FR3- Structure and functional anatomy of bacteria

Question 1

Explain the structure of peptidoglycan:

How are the NAG and NAM residues arranged?

Answer 1

• Peptidoglycan is composed of many identical subunits. Each subunit within the sacculus contains two sugar derivatives, N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM), and several different amino acids.
• The amino acids form a short peptide, sometimes called the stem peptide, consisting of four alternating d- and l-amino acids; the peptide is connected to the carboxyl group of NAM
• Three of the amino acids are not found in proteins: d-glutamic acid, d-alanine, and meso-diaminopimelic acid. The presence of d-amino acids in the stem peptide protects against degradation by most peptidases, which recognize only the l-isomers of amino acid residues.
• The peptidoglycan sacculus is formed by linking the sugars of the peptidoglycan subunits together to form a strand; the strands are then cross-linked to each other by covalent bonds formed between the stem peptides extending from each strand.The backbone of each strand is composed of alternating NAG and NAM residues

Question 2

What does the peptidoglycan subunit look like?

Answer 2

Question 3

There are two types of cross-links: direct and indirect via a peptide interbridge

Answer 3

A direct cross-link is characterized by connecting the carboxyl group of an amino acid in one stem peptide to the amino group of an amino acid in another stem peptide.

Bacteria that have indirect linkage use a peptide interbridge (also called an interpeptide bridge), a short chain of amino acids that links the stem peptide of one peptidoglycan strand to that of another

Question 4

Motile bacteria do not move aimlessly. Rather, motility is used to move toward nutrients such as sugars and amino acids and away from many harmful substances and bacterial waste products

Answer 4

Movement toward chemical attractants and away from repellents is known as chemotaxis. Motile bacteria also can move in response to environmental cues such as temperature (thermotaxis), light (phototaxis), oxygen (aerotaxis), osmotic pressure (osmotaxis), and gravity

Question 5

For many bacteria in an aquatic environment, flagellar rotation results in two types of movement:

Answer 5

1. A smooth swimming movement often called a run, which actually moves the cell from one spot to another,
2. A tumble, which serves to reorient the cell

Alternating between smooth swims and changes in direction is important for responding to environmental conditions

Question 6

What rotations do monotricious bacteria use for a run?

Answer 6

Polar flagella use a counterclockwise rotation for a run

When rotation is reversed, the cell tumbles

Question 7

What rotations do peritricious bacteria use for a run?

Answer 7

To move forward in a run, the flagella rotate counterclockwise. As they do so, the flagella bend at their hooks to form a rotating bundle that propels the cell forward. Clockwise rotation of the flagella disrupts the bundle and the cell tumbles

Question 8

Name two other types of swiming motility

Answer 8

• Rhodobacter sphaeroides cells alternate between rotating their single flagellum in one direction (run) and no rotation, a so-called run-stop motility. When the cells are stopped, molecules in the environment bombard the cells and cause them to make small changes in orientation. When they resume a run, they move in a new direction
• Another type of swimming motility is seen with the monotrichous bacterium Vibrio alginolyticus. It uses a run-reverse-flick pattern. It swims forward (run) when the flagellum rotates in one direction. When rotation reverses, the cell moves backward (reverse). Just as the rotation switches again for a run, the flagellum flicks, causing the cell to change its orientation and move in a new direction

Question 9

How can PMF (proton motive force) be used to power the flagellar motor?

Answer 9

PMF is a difference in charge and pH across the plasma membrane

• The channels created by the MotA and MotB proteins allow protons to move across the plasma membrane from the outside to the inside
• Thus the protons move down the charge and pH gradient. This movement releases energy that is used to rotate the flagellum
• The speed of flagellar rotation is proportional to the magnitude of the PMF

Question 10

What is the svedberg unit a measure of?

Explain the composition of bacteria ribosomes

Answer 10

• This is the unit of the sedimentation coefficient, a measure of sedimentation velocity in a centrifuge; the faster a particle travels when centrifuged, the greater its Svedberg value or sedimentation coefficient. The sedimentation coefficient is a function of a particle’s molecular weight, volume, and shape. Heavier and more compact particles normally have larger Svedberg numbers and sediment faster
• Bacterial ribosomes are composed primarily of ribosomal RNA (rRNA) molecules. The small subunit contains 16S rRNA, whereas the large subunit consists of 23S and 5S rRNA molecules. Approximately 55 proteins make up the rest of the mass of the ribosome: 21 in the small subunit, and 34 in the large subunit.

