Biology Review- Chapter 5 (Microbiology)

Psychrophiles

Cold-loving microbes

Thermophiles

Heat loving microbes that survive in boiling hot springs or near geothermal veins in the ocean floor

If antibodies to a viral capsid protein are ineffective in blocking infection, what might this indicate about the virus?

It suggests that the virus is enveloped, so the antibody cannot reach its epitope on the capsid surface in infectious virus.

Do (-) strand RNA viruses use host enzymes to catalyze RNA production in transcription or in replication of the genome?

Neither. Viral RNA-dependent RNA polymerase first makes the (+) strand as mRNA and then uses the (+) strand as the template to replicate new (-) strand genomes.

Photoheterotrophs

Organisms that get their energy from the sun, but require organic molecule made by another organism as their carbon source

Chemoheterotrophs

Organisms that require organic molecules such as glucose made by other organisms as their carbon source and for energy (humans are this)

Obligate Anaerobes

Organisms that require the absence of oxygen as oxygen is toxic for them

Photoautotrophs

Organisms that use only CO₂ as carbon source and obtain their energy from the sun (plants are this)

Why might a bacteriophage inject its DNA, while animal viruses do not?

Phage must puncture the bacterial cell wall, while animal viruses can be internalized whole into animal cells (since they do not have a cell wall)

Why would a bacterial gene, carried with a virus and integrated with viral genes into a new bacterial genome, not be repressed along with the viral genes during lysogeny?

Prophage latency results from a viral repressor protein binding to viral DNA in a sequence-specific manner. The specific DNA sequence to which the repressor binds is present in the viral genes but not in the bacterial genes, so the bacterial genes can be expressed while the viral genes are repressed.

Given the limited information that viruses may contain in their genomes, why carry genes for an enzyme processed by the host?

The host cell will only make dNTPS in preparation for replication. If the virus wants to reproduce without waiting for the host to do so, it must encode its own enzymes for the synthesis of DNA building blocks.

True or false: viruses are not cells or even living organisms

True

Naked Viruses

Viruses which do not have envelopes. All phages and plant viruses are naked.

What is one potential consequence of the lysogenic cycle?

When the viral genome activates, excising itself from the host genome, it may take part of the host genome along with it. When the virus replicates, the small piece of host genome will be replicated and packaged with the viral genome.

Can prion disease be genetically linked or spontaneously arise?

Yes. Prion diseases can also be genetically linked, through mutations in the gene that codes for the prior protein. They can also arise spontaneously.

(+) RNA Viruses

• A piece of single-stranded viral RNA which serves as mRNA • Must encode RNA-dependent RNA pol (and not have to carry it); the role of which is to copy RNA genome so it can replicate itself

Prions

• Self-replicating proteins; contain no DNA or RNA • When the normally folded protein (Prpᶜ) comes into contact with the prior (PrPˢᶜ), it too becomes infectious

Conjugation

• Similar to sexual reproduction in animals. A sex plasmid is transferred through a bridge between two bacteria. The pilus extends from one bacterium (often referred to as F+; male) to another bacterium (known as F-; female) and creates a conjugation bridge • F+ factor itself is transferred to the new bacterium as well, creating a new F+ cell.

The Productive Cycle

• Similar to the lytic cycle but does not destroy the cell • Enveloped viruses exist the host cell by budding through the host's cell membrane, becoming coated with this membrane in the process. The lipid bilayer membrane can reseal as the virus leaves.

Glycolax (capsule)

• Sticky layer of polysaccharide "goo" surrounding the bacterial cell and often surrounding an entire colony of bacter • Makes bacteria more difficult for immune system cells to eradicate • Enables bacteria to adhere to smooth surfaces

What is the purpose of the tail fiber, base plate, and sheath of a bacteriophage?

