is controlled by antibiotics like tetracycline, erythromycin,streptomycin and chloramphenicol.Inhibition of metabolism can be targeted by sulfanilamide inhibition of transcriptioncan be controlled by antibiotics rifamycin and inhibition of DNA replication had beentargeted by quinolones.So, again you can see looking at the composition and of the cell wall and different membranesa different type of antibiotic targets they try to damage the bacterial cell wall andtry to control bacteria for many infections.So, bacterial diseases I am sure we have all encountered one of the other bacterial infectionmany bacteria they are human pathogens.Just shown here is one of the example for anthrax disease which is caused by bacteriaknown as Bacillus anthracis.Which can infect through the skin lung or the stomach.So, bacteria has both beneficial as less harmful impact on humans if you think about the broaderenvironmental issues.So, bacteria plays a major positive role in the recycling of chemical elements betweenthe living and the nonliving components of ecosystems.The Chemoheterotrophic prokaryotes they function as decomposers which could break down deadorganisms as well less waste products.Prokaryotes they can also increase the availability of nitrogen phosphorus and potassium for theplant growth.Prokaryotes also a form a biotic relationship with larger organisms and that can be veryuseful.So, we have seen that bacteria on one hand are very harmful they can cause many diseasesand on other hand they can be very helpful especially for many environmental relatedissues.So, scientists have been trying to harness the benefits out of these Prokaryotes andthis is one of the hot topic in research and technology development.Experiments have been performed using prokaryotes which have led to some important advancementsin the DNA technology for example Escherichia coli has been used for the gene cloning.We have discussed that how agrobacterium tumefaciens can be used to produce transgenic plants.They are various niches or plastics, antibiotics, vitamins, ethanol production all of theseare governed by prokaryotes.So, as the bioremediation which is really important from the environmental point ofview.Here there are some examples shown that how bacteria can synthesize and store poly hydroxyalkenoate which can be used for making biodegradable plastics.One of the key areas for research the fertilizer spray they can stimulate bacteria growth whichcan metabolize even oils.Or one could develop bacteria to produce ethanol fuel from the renewable plant products.Some of these are you know some remarkable examples.How research on prokaryotes can be so beneficial for many type of products and processes.Let us now move on and talk about viruses.So, what are viruses these are much smaller.And much simpler as compared to a eukaryotes and of course they are even if you compareto the bacteria, right?So, they are very small infectious particles which has their own genetic material and theprotein coat.They are obligate intracellular parasite which can reproduce only when they are present insidea host cell.They infect almost all the members of the three cellular forms of life with a bacteria,archaea, or Eukaryote the question comes are viruses alive or they have the kind of a borrowedlife.Viruses lack their energy metabolism are all viruses very small no not all viruses arevery small.In fact people are studying different types of viruses and they are reported that thereare some large DNA viruses which are extremely useful to study evolution and biology.They are example like vaccinia virus 190 kb genome, pandora virus which is 2.5 mb genomeand Mimi virus which is 1.2 mb genome.So, such you know large DNA viruses are they alive?why are they so big? you know how do they invade the host?how do they manage to package their genome inside the capsid.There are many interesting aspects of your studying viruses and which are still prettymuch unknown and one of the hot areas of research also looking at the evolutionary context.Broadly virus consist of a nucleic acid surrounded by the protein coat.Historically scientists were able to detect viruses indirectly before they were even actuallyable to see them under the microscope.For example tobacco was a virus which causes tobacco mosaic disease.It stunts growth of tobacco plants and give their leaves a mosaic kind of coloration.So, shown here is the healthy leaf and then compare with the tobacco mosaic virus infectedleaf.What are the bacteriophages?Bacteriophages virus can infect and set in motion a genetic takeover of bacteria suchas E Coli Are the tiny virus infecting this E coli cells alive that I think an interestingtopic for you to go back and study and then think about how these viruses infect bacteriacell.Let us now think about viruses structure.the viruses are made of nucleic acid DNA or RNA and then enclosed in a protein coat whichis capsid.Capsid is a protein shell that encloses the viral genome which can have various structures.Some viruses have envelopes, membranous covering which are derived from the membrane of hostcells.So, bacteriophages have most complex capsid structure as you can see on the screen thebacteriophage T4 is shown but the complex capsid which consists of an icosahedral headand a tail apparatus.E coli and its viruses are used as a model system for many type of research?Let us now talk about RNA virusesRetroviruses such as human immune deficiency virus they use enzyme called reverse transcriptase.This can help to copy their RNA genome into DNA which can then be integrated into thehost genome as a pro virus.Here on the screen you can see one of the major disease caused by viruses which is poliomyelitis or the infantile paralysis which is caused by polio virus.The polio virus invades the nervous system which causes paralysis in one out of every200 children.Polio still remains endemic in several parts of the world including Afghanistan, Nigeriaand Pakistan.Let us now look at another type of virus which is SARS virus or severe acute respiratorysyndrome.The SARS causing agent is a coronavirus lake what is shown on the screen here the namecomes from the corona of glycoproteins spikes protruding from the envelope.There are many viral diseases which one could observe in the plants.There are more than 2000 types of viral disease of plants which are already known the commonsymptoms of these vital diseases and these viral infections include the spots on theleaf and fruit stunted growth and damaged flowers or roots.Let us now talk about find flu swine origin H1N1 influenza viruses a respiratory diseaseof pigs caused by type A influenza virus.Its symptoms include fever, chills, cough, sore throat, body ache, headache, fatigueetc.It is very contagious it spreads mainly from person to person through the cough or sneezingand often by touching mouth or nose of the infected individuals.How influenza A viruses can be classified.Let us look at their structure so there are surface glycoproteins which is having twomajor components a hemagglutinin or HA and Neuraminidase which is NA and this what givesgive the term H1N1.So, influenza viruses classified on the basis of antigenicity of HA and any surface glycoproteinsand there in fact 16 HA subtypes H1 to H16 as well as 9 NA N1 to N9 of these proteins.The HA proteins are very important for the cellular receptor binding fusion of vitaland Endosomal membranes whereas any proteins the help to virus to release from the infectedcells with lot of these heterogeneity of H and N proteins.Now let us briefly look at evolution of H1N1.The swine origin influenza A or H1N1 virus es they resulted from the reassortment ofavian or human or swine.The triple reassortment viruses with Eurasian Avian swine viruses cross sort of importantto note here that because of lot of phonetic reassortment which is happening in the viruses.They can give rise to new type of viruses and actual N1 got evolution from similar kindof reassortment.So, studying viruses actually it can be very helpful and there are many challenges aheadwhich can be posed by viruses.For example risk of generating novel viruses through reassortment.Resistance against drug or inhibitors is very much possible and for us to scale up or themass production of vaccines is very challenging.It also signifies that is studying viruses can be very helpful from the evolutionaryaspects if we know their genetic makeup if you know the possibilities of genetic reassortmentsthen you know in case of new species arises.I think one could still make some sort of guess that help control that kind of viralinfection.So, in summary today we briefly discussed about a different bacteria and viruses wediscussed about the rapid reproduction and bacteria mutation and genetic recombinationwhich promotes genetic diversity in prokaryotes.Viruses they consist of nucleic acid surrounded by a capsid proteins.They replicate only in host cell which poses a question are they alive? we also lookedat how genetic reassortment can give rise to different strains of viruses.And therefore studying viruses are very important in terms of the evolutionary aspects.We will stop here and continue on the next topic in next lecture.Thank you.