Microbial Metabolism and Recombination

Chemical energy

The currency that runs the metabolic processes of the cell

Metabolism

The sum of all chemical reactions that occur in living organisms in order to maintain life. These processes allow organisms to grow, reproduce, maintain their structures, and respond to their environments

Catabolism

• Breaks down complex molecules into simpler ones

• Generally hydrolytic reactions and exergonic

• e.g. cellular respiration

Anabolism

• Building of complex substances from simpler ones

• Often involve dehydration and endergonic

• Uses energy to construct components of cells such as proteins and nucleic acids

Bioenergetics

Refers to the study of the production and use of energy by cells

Adenosine triphosphate

• The chemical substance that serves as the currency of energy in the microbial cell

• Energy released during the reactions of catabolism and the energy trapped in anabolic reactions such as photosynthesis

• The most important molecule for capturing and transferring free energy in biological system

Adenine

A part of ATP that is a double ring of carbon and nitrogen atoms

ribose

Attached to the adenine molecule in ATP is a small five-carbon carbohydrate called __________.

phosphate groups

Attached to the ribose molecule of ATP are three __________ which are linked by covalent bonds

Oxidation

The removal of electrons from an atom which is a reaction that often produces free energy

Reduction

The gaining of electrons

Phosphorylation

The addition of a phosphate group to a protein molecule or a small molecule

Enzymes

• Biological catalysts

• Chemical reactions in microorganisms operate in the presence of this

Substrate

The substance acted on by an enzyme

End products

The products of an enzyme-catalyzed chemical reaction

Coenzymes

May assist the enzyme by accepting atoms removed from the substrate or by donating atoms required by the substrate

NAD, NADP, FAD

3 most important coenzymes

Glycolysis

• Converts glucose into pyruvic acid with the production of some (2) ATP and energy containing (2) NADH

• The net yield is 2 ATPs for each glucose converted to pyruvate

• Reaction takes place both in the presence and absence of oxygen in the cytoplasm of the cell

tricarbocylic acid cycle

In the presence of oxygen, pyruvate is further oxidized in the mitochondria to carbon dioxide and water via the __________.

fermentation

In the absence of oxygen, pyruvate is converted to lactate or ethanol through __________.

Tricarbocylic acid cycle

• Pyruvic acid is still an energy-rich molecule, containing a number of extractable hydrogen and electrons to power ATP synthesis

• Pyruvic acid is converted to carbon dioxide and water

• 2 pyruvic acid yield 6 CO2, 2 FADH2, 8 NADH2, and 2 ATP

Respiratory chain: Electron transport and oxidative phosphorylation

• Final processing mill for electrons and hydrogen and the major generator of ATP

• Electrons progressively transferred from donor to acceptors. The flow of electrons down this chain is highly energetic and pays off ATP at various points

• In prokaryotic cells, it occurs in the cell membrane, while in eukaryotic cells, it occurs in the inner membrane of the mitochondria

• Electrons are passed from NADH and FADH2 to electron carriers in the membrane and ends at the terminal electron acceptor (oxygen), forming water

Fermentation

• An anaerobic process in which energy can be released from glucose even though oxygen is not available

• Occurs in yeast cells and also in some bacteria

• Glucose is still changed to pyruvic acid via glycolysis

• Pyruvic acid is first converted to acetaldehyde and then to ethyl alcohol

• The net gain of ATP is 2 molecules (as normally produced in glycolysis)

Alcohol fermentation

The process that yields beer, wine, and other spirits

Recombination

A new chromosome with a genotype different from that of the parent results from the combination of genetic material from 2 organisms. This new arrangement of genes is usually accompanied by new chemical or physical properties

General recombination

• The most common form of recombination

• Usually involves a reciprocal exchange of DNA between a pair of DNA sequences

• Occurs anywhere on the microbial chromosome

Site-specific recombination

• Second type of recombination

• Involves the integration of a viral genome into the bacterial chromosome

Replicative recombination

• Third type of recombination

• Due to the movement of genetic elements as they switch position from one place on the chromosome to another

chromosome

Prokaryotes such as bacteria possess a single circular __________ composed of double-stranded DNA in a single circular loop with associated protein.