• Tail fibers attach to the surface of the host cell as does the base plate • The sheath contracts using the energy of stored ATP, injecting the genome into the host

Exotoxins

• Very toxic substances secreted by both gram-positive and gram-negative bacteria into the surrounding. • Helps bacterium compete with other bacterial species

Retrovirus

• Virus that contains RNA as its genetic information • Must encode reverse transcriptase (RNA-dependent DNA polymerase)

Lytic Cycle

1. Attachment of phage and injection of phage chromosome 2. Breakdown of bacterial chromosome with phage-specific enzyme 3. Replication of phage chromosome using bacterial materials and phage enzymes 4. Expression of phage genes to produce phage structural components 5. Assembly of progeny phage particles 6. Release of progeny phage by lysis of bacterial wall

Lysogenic Cycle

1. Phage binds to bacterium 2. Phage DNA enters the host cell 3. Phage DNA integrates and becomes a noninfective prophage 4. Chromosome with integrated prophage replicates 5. In rare cases, the prophage may separate and the cell will be induced to lyse

Viral Envelope

A liquid bilayer that surrounds the capsid of an animal virus. The envelope is acquired as the virus out through the plasma membrane of its host cell. Not all animal viruses possess an envelope.

What does the viral genome consist of?

A viral genome many consist of either DNA or RNA that is either single-or double0stranded and either linear or circular

Treatment of an enveloped animal virus with a mild detergent solubilizes several proteins from the virus, although the genome does not become accessible. Which of the following is consistent with this scenario? A) Some of the proteins that are released by detergent may be encoded by the genome of the infected cell. B) The infectivity of the virus is not affected by detergent treatment. C) The proteins released by detergent are capsid proteins. D) All the proteins released by the detergent are encoded by the viral genome.

A) Some of the proteins that are released by detergent may be encoded by the genome of the infected cell.

If the ration of adenine to thymine in a DNA virus is not one to one, what can be said about the genome of this virus?

Adenine base pairs with thymine in double-stranded DNA. Thus, for every A there should be one T for a one to one ratio of A to T. If the ratio differs from this, the genome must be single-stranded DNA, or RNA, which has no T

What is the problem with the lytic cycle?

All host cells are destroyed which is an evolutionary disadvantage

What is the structure of viruses?

All viruses possess a nucleic acid genome packed in a protein shell (which helps convey the genome from one cell to infect other cells)

Lysozyme

An example of a late gene; destroys bacterial cell walls

A virus is a what?

An obligate intracellular parasite that relies on host machinery whenever possible

Autotrophs

An organism that can makes its own good, typically using CO₂ as a carbon source

Heterotrophs

An organism that cannot make its own food, and thus must ingest other organisms

Facultative Anaerobes

An organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation if oxygen is absent

Facultative Aerobes

An organism that makes ATP by anaerobic respiration. These organisms do not require oxygen but can survive in presence of oxygen. They generate ATP by aerobic respiration.

Chemotrophs

An organism that relies on a chemical source of energy (such as ATP) instead of using light to make ATP

Phototrophs

An organism that utilizes light as its primary energy source

Cyanide (an inhibitor of the electron transport chain) is added to a culture of virus-infected mammalian cells. The virus has none of the components of the electron transport chain or any of the proteins are inhibited by cyanide. Which of the following best describes the effect of cyanide? A) The mammalian cells will die, and all viruses will be destroyed as well, regardless of their stage of development B) Mammalian cells are killed, and viral replication halted, but the culture remains infectious C) Mammalian cells stop growing, and viral replication is unaffected D) Mammalian cells continue to grow, but viral replication is halted

B) Mammalian cells are killed, and viral replication halted, but the culture remains infectious ➡ Any viruses that had already completed the replication process when the cyanide was added well not be affected

Motile Bacteria

Bacteria that possesses one or more flagella

Death Phase of Bacterial Growth

Bacteria die off. This could be caused by lack of nutrients, environmental temperature above or below the tolerance band for the species, or other injurious conditions.

