GRE-The Genetics of Viruses and Bacteria

GRE-The Genetics of Viruses and Bacteria

memorize.aimemorize.ai (lvl 286)
Section 1

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Emerging Viruses

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Date created

Mar 14, 2020

Cards (70)

Section 1

(50 cards)

Emerging Viruses

Front

Viruses that appear suddenly or that suddenly come to the attention of medical scientists. Class examples: HIV and AIDS

Back

Adenoviruses

Front

Type of virus that infects the respiratory tract in animals. Capsid is arranged in a polyhedral with a glycoprotein spike at each vertex.

Back

Reproductive Cycle of an Animal Virus Equipped with a Viral Envelope with an RNA Genome

Front

1. Glycoproteins on the viral envelope bind to specific receptor molecules on the host cell, promoting viral entry into the cell. 2. The capsid and viral genome enter the cell by fusion of the envelope with the cell's plasma membrane or by endocytosis and digestion of the capsid by cellular enzymes releases the viral genome. 3. The viral genome functions as a template for synthesis of complementary RNA strands by a viral enzyme and copies continue to be made from subsequent copies. 4. Complementary RNA strands also function as mRNA, which is translated into both capsid proteins in the cytosol and glycoproteins for the viral envelop in the ER. 5. Vesicles transport envelope glycoproteins to the plasma membrane. 6. A capsid assembles around each viral genome molecule. 7. Each new virus buds from the cell with an envelope studded with glycoproteins embedded in the membrane.

Back

Retroviruses

Front

The RNA animal viruses with the most complicated reproductive cycles (class VI). E.g. HIV. They have reverse transcriptases, which provide an RNA to DNA information flow, the opposite of the usual direction. Enveloped viruses that contain two identical molecules of single-stranded RNA and two molecules of reverse transcriptase.

Back

Reverse Transcriptase

Front

Enzymes in retroviruses that transcribe an RNA template into DNA, providing an RNA to DNA information flow, which is the opposite of the usual direction.

Back

Prophage

Front

The viral DNA that has become integrated into the host cell's (bacteria's) chromosome during the lysogenic cycle. One prophage gene codes for a protein that prevents transcription of most of the other prophage genes, leaving the phage genome mostly silent within the host (though in some cases, it can cause a change in the host cell's phenotype).

Back

Virus' Effects on Cells and Symptoms

Front

Some may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes; some cause host cells to produce toxins that lead to disease symptoms; some have molecular components that are toxic, such as their envelope proteins. How much damage a virus causes depends partly on the ability of the infected tissue to regenerate by cell division. Many of the temporary symptoms associated with viral infections, such as fever and aches, actually result from the body's own efforts at defending itself against infection.

Back

Transformation in E. Coli

Front

E. Coli and some other types of bacteria seem to lack the mechanism of transformation. However, placing E. Coli into a culture medium containing a relatively high concentration of Ca ions will artificially stimulate the cells to take up small pieces of DNA. This is used in biotechnology.

Back

Plasmid

Front

Small, circular, self-replicating DNA molecule separate from the bacterial chromosome. Smaller than the other bacterial chromosomes. Some can undergo reversible integration into the cell's chromosome. Have a small number of genes that under normal conditions are not required for the survival and reproduction of the bacterium but they can confer advantages for bacteria living in stressful environments.

Back

Replication of Bacterial Chromosomes

Front

From a single origin or replication, DNA synthesis progresses in both directions around the circular chromosome. Enzymes that cut, twirl, and reseal the double helix prevent the DNA from tangling.

Back

Plant Viruses

Front

Mostly have an RNA genome. Many have rod-shaped capsids while others have a polyhedral capsid. Once a virus enters a plant cell and begins reproducing, viral components can spread through the plant by passing through the plasmodesmata--proteins encoded by the viral genes are capable of altering the diameter of plasmodesmata to allow passage of viral proteins or genomes. Scientists have not yet devised cures for most viral plant diseases.

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Antiviral Drugs

Front

Mostly resemble nucleosides and as a result interfere with viral nucleic acid synthesis.

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Vertical Transmission

Front

One of the major routes by which plant viral disease spread. In this route, a plant inherits a viral infection from a parent. Can occur in asexual propagation (e.g. by taking cuttings) or in sexual reproduction via infected seeds.

Back

Binary Fission

Front

Mechanism by which bacterial cells divide. Preceded by replication of bacterial chromosomes. An asexual process--producing genetically identical offspring.

Back

Three Processes That Bring Together Bacterial DNA from Different Individuals

Front

Transformation, transduction, and conjugation.

Back

Bacteriophages (or phages)

Front

Viruses with some of the most complex capsids found. Their capsids have elongated icosahedral heads (having 20 triangular facets) enclosing their DNA. Attached to the head is a protein tail piece with fibers that the phages use to attach to a bacterium (seen in the "T-even" phages: T2, T4, and T6). The tail piece consists of a tail sheath and tail fibers. Infect bacteria.

Back

Pathogen

Front

A disease causing agent.

Back

Reproductive Cycle of an Animal Virus Equipped with a Viral Envelope with a Double-stranded DNA Genome

Front

Similar to the of an animal virus equipped with a viral envelope with an RNA genome except that the envelope is derived from the nuclear membrane of the host. E.g. the herpesvirus. These viruses also reproduce within the host's nucleus, using a combination of viral and cellular enzymes to replicate and transcribe their DNA.