Plasmid

• Many bacteria also possess this which exist and replicate independently of the chromosome

• Have relatively fewer genes (fewer than 30)

• Its genetic information is usually not essential to survival of the host bacteria

Curing

• Plasmids can be removed from the host cell in this process

• May occur spontaneously or may be induced by treatments such as ultraviolet light

episomes

Certain plasmids called __________ may be integrated into the bacterial chromosome.

conjugative plasmids

Other plasmids contain genes for certain types of pili and are able to transfer copies of themselves to other bacteria. Such plasmids are referred to as __________.

Fertility (F) factor

• A special plasmid that plays an important role in conjugation

• Contains genes that encourage cellular attachment during conjugation and accelerate plasmid transfer between conjugating bacterial cells

• Can exist outside the bacterial chromosome or may be integrated into the chromosome

F+ (donor) cells

Cells contributing DNA

F- (recipient) cells

Cells receiving DNA

Bacteriocins

Bacterial proteins capable of destroying other bacteria

Bacterial conjugation

• First populated in the 1940s by Joshua Lederberg and Edward Tatum while experimenting with E. coli

• Two bacterial cells come together and mate such that a gene transfer occurs between them

• The donor cell gives up DNA and the recipient cell receives the DNA

• The transfer is nonreciprocal and a special pilus, called the sex pilus, joins the donor and recipient during the transfer

• The DNA most often transferred is a copy of the F factor plasmid. The factor moves to the recipient, and when it enters the recipient, it is copied to produce a double-stranded DNA for integration

Bacterial transformation

• Was discovered by Frederick Griffith in 1928

• Worked with pneumococci that cause bacterial pneumonia

• He discovered that if he mixed fragments of dead pathogenic pneumococci with specimens of live harmless pneumococci, the harmless bacteria took on genes of the bacterial fragments and became pathogenic

• A bacterial cell becomes genetically transformed after the uptake of DNA fragments from the environment. Extracellular pieces of DNA can only penetrate the cell wall and cell membrane of certain bacteria

• A competent cell takes up DNA and destroys one strand of the double helix. A single-stranded fragment then replaces a similar but not identical fragment in the recipient organism

Competence

The ability to absorb naked DNA into the cell

Competent bacteria

Bacteria capable of taking up naked DNA molecules

Bacterial transduction

• Means to “carry across”

• Some bacterial genetic material may be carried across from one bacterial cell to another by a bacterial virus

Bacterial virus (bacteriophages)

• Transfer DNA fragments from one bacterium to another bacterium

• Contain a strand of DNA enclosed in an outer coat of protein

Lytic cycle

After a bacteriophage (or phage, in brief) enters a bacterium, it may encourage the bacterium to make copies of the phage. At the conclusion of the process, the host bacterium undergoes lysis and releases new phages. What is this process called?

Lysogenic cycle

The virus may attach to the bacterial chromosome and integrate its DNA into the bacterial DNA. It may remain here for a period of time before detaching and continuing its replicative process. What is this process called?

temperate phage

Under the lysogenic cycle, the virus does not destroy the host bacterium, but remains in a lysogenic condition with it. The virus is called a __________.

Mutation

• A permanent alteration in the sequence of nitrogenous bases of a DNA molecule

• The results of this is generally a change in the end product specified by that gene

• In some cases, this can be beneficial if a new metabolic activity arises in a microorganism or it can be detrimental if a metabolic activity is lost

Point mutation

• Most common type of mutation and involves a single base pair in the DNA molecule

• A different base is substituted for the normal base, thus altering the genetic code

missense mutation

Should a new amino acid be substituted in the normal protein, the mutation is known as __________.

nonsense mutation

Certain mutations change the genetic code and destroy the information it contains. Such a mutation is referred to as __________.

Mutagens

Physical and chemical agents capable of bringing about mutations

Nitrous acid

This chemical mutagen converts adenine to hypoxanthine, a molecule that will not pair with thymine, and thus interrupts the genetic code

Base analog

A chemical mutagen that resembles a nitrogenous base and is incorporated by error into a DNA molecule. Such a DNA molecule cannot function in protein synthesis

Physical mutagens

Include X-rays, gamma rays (which break the covalent bonds in the DNA molecules, thereby producing fragments), and ultraviolet rays (binds together adjacent thymine bases, forming dimers, which cannot function in protein synthesis, and the genetic code is thereby interrupted).

photoreactivation

Radiation damage can be repaired by certain bacterial enzymes, a process known as __________.