Retroviruses are theoretically not required to carry reverse transcriptase, only to encode it. Why?

Because the viral RNA genome can be translated by host ribosomes; thus reverse transcriptase may be made after the viral genome enters the host.

Septic Shock

Condition that occurs when an overwhelming bacterial infection affects the body. It results in drop in blood pressure, and other problems, which may be fatal.

Many animal viruses enter cells by __________

Endocytosis (a process whereby the host cell engulfs the virus and internalizes it )

Amphitrichous

Flagella at both ends of cell

Peritrichous

Flagella dispersed over surface of cell

Why does gram-negative cells stain pink?

Gram-negative contain an outer membrane , a periplasmic space with peptidoglycan cell wall, and an inner membrane. The increased protection from the environment is reflected in their weak staining, as well as their increased resistance to antibiotics.

What configuration of amino acids are found in humans?

Humans only have L configuration amino acids

Phases of Bacterial Growth

Lag phase, log phase, stationary phase, death phase

Flagella

Long, whip-like filament, which are involved in bacterial motility

Which bacteria would be more susceptible to lysis when treated with lysozyme: gram-positive or gram-negative?

Lysozyme hydrolyzes linkages in peptidoglycan to weaken the cell wall. The peptidoglycan in gram-positive cells are more accessible, since these cells do not possess an additional outer layer; therefore, gram-positive cells will lyse more easily when treated with lysozyme.

Mesophiles

Moderate temperature loving microbes

Are viruses able to perform any of the chemical reaction charactersistics of life such as the synthesis of ATP and macromolecule?

No

A disease agent that is isolated from a human cannot reproduce on its own in cell-free broth but can reproduce in a culture of human cell. In its pure form it possesses both RNA and DNA. Is it possible that the disease agent is a virus?

No, it cannot be a virus. Viruses possess only one kind of nucleic acid. The disease agent is another kind of obligate intracellular parasite (can only reproduce inside host cells)

After integration of a retrovirus into the cellular genome, a reverse transcriptase inhibitor is added to the cell. Will the production of new viruses be blocked?

No, it will not. Reverse transcriptase is required for only phase of the retrovirus life cycle: the copying of the viral genome into DNA so that it can integrate into the host genome and be transcribed. Once the viral genome has integrated, transcription to produce viral mRNA and new viral RNA genomes does not involve reverse transcriptase. It can proceed with normal host-cell enzymes.

Will an infectious virus be produced if the genome of an enveloped (+) strand RNA virus is added to an extract prepared from the cytoplasm of eukaryotic cells that retains translational activity but lacks DNA replication or transcription of host genes?

No. The (+) strand RNA virus will be able to viral genome and proteins, but progeny will not be able to acquire the envelope they need to be infectious.

If lysozyme were an early gene, would this be advantageous to the virus?

No. The host cell would lyse before the phage had time to replicate and assemble.

Can viruses move via flagellar propulsion to find host cells?

No. Viruses lack any means of energy production on their own and any means of active movement. They rely on diffusion to find host cells.

Endotoxins

Normal component of the outer membrane of Gram-negative bacteria that aren't inherently poisonous. However, they cause our immune system to have such an extreme reaction that we may die as a result. Cells of the immune system release so many chemicals that the patients goes into septic shock.

Chemoautotrophs

Organism that builds organic molecules from CO₂ using the energy of chemicals. They obtain energy by oxidizing in organic molecules like H₂S

Double-Stranded DNA Viruses

Often encode enzymes required for dNTP synthesis and DNA replication

What happens after a virus enters an animal cell?

Once inside the host, the viral genome is uncoated, meaning it is released from the capsid. Alternatively, some viruses fuse with the plasma membrane to release virus into the cytoplasm.

What is the purpose of the bacterial cell wall?

Provides support for the cell, preventing lyssi due to osmotic pressure

Obligate Aerobes

Require oxygen for metabolism

Bacteria are often classified based on their shape and fall into one of 3 categories:

Round (cocci), rod-shaped (bacilli), and spiral-shaped (spirilli or spirochetes).