Question 11

What is the function of chemoreceptors?

Answer 11

Attractants and repellents are detected by chemoreceptors, proteins that bind chemicals and transmit signals to other components of the chemosensing system. Chemosensing systems are very sensitive and allow the cell to respond to very low levels of attractants (about 10−8 M for some sugars)

Question 12

Chemotactic behaviour of E.Coli:

What happens in the absence of a chemical gradient?

What happens in the presence of an attractant?

What happens in the presence of a repellant?

Answer 12

• In the absence of a chemical gradient, E. coli cells move randomly, switching back and forth between a run and a tumble. During a run, the bacterium swims in a straight or slightly curved line. After a few seconds, the bacterium stops and tumbles. The tumble randomly reorients the cell so that it is facing in a different direction. Therefore when it begins the next run, it usually goes in a different direction
• In contrast, when E. coli is exposed to an attractant, it tumbles less frequently (or has longer runs) when traveling toward the attractant. Although the tumbles can still orient the bacterium away from the attractant, over time the cell gets closer and closer to the attractant
• The opposite response occurs with a repellent. Tumbling frequency decreases (the run time lengthens) when the bacterium moves away from the repellent

Question 13

Describe E.Coli’s mechanism for sensing that it is getting closer to an attractant (or moving away from the repellent)

Answer 13

• The behavior of the bacterium is shaped by temporal changes in chemical concentration.
• The cell is able to compare the current concentration with the concentration a few seconds earlier.
• If the concentration of the attractant is increasing, tumbling is suppressed.
• Likewise, E. coli moves away from a repellent because it senses that the concentration of the repellent is decreasing.
• The bacterium’s chemoreceptors play a critical role in this process

Question 14

What are endospores?

Which bacteria produce these structures?

Answer 14

Endospores, dormant cells formed within a so-called mother cell are bacterial structures only produced by certain members of the genera Bacillus and Clostridium (rods), and Sporosarcina (cocci) within the phylum Firmicutes

Endospores are extraordinarily resistant to environmental stresses such as heat, ultraviolet radiation, gamma radiation, chemical disinfectants, and desiccation

Question 15

why have endospores long held the interest of microbiologists?

Give examples of dangerous endospore producing bacteria

Answer 15

• Several species of endospore-forming bacteria are dangerous pathogens.
• For example, Clostridium botulinum causes botulism, a food-borne disease that results from ingestion of botulinum toxin, the deadliest toxin known.
• In order to prevent botulism, food must be prepared and stored properly.
• The extreme heat resistance of C. botulinum’s endospores is a major concern of the food industry.
• Bacillus anthracis causes the deadly disease inhalational anthrax, which occurs when spores are inhaled and germinate in the lungs. B. anthracis spores can be produced in a laboratory and used as a bioterrorism agent

Question 16

Bacteria cycle between two states:

Answer 16

vegetative growth and survival as an endospore.

• Vegetative growth is the normal, continuous cycle of growth and division. By contrast, sporulation is a complex process that occurs in a highly organized fashion over several hours.
• Sporulation normally commences when growth ceases due to lack of nutrients. Thus it is a survival mechanism that allows the bacterium to produce a dormant cell that can survive until nutrients are again available and vegetative growth can resume

Question 17

Give examples of endospore location and size

Answer 17

Question 18

State the 7 stages of sporulation:

Answer 18

• The cell’s DNA is replicated (stage I), followed by an inward folding of the cell membrane to enclose part of the DNA and produce the forespore septum (stage II).
• The mother cell membrane continues to grow and engulfs the immature endospore in a second membrane (stage III).
• Next, cortex is laid down in the space between the two membranes, and both calcium and dipicolinic acid are accumulated (stage IV).
• Protein coats are formed around the cortex (stage V), and maturation of the endospore occurs (stage VI).
• Finally, lytic enzymes destroy the sporangium, releasing the spore (stage VII).

