AP Biology Bacteria

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In today's lecture, we are going to continue our discussion of the diversity of life by focusing on the domain bacteria.0002

We are going to begin with the review of some general characteristics of bacteria and archaea, and these are members of two separate domains.0009

What I am doing right now is just a comparison, and then, we will go on to focus on bacteria,0016

so comparison of members of domain Archaea and domain Bacteria.0023

And recall that archaea and bacteria were once grouped together under kingdom Monera.0032

But they were separated out because they have some fundamental differences.0038

The archaea, which were once known as archaebacteria, include groups such as the extremophiles.0042

And as you will recall from the previous lecture on classification, when I talked about the domain archaea,0050

extremophiles include halophiles or salt lovers that can live in environments with very high salinity such as the Great Salt Lake.0055

And extremophiles may also be thermophiles.0070

These are archaea that are able to tolerate very high temperatures such as in the hot springs in Yellowstone or near hydrothermal vents deep in the ocean.0075

Archaea also includes methanogens that can produce methane from hydrogen.0088

Members of Bacteria include a broad array of pathogenic or disease-causing bacteria and non-pathogenic bacteria.0097

Starting out with some similarities, both all the members of Archaea, and all the members of Bacteria are prokaryotes.0106

These cells, therefore, lack a true nucleus, and they lack membrane-bound organelles.0112

The organization of their genetic material, the organization of their genomes is that of a circular genome, so these consist of circular strands of DNA.0119

Bacteria do not contain histones, whereas, members of Archaea like members of the Eukarya may have histones associated with their DNA.0130

The cell walls of Bacteria contain a substance called peptidoglycan. Archaea do not contain peptidoglycan.0140

Another difference between the two is that the number of types of RNA polymerase in Archaea can be multiple types, and this is also true of Eukarya.0150

That is different, though, in Bacteria. Bacteria contain only one type of RNA polymerase.0164

The membrane lipids: if you look in the cell membrane at lipid structure, the structure of the membrane lipids is different between Bacteria and Archaea.0174

And one thing that we can focus on is the bond.0182

And if you look at Archaea, the bond is a glycerol ether bond, whereas, the bond in Bacteria is a glycerol ester bond.0187

So, this is just a different structure bonding the lipids to the glycerol group.0202

A bond between the glycerol group and the lipids can either be an ether bond in Archaea or an ester bond in Bacteria.0208

Finally, introns: remember that these are non-coding sequences of DNA.0214

Within a genome, you have DNA that contains genes that code for a protein or another product, and between those, in eukaryotes, we have introns.0220

Also in Archaea, in some genes are introns, whereas, Bacteria do not contain introns.0233

So, you should be familiar with the similarities and differences between Archaea and Bacteria.0239

For the rest of this lecture, we are going to be focusing exclusively on Bacteria starting out with just an overview.0244

As I mentioned, Bacteria can be pathogenic or non-pathogenic.0249

A pathogen is an organism that causes disease. Some examples of bacteria that cause disease are Mycobacterium tuberculosis.0254

I am just going to say Mycobacterium TB.0271

Mycobacterium tuberculosis causes the respiratory disease tuberculosis, another example: Clostridium botulinum causes botulism.0273

If food is canned improperly, and these bacteria are in there, they produce a toxin called botulism toxin.0287

And this toxin in extremely dilute amounts is also now used for medical purposes.0295

So, it is a pathogen, but we found some uses for this, as well.0301

There are many other pathogens like Salmonella.0304

Strep throat is caused by a bacteria, a Streptococcus bacteria, numerous other pathogens.0308

However, there are bacteria that are beneficial, as well. Bacteria have important roles in the environment.0314

One important role is that they may be decomposers. Decomposers break down organic material, which allows those components to be recycled.0321

Now, let's focus on some of the contributions of bacteria, which is to act as decomposers allowing organic materials to be recycled.0331

They also function to fix nitrogen.0340

In some plants, there are bacteria with the symbiotic relationship, where they take nitrogen from the atmosphere that plants cannot utilize and fix it to0343

form ammonia which plants can utilize, and which will be discussed in detail when we talk about plants in a series of separate lectures.0353

Before we go on to talk more about types of bacteria, I want to mention that bacteria can be classified as aerobic or anaerobic.0363

Aerobic bacteria require the presence of oxygen for cellular respiration, whereas, anaerobic bacteria do not require oxygen for cellular respiration.0380

In the lectures on cellular respiration, we talked about different pathways for respiration- some requiring oxygen, some which did not.0390

One thing to note is that oxygen can actually be toxic to some anaerobic bacteria.0400

These bacteria are called strict anaerobes. They can only function in the absence of oxygen.0405

They must have an anaerobic environment, whereas, facultative anaerobes use oxygen if it is available.0413

And if it is not available, they will perform anaerobic respiration, so these are facultative anaerobes versus strict anaerobes.0420

In the lecture in classification, I mentioned how to classify organisms according to nutritional modes0437

and the type of energy that they utilize and, therefore, categories that they can fall into.0442

If you look at the whole range of domain Bacteria, there are some members that fall into each of these groups. They fall into all four groups.0449

Just reviewing now, first, classifying organisms based on the source of energy that they use,0458

there are two ways that an organism can obtain energy- can obtain it from light or from chemical bonds.0464

Phototrophs obtain energy from light.0472

Looking at another kingdom- plants, plants obtain energy from light so do some bacteria like cyanobacteria.0483

Chemotrophs obtain energy from chemicals.0498

During cellular respiration, the energy can be released from chemical bonds to form ATP to form energy that can be utilized by the cell.0515

These are methods of obtaining energy, categorizations by how a cell or an organism obtains its energy.0525

Now, we can also categorize organisms according to how they obtain organic compounds,0534

whether they are producers of organic compounds or consumers of organic compounds.0539

Some organisms are autotrophs. Autotrophs are producers of organic compounds.0544

They can make or produce organic compounds from inorganic compounds.0555

OK, so, they can make organic compounds from inorganic compounds, whereas, heterotrophs are consumers.0581

They cannot make organic compounds from inorganic components.0593

They can take organic compounds that are building blocks to make other organic compounds.0601

But they cannot make organic compounds from inorganic compounds.0605

OK, now, if you put these together, you are going to get four different categories.0613

The first category is photoautotrophs.0621

And these are organisms that are going to obtain energy from light, and they are able to produce organic compounds.0633

They can perform photosynthesis.0641

The next category are the photoheterotrophs.0647

The photoheterotrophs can use light as a source of energy, but they cannot produce organic compounds from inorganic compounds.0652

So, they need to consume other organisms as a source of organic carbon.0661

Next, we have the organisms that obtain energy from chemicals- the chemotrophs.0667

The organism can perhaps be a chemoautotroph. That is one category.0675

A chemoautotroph is going to obtain energy from compounds.0681

There are actually some bacteria that can oxidize inorganic compounds to obtain energy.0686

And they can form organic compounds from inorganic compounds.0693

Finally, we come to the chemoheterotrophs.0699

The chemoheterotrophs obtain energy from chemicals, and they also need to obtain organic compounds to make other organic compounds.0702

They cannot make organic compounds from inorganic building blocks.0714

Bacteria fall into all four categories: photoautotrophs, photoheterotrophs, chemoautotrophs, chemoheterotrophs.0718

There are a certain bacteria that fall into various categories between all different bacteria. We have all four categories represented.0725

So, we talked about some classification based on nutrition and based on energy consumption.0734

There are other ways to categorize bacteria, and some of these are based on structure.0742

First, talking about different shapes of bacteria, bacteria can be round.0747

And bacteria that are round, we put the term cocci on the end such as Streptococci or Streptococcus- singular.0755

And these are bacteria that are spherical or round, 3-dimensional, so they are spherical.0769

The next shape is rod-shaped, and these bacteria are known as bacilli, and an example, Salmonella are bacillus, so rod-shaped.0777

Some bacteria are actually shaped more like a comma or a curved rod, and these are known as Vibrios.0798

Cholera is an example. Actually, cholera can be known as Vibrio cholerae.0807

I am going to put that they are shaped like a comma or curved, so they are like a curved rod.0814

Finally, some bacteria form spirals or tight coils. These are the spirochetes.0819

An example are organisms that cause Lyme disease and syphilis. I am just going to put Lyme disease in here and spiral-shaped.0829

So, those are the structures.0842

If you looked through a microscope, and you saw a comma-shaped, that would be a vibrio versus some clusters of spheres- cocci.0844

Now, just to look at a single organism and its structure, a single bacterium here, bacteria have a plasma membrane that consists of a lipid bilayer.0855

And again, in an earlier lecture on prokaryotic and eukaryotic cell structure, I went into detail.0875

And I also talked in detail about lipid bilayers and cell membrane and transport across cell membrane.0882

So, this is just a brief review, but bacteria do, of course, have plasma membranes. In addition, they also have cell walls.0888

The cell walls are located outside the plasma membrane and provide protection for the bacteria.0898

They also provide support and help to prevent the cell from lysing in a hypotonic environment because water would enter the cell, and it causes lysis.0905

Cell walls in bacteria contain peptidoglycan.0916

And we are going to talk in a second about ways of categorizing bacteria based on the amount of peptidoglycan they have.0920

But first, we are just going to finish up talking about bacterial structure.0926

As I mentioned, the genome is circular.0929

Bacteria do not have a true nucleus. However, they do have what is called a nucleoid region with a circular genome.0933

Bacteria may also have a few genes located on a small circular piece of DNA outside the nucleoid region. These are called plasmids.0949

Here is an example of a bacterium containing a plasmid.0962

Some bacteria are also covered with what is called a capsule, and this is a layer, it is outside the cell wall; and it is generally composed of polysaccharides.0969

And what it does is that it helps bacteria to evade the immune system.0981

Some pathogenic or disease-causing bacteria have this. This is present on some but certainly not all bacteria.0985

So, I am just going to add it right here. This is a capsule.0993

Other structures that bacteria can have: flagella.0997

Flagella allow for motility, so I am just going to draw a flagella here on the end; and eukaryotes can have flagella, as well.1001

But keep in mind that the structure of eukaryotic flagella is different than that of prokaryotic flagella.1012

The prokaryotic flagella consist of three parts. The first part that we are going to look at is the motor.1018

This is located in what is called the basal apparatus, and it contains the element that powers the flagella; and there is a pump that is powered by ATP.1027

This provides the energy for the flagella to move.1045

The next section is called the hook, and this hook region is what attaches the basal apparatus to the filament, so this final region is the filament.1047

Three regions: the basal apparatus, the hook, and the filament.1059

The filament is the part that actually moves around and does the work of allowing the bacterium to be mobile.1063

The flagella is made of a protein called flagellin, OK?1074

Now, in addition, there can be other structures on the bacteria called pili or fimbriae.1082

We are going to talk about sex pili, which are important for conjugation in bacteria. They allow some bacteria to exchange genetic material.1095

These are also other types of pili that can allow bacteria to attach to a substrate, which is another word for a surface.1103

Not all bacteria have all these features, but they do all have a cell wall, the cell membrane.1113

They have ribosomes, but their ribosomes are different than ribosomes found in eukaryotes.1118

They are free in the cytoplasm. They are not attached to anything.1125

These are the major features of the structure of bacteria.1131

I mentioned that they can be classified according to their peptidoglycan, so there are two types: Gram-positive bacteria and Gram-negative.1135

When a staining process is done, gram-positive bacteria will stain purple, and the reason is they have a thicker layer of peptidoglycan.1147

I am just going to say more peptidoglycan in the cell wall.1159

Staining procedure is done, and a dye called crystal violet is used that will stain these bacteria purple.1165

In the staining procedure, the crystal violet is added, and then, the bacteria are rinsed; and the purple stain stays really well with the peptidoglycan.1175

If there is not a lot of peptidoglycan, it will rinse off, and then, a counter stain is done using safranin, which is a pinkish dye.1186

If bacteria do not have much peptidoglycan in their cell walls, they will stain pink.1193

And these are called Gram-negative bacteria, and they have less peptidoglycan in their cell walls.1199

And this is called a Gram stain, and this is useful in medicine allowing us to categorize quickly what type of bacteria we are dealing with,1210

what type of infection, what antibiotics might work well for this, but there are numerous other ways to categorize bacteria, as well.1218

If you look at bacteria, you know the shape, the gram staining, that can give you some ideas of what kind of bacteria that you are working with.1227

Now, bacteria are unicellular organisms.1234

The entire domain Bacteria consist of unicellular organisms. However, they can sometimes aggregate together and form what is known as a biofilm.1237

These bacteria, sort of, stick together on a surface, on a substrate, and this is due to secreted substances in various proteins.1246

And they can communicate with each other through these secreted substances or signaling molecules.1255

The plaque that forms on people's teeth and can cause decay, dental carries, is partly due to a biofilm from the formation of bacteria in the mouth.1261

So, now that we have talked about the structure of bacteria, we are going to briefly review bacterial genomes and reproduction.1275

Again, a detailed discussion of bacterial genetics is given earlier on the course.1281

The bacterial genome is a single, circular molecule of DNA. As I mentioned, it is found in the nucleoid region.1287

And there may be additional genes, just a few genes usually, located on small circular structures that are outside the nucleoid region.1294

They are outside the main genome.1304

These plasmids often contain what is called virulence genes that give the bacteria properties that might make it more infectious.1307