Aerotolerant Anaerobes

Similar to obligate anaerobes in that they can only engage in anaerobic metabolism, but the presence of oxygen is not toxic to them

Monotrichous

Single flagellum at one end

Prions are self-replicating proteins. Why does this violae the central dogma?

The central dogma states that the information flows in its nucleotide form from DNA to RNA (transcription), and then in its amino acids form from RNA to proteins (translation). Prions take both transcription and translation out of the process and have proteins being shaped base on other proteins.

What is a factor likely to limit the size of RNA genomes?

The error rate in RNA synthesis is much higher than in DNA synthesis, in part because there are mechanisms to proofread and correct errors in DNA synthesis (but not in RNA synthesis). If an RNA genome were too large, every copy of the viral genome synthesized would suffer from so many errors that no infectious virus would be produced.

What is the likely result if a viral genome is tripled in size?

The exterior protein shell of a virus is typically a rigid structure of fixed size that cannot expand to accommodate a larger genome. The viral genome will probably no longer fit within the normal viral structure, and the genome will therefore not be packaged into infectious viral particle.

When phage are first added to a bacterial culture, the number of infective viruses initially decreases before it later increases. Why does this occur?

The initial decrease is due to the simple fact that many phage have injected their genome into hosts and are no longer infectious

What is the component of the prokaryotic cell wall?

The most important component of the cell wall is a polysaccharide known as peptidoglycan, which helps provide the rigid support for the cell.

Log Phase of Bacterial Growth

The second of the four phases of bacterial growth, in which cells divide at an exponential rate.

Transformation

The simplest of these gene transfer mechanisms is transformation, which involves bacteria absorbing genetic material directly from the environment. This mechanism does not involve an external carrier of foreign DNA.

Bacteria cultured in the presence of ³⁵S-labeled cysteine and ³²P-labeled phosphates are infected with phage T4. When phage from this culture is used to infect a new nonradiolabeled bacterial culture, which of the isotopes will be found in the interior of the newly infected bacteria?

The ³⁵Cysteine will be incorporated into viral coat proteins and the ³²Phosphates will be incorporated into the viral nucleic acid genome. (Proteins contain no P and nucleic acids contain no S). When these viruses infect bacteria, their nucleic acids are injected into the bacteria while the capsid proteins remain on the exterior, which means that only the ³²P will be found on the interior of the newly infected cells.

If a viral genome is (+) strand RNA, what is used as a template by the RNA-dependent RNA polymerase?

To make (+) strand copies of the genome, the virus needs the complementary strand as a template: the (-) strand RNA. Thus, the RNA-dependent RNA polymerase produces a (-) strand intermediate before generating new (+) strand genomes.

Some DNA viruses induce infected host cells to enter mitosis and may even override cellular inhibition of cell division so strongly that the cell becomes cancerous; what is the advantage to the virus of inducing host-cell division?

To replicate, the DNA virus must either provide all of the necessary components (such as dNTPs) itself, infect a cell that is already dividing, or induce the cell it infects to enter mitosis and produce the ingredients for DNA synthesis.

Transduction

Transduction is the process by which DNA is transferred from one bacterium to another by a virus

Mutation of the cell-surface receptor that viruses attach to would be a means for an organism to become resistant to viral infection. Why is this mechanism not common?

Two reasons 1. The receptor has a specific role in the normal physiology of the host, which a mutation might compromise 2. Viruses generally evolve so rapidly that they can keep up with any changes in the host, but this is not an absolute rule.

How do ribosomes used to translate viral proteins compare to host ribosomes?

Viral and host proteins are translated by the same ribosomes.

Is viral infection random or specific?

Viral infection is not a random process, but highly specific. A virus binds to a specific receptor on the cell surface. Only cells with a receptor that matches the virus will become infected.

Bacteriophage

Virus that infects bacteria

Why don't phages and plant viruses have viral envelope?

Viruses acquire envelopes by budding through host membranes. Phages and plant viruses infect hosts that possess cell walls. When viruses begin to exit the cell, the cell wall is destroyed, and host membranes rupture. Thus there is no membrane through which the remaining viruses must bud; they simply escape in a lytic explosion.

The binding of the HIV virus protein gp120 to a T cell membrane protein termed CD4 is one of the first steps in HIV infection. Would treatment of an HIV-infected person with a soluble form of CD4 protein affect the infectivity of the virus?

Yes, it would. The soluble CD4 protein would bind to the virus's CD4 receptor (gp120) and block attachment of the virus to the T cells.

Lag Phase of Bacterial Growth

• Bacteria adapt to a new environment • During the lag phase of the bacterial growth cycle, synthesis of RNA, enzymes, and other molecules occurs. • Period of little to no cell division (only growing in cell size)

Prophage

• Bacteriophage DNA that is embedded in the bacterial host's DNA • Silent; its genes are not expressed and viral progeny is not produced. Eventually, the prophage becomes activated and removes itself from the host genome.

Transmission Spongiform Encephalopathies (TSEs)

• Caused by prions • Cause degeneration in the nervous system, especially the brain where characteristic holes develop, and are always fatal • Misfolded proteins are very resistant to degradation by chemicals or heat, making them hard to destroy

Gram-Positive

• Cells have a thick layer of peptidoglycan outside the cell membrane • Stains purple

Gram-Negative

• Cells have only a thin layer of peptidoglycan in the cell wall • Also have an additional outer membrane with lipopolysaccharide • Resistance to antibiotics • Stains pink

Describe the structure of the prokaryotic flagellum?

• Contain the filament, the hook, and the basal structure. The basal structure contain rings that anchor flagellum to the inner and/or outer membrane and serve to rotate the rod and the attached flagellum in a CW or CCW manner) • The structure of prokaryotic and eukaryotic flagellum differ

Provirus

• Dormant virus of animal cells • Analogous to the prophase • After an infection, it may remain dormant as a provirus for an indefinite period of time. Then one day, usually when the host encounters stress, the virus reactivates

Bacteriophage Life Cycle

• First step is binding to the exterior of a bacterial cell in a process termed attachment or adsorption • Injection of the viral genome into the host cell in a process called penetration or eclipse; capsid remains on the outer surface • Phage follows one of two different paths: lytic cycle or lysogenic cycle

What are the three main retroviral genes?

• Gag: codes for viral capsid proteins • Pol: polymerase codes for reverse transcriptase • Env: envelope codes for viral envelope proteins

(-) RNA Viruses

• Genome of a (-) RNA virus is complementary to the piece of RNA that encodes viral proteins (template for vital mRNA production) • Must carry RNA-decedent RNA pol (and, of course, encode it too)

One of the first viral gene products made is sometimes an enzyme called hydrolase. What does it do?

• Hydrolase is a hydrolytic enzyme that degrades the entire host gene • An example of an early gene; one of a group of genes that are expressed immediately after infection and which includes any special enzymes

Stationary Phase of Bacterial Growth

• New cells are produced at the same rate as the old cells die, leaving the number of live cells constant. • Often due to a growth-limiting factor such as the depletion of an essential nutrient, and/or the formation of an inhibitory product such as an organic acid

How does viruses adapt to the size constraint of their fixed rigid protein coat?

• One adaptation is for the viral genome to carry very few genes and for the virus to rely on host-encoded proteins for transcription, translation, and replication. • Another adaption is the ability to encode more than one protein in a given length of the genome by utilizing more than one reading frame.

Capsid

• Outer protein coat of a virus • Various shapes such as helical and polyhedral

Binary Fission

• Reproduction in bacteria • Similar to mitosis in that binary fission also results in the formation of two identical cells