Sporulation requires about 8 to 10 hours.

Question 19

The transformation of dormant spores into active vegetative cells is almost as complex as sporulation. It occurs in three stages:

Answer 19

(1) activation, (2) germination, and (3) outgrowth.

• Activation is a process that prepares spores for germination and can result from treatments such as heating.
• This is followed by germination, the breaking of the spore’s dormant state.
• It begins when proteins called germinant receptors, located in the inner membrane, detect small molecules such as sugars and amino acids.
• Upon detection of these molecules by the germinant receptors, a series of events occur.
• These include release of the Ca-DPA complexes, breakdown of the peptidoglycan in the cortex, and water uptake.
• Eventually water levels inside the germinating spore reach those characteristic of vegetative cells and enzymes in the core become active.
• This allows the spore to begin synthesizing various molecules needed to initiate spore outgrowth and return to a vegetative state

Question 20

What is the transfer of genes from parents to progeny called?

Answer 20

vertical gene transfer

This type of gene transfer is observed in all organisms

Question 21

Bacteria and archaea have evolved three major mechanisms for creating recombinants. These mechanisms are referred to collectively as

Answer 21

Horizontal (lateral) gene transfer (HGT)

Question 22

What is the difference between vertical and horizontal gene transfer?

Answer 22

HGT is distinctive from vertical gene transfer because genes from one independent, mature organism are transferred to another mature organism, often creating a stable recombinant having characteristics of both the donor and the recipient

Question 23

Give an example of the imporance of HGT

Answer 23

• Some archaea respond to UV radiation by increasing their ability to carry out HGT so that they can obtain and use DNA from other cells to repair any UVdamaged DNA in their genomes.
• Another important example is the transfer of groups of genes encoding virulence factors from pathogenic bacteria to other bacteria. These groups of genes are called pathogenicity islands,

Question 24

What happens during horizontal gene transfer?

Answer 24

During HGT, a piece of donor DNA, sometimes called the exogenote, enters a recipient cell. The transfer can occur in three ways:

• direct transfer between two cells temporarily in physical contact (conjugation)
• transfer of a naked DNA fragment (transformation)
• transport of DNA by viruses (transduction)

Question 25

What are transposable elelments?

Answer 25

specific DNA segments that can repeatedly insert into one or more sites or into one or more genomes

The enzymes that function in transposition are collectively termed recombinases

Question 26

What does conjugation depend on?

Answer 26

Conjugation, the transfer of DNA by direct cell-to-cell contact, depends on the presence of a conjugative plasmid.

Perhaps the best-studied conjugative plasmid is F factor. It plays a major role in conjugation in E. coli, and it was the first conjugative plasmid to be described

Question 27

How is bacterial conjugation different in gram positive bacteria compared to gram negative bacteria?

Answer 27

Unlike Gram-negative bacteria, which establish contact by way of the sex pilus, cell-to-cell contact in these Gram-positive bacteria is established by surface substances that enable cells to directly adhere to one another

Question 28

Define transformation

Answer 28

Another HGT mechanism is transformation, discovered by Fred Griffith in 1928. Transformation is the uptake by a cell of DNA either a plasmid or a fragment of linear DNA, from the surroundings and maintenance of the DNA in the recipient in a heritable form

Question 29

What is the transformation frequency of very competent cells?

Answer 29

The transformation frequency of very competent cells is around 10²³ for most genera when an excess of DNA is used. That is, about one cell in every thousand will take up and integrate the gene

Question 30

Describe the steps involved in natural transformation

Answer 30

Double-stranded (ds) DNA must first bind a competent cell. One strand is then hydrolyzed as the remaining intact strand is brought into the cell. The incoming single-stranded (ss) fragment then interacts with proteins that integrate the DNA into the recipient’s chromosome by homologous recombination

Question 31

How can bacteria be made artificially competent?

Answer 31

• bacteria must be made artificially competent by certain treatments.
• Two common techniques are electrical shock and exposure to calcium chloride.
• Both approaches render the cell membrane temporarily more permeable to DNA

Question 32

Which mode of HGT is mediated by viruses?

Answer 32

Transduction

Question 33

Two kinds of bacterial transduction have been described:

Answer 33

generalized and specialized.