Plasmids are also very important for molecular biology techniques, genetic engineering,1320

because they allow us to transfer genes from one cell to another cell.1326

And we are going to talk about some means for doing that in a minute.1331

Reproduction of bacteria is through binary fission, so this is asexual reproduction through binary fission.1334

Bacterial DNA, during binary fission, is replicated, and one copy of the genome is passed to two identical daughter cells; so this is asexual reproduction.1342

One thing to note about bacteria is that they can reproduce very rapidly.1357

In good conditions, there can be as little as even 20 minutes for a bacteria to reproduce.1361

And because they can reproduce so quickly, many generations will occur in a short time.1367

Bacteria can, therefore, adapt to their environment, adapt to changing conditions, and it also makes them very useful in the laboratory.1371

And using bacteria in the laboratory, we have been able to develop new immunizations, medications, treatments for diseases.1380

For example the immunization for hepatitis B uses genetic engineering techniques.1387

I also talked about biotechnology in an earlier section of the course.1394

But we are going to review a couple of techniques that are found in nature and in the lab.1399

One technique is transformation. Transformation is a genetic engineering technique, but it is also something that occurs in nature.1407

So, I want to be clear that this is just not a genetic engineering technique, it occurs with bacteria in nature.1418

When we say that transformation occurs, what we are saying is that a bacteria can take up DNA from its surroundings, from the environment.1423

It is a process by which bacteria take up DNA from the environment.1432

Transformation can make bacteria more virulent. For example, a bacterial cell might take up a gene that allows it to make a capsule.1445

So, one bacteria might be able to make a capsule, another cannot.1455

The bacteria that can make the capsule dies, and another bacteria can take up this DNA through transformation1460

and may incorporate that gene into its genome through recombination between homologous segments of DNA.1467

In the lab, we use transformation to get genes into bacterial cells so that we can express the genes and use or study the products.1475

When we do that, what we do is we put the genes that we are studying into a vector.1484

A vector is a small piece of DNA that we use to carry genes that we want to express or study. An example of a vector is a plasmid.1490

You can take a plasmid, put in the genes that you want through molecular biology techniques and then, use transformation to get it into the cell.1503

And in order to get DNA into the cell, the cells need to be, what we call, competent.1512

It means that they are in a state - the bacteria - in which they will take up. This means that the cell is able to take up DNA.1518

And there is a method that you may have used in your AP biology lab called the heat1530

shock method that causes bacteria to be competent and ready to take up DNA.1534

Although bacteria reproduce asexually, as I mentioned through binary fission, they can exchange genetic material both1541

through taking up through transformation and also through a primitive form of sexual reproduction known as conjugation.1549

So, we are going to review conjugation here, and I mentioned pili.1556

And this structure here is what is called a sex pilus, and the sex pilus allows the transfer of DNA from the cell with the pilus to the other cells.1562

This is just a one-way transfer. They are not exchanging DNA.1573

This cell is simply donating DNA to the other cell.1576

Now, a cell that is able to make a sex pilus is called an F⁺ cell, if it carries the genes allowing it to make the pilus on the plasmid.1580

F⁺ cells carry the F-plasmid, and that is what is shown here.1597

There is going to be these genes here on this F-plasmid, and then, here is an F⁺ cell.1607

A cell that cannot make a sex pilus is called an F^- cell.1614

What happens during conjugation is that these two cells are joined through this pilus.1621

And then, one strand of the DNA from the plasmid is transferred from the F⁺ cell to the F^- cell.1627

What we are left with is a single strand of DNA here and a single strand of DNA here.1637

And then, each cell can make the complementary strand because it donated one strand.1643

And this cell can make the complementary strand, and then, they both end up with the double-stranded plasmid.1649

One type of plasmid that is important is called the (R)plasmid, and there is various types.1654

So, it is actually (R)plasmids, and these carry genes for antibiotic resistance.1659

And the reason that this is important is it means that resistant bacteria can transfer that resistance to other bacteria.1667

If you are treating an infection, let's say someone has an ear infection, and the physician treats that with an antibiotic such as amoxicillin,1674

and the ear infection gets partly better but not all the way better, what may be happening is that some bacteria that have survived that are resistant to amoxicillin.1684

And the problem is that those bacteria can transfer the resistant to other bacteria,1693

And because of the widespread use of antibiotics, in the United States, we are encountering more and more resistance,1699

so we have to keep coming up with new antibiotics and new ways so the bacteria have not figure it out yet to get around antibiotic resistance to treat infections.1706

Now, another way that a bacteria can perform conjugation is to carry the F-factor.1716

What the F-plasmid carrying these genes, what these genes are, are called F-factor, and this stands for fertility factor.1726

So, a plasmid can carry the F-factor, or the F-factor can actually be integrated into the bacterial genome.1738

Let's say I have a bacteria, and it is carrying the F-factor, not on a plasmid, but over here within the genome.1748

These cells are not called F⁺ cells.1760

They are called Hfr cells, and this stands for High frequency of recombination; and they are also able to donate DNA to another cell.1762

OK, in example one: as we review what we have just learned about bacteria,1782

species A are bacteria that use sunlight as an energy source and form organic compounds from inorganic molecules, so this is one species of bacteria.1787

We have another species. Species B obtain energy from organic compounds. Members of species B cannot form organic compounds from inorganic molecules.1798

Which of the following describe these species?1808

So, let's look at species A first. They use sunlight as energy.1810

Recall that phototrophs use light as an energy source, so this species A is either a photoautotroph or a photoheterotroph.1816

Chemotrophs use chemical sources of energy.1832

I have this narrowed down, and I know that they use sunlight as an energy source.1842

And I also know that these members of species A form organic compounds from inorganic molecules.1847

So, autotrophs form organic compounds from inorganic molecules. The correct answer is - for species A - that species A is photoautotrophic.1858

It uses light as energy, and it is able to form organic compounds from inorganic molecules, so this might be a photosynthetic type of bacteria.1875

Species B: members of species B cannot form organic compounds from inorganic molecules, and they obtain energy from organic compounds.1885

Let's take this part first. They obtain energy from organic compounds, so they obtain energy from chemicals.1897

Therefore, they are chemoautotrophic or chemoheterotrophic- one of these.1904

So, I have the first half.1914

Species B cannot form organic compounds from inorganic molecules. Well, autotrophs can form.1915

Autotrophs form organic compounds from inorganic molecules, and since this organism is not capable of doing that, it is not a chemoautotroph.1923

It is actually a chemoheterotroph.1942

Species A is photoautotrophic. Species B is chemoheterotrophic.1944

Example two: although bacteria reproduce asexually through binary fission, exchange of genetic material can occur between bacteria.1952

Describe two mechanisms through which this can take place.1962

There are two ways that we discussed through which bacteria can exchange genetic material or take up genetic material.1967

The first one is transformation. This is the process through which bacteria take up DNA from their environment or from their surroundings.1975

The second method we discussed is conjugation. This is a primitive form of sexual reproduction.1994

And it is the transfer of genetic material through a sex pilus, and this sex pilus is coded for by the F-factor,2001

which can be carried on a plasmid in F⁺ cells or integrated into the bacterial genome in Hfr or High frequency of recombination cells.2019

Example three: what are two ways in which bacteria are beneficial to other organisms?2029

We talked about pathogenic or disease-causing organisms. The bacteria are beneficial, as well.2035

One role that they play that is very important is they act as decomposers. Bacteria can break down organic material.2040

So, if a plant or animal dies, certain types of bacteria will break down the components of these organisms2048

and allow for reuse of some of those organic compounds that are building blocks for other organisms.2055

Second important function: decomposers. That is important because they are able to help recycle organic compounds.2062

A second important function of bacteria is they act as nitrogen fixers, and they convert atmospheric nitrogen into ammonia which plants can use.2071

I am going to say for plants to use.2086

So, two very important functions of bacteria in the environment.2088

A prokaryotic unicellular organism is discovered living underground in an acidic environment.2094

Observation and testing reveal that its genetic material is in circular form and is associated with histones. It has a cell wall that is lacking peptidoglycan.2102

Several genes are studied and are noted to contain introns.2113

Should this organism be classified as a member of domain Bacteria or domain Archaea?2117

It is a prokaryote, so it could be either; but then, we look a little more closely.2124

And it is in an acidic environment, sort of, an extreme environment, which makes me think Archaea, but that is not enough to go off of.2128

I am looking and seeing that it has a circular genome, still could be either. However, the genetic material is associated with histones.2135

It is a prokaryote, unicellular and has circular genome associated with histones.2147

That is describing Archaea. Let's just go on to confirm.2154

It has a cell wall lacking peptidoglycan.2157

Recall that in the domain Bacteria, cell walls contain peptidoglycan, Archaea do not- still looking like Archaea.2160

Several genes are studied and noted to contain introns.2170

Bacterial genes do not or Bacterial DNA does not contain introns, whereas, Archaea sometimes do. Therefore, this is a member of domain Archaea.2174

It is a prokaryote. It has circular genome.2186

However, the cell wall does not have peptidoglycan.2191

There are histones. There are introns, and this all leads to domain Archaea.2196

That concludes this lecture on bacteria.2201

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