Back

Two Major Routes that Plant Viral Disease Spread By

Front

Horizontal transmission and vertical transmission

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How Viruses Synthesize New Viral Genomes

Front

Most DNA viruses use the DNA polymerase of the host cell to synthesize new genomes along the templates provided by the viral DNA. In contrast, to replicate their genomes, RNA viruses use special virus-encoded polymerases that can use RNA as a template. After all the components have been synthesized, the new viruses usually assemble spontaneously. The simplest type or viral reproduction ends with the exit of hundreds or thousands of viruses from the infected host cell, usually destroying the host--causing some of the symptoms of viral infection.

Back

Sex Pilus

Front

A bacterial appendage that is used during conjunction.

Back

Horizontal Trasmission

Front

One of the major routes by which plant viral disease spread. In this route, a plant is infected from an external source of the virus. Since the virus must get past the plant's outer protective layer of cells (epidermis), plants that are damaged by by wind, injury, or insects are more susceptible to viral infections. Insects can be carriers. Farmers can act in the transmission through tools that they use.

Back

HIV

Front

A retrovirus.

Back

Structure of a Virus

Front

Only 20nm long--smaller than a ribosome. Not cells but rather infectious particles consisting of nucleic acid enclosed in a protein coat, in and some cases a membranous envelope. Genomes can consist of double-stranded DNA, double-stranded RNA, or single-stranded RNA/DNA. Their genomes are organized into a single linear or circular molecule of nucleic acid. Enclosed in a capsid

Back

Lytic Cycle

Front

A phage reproductive cycle that culminates in the death of the host cell (bacteria). Steps: 1. The phage uses its tail fibers to bind to specific receptor sites on the outer surface of the host cell. 2. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell's DNA is hydrolyzed. One of the first phage genes translated after the viral DNA enters the host cell codes for an enzyme the degrade the host cell's DNA (phage DNA is protected from this because it contains a modified form of cytosine that is not recognized by the enzyme). 3. The phage DNA directs production of phage proteins and copies of the phage genome by host enzymes within the cell. 4. Three separate sets of proteins self-assemble to form phage heads, tails and tail fibers. The phage genome is packaged inside the capsid as the head forms. 5. The phage directs production of an enzyme that damages the host cell wall, allowing fluid to enter, the cell to swell and then ultimately burs (lyse)t, releasing the phages.

Back

Lyses

Front

Breaks open.

Back

Viroids

Front

A class of pathogens. They are circular RNA molecules that infect plants. Do not encode proteins but can replicate in host plant cells, using cellular enzymes. The small RNA molecules seem to cause errors in the regulatory systems that control plant growth. Symptoms for plants include abnormal development and stunted growth.

Back

Transduction

Front

A process that brings together bacterial DNA from different individuals. In this process, phages carry bacterial genes from one host cell to another as a result of atypical behavior in the phage reproductive cycle; a small piece of the host cell's degraded DNA is accidentally packaged within a phage capsid in place of the phage genome.

Back

Tobacco Mosaic Virus (TMV)

Front

A virus that stunts the growth of tobacco plants and gives their leaves a mosaic colorization. Have a rigid-rod shaped capsid made from over a thousand molecules of a single type of protein in a helix.

Back

Influenza Virus

Front

A type of virus found in animals. Have a membranous envelope surrounding the capsids that help in their infection of a host. Outer envelope is studded with glycoprotein spikes. Genome consists of eight different RNA molecules, each wrapped in a helical capsid.

Back

Host Range

Front

The limited range of host cells that each type of virus can infect. Host specificity results from the evolution of recognition systems by the virus--"lock and key" fit between proteins on the outside of the virus and specific receptor molecules on the surface of the host cells.

Back

Two Mechanisms by Which Phages Reproduce

Front

The lytic cycle and the lysogenic cycle.

Back

Transformation

Front

A process that brings together bacterial DNA from different individuals. The process is the alteration of bacterial cell's genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment. Many bacteria have cell surface proteins that recognize and transport DNA from closely related species into the cell, which can then incorporate the foreign DNA into the genome.

Back

Restriction Enzymes

Front

(Restriction Endonucleases) A cellular enzyme (found in bacteria) that cuts up phage DNA after it has been detected as foreign by the host bacteria. Just as natural selection favors bacteria with effective restriction enzymes, it also favors bacteria mutants that are resistant to these enzymes; thus, the parasite-host relationship is in constant evolutionary flux.

Back

Lysogenic Cycle

Front

A phage reproductive cycle in which the genome is replicated without destroying the host (bacteria). In this cycle, the phage attaches to a host cell and injects its DNA, which then circularizes. The DNA molecules is then incorporated by genetic recombination (crossing over) into a specific site on the host cell's chromosome, becoming a prophage. One prophage gene codes for a protein that prevents transcription of most of the other prophage genes, leaving the phage genome mostly silent within the host (though in some cases, it can cause a change in the host cell's phenotype). Every time the host cell prepares to divide, the phage DNA is replicated along with the host DNA and is passed on to daughter cells. At some point, the phage genome can exit the host;s chromosome and initiate the lytic cycle; usually triggered by some environmental signal like radiation or the presence of a certain chemical.

Back

Nucleoid

Front

The dense region of DNA in bacteria that is not bounded by membrane like the nucleus of a eukaryotic cell.

Back

Capsomeres

Front

Large protein subunits that are the building blocks of capsids.

Back

Prions

Front

Proteins that appear to cause a number of degenerative brain disease in various animal species. Causes mad cow disease, Creutzfeldt-Jakob Disease in humans, and scrapie in sheep. Most likely transmitted through food. Very slow acting. Incubation period until symptoms appear is about 10 years. Virtually indestructible; not destroyed or deactivated by heating to normal cooking temperatures. No known cure for prion disease. Most likely a misfolded form of a protein normally present in the brain which converts the normal protein like itself to the prion version of itself.

Back

Reproductive Cycle of Retroviruses

Front

After the virus enters the cell, its reverse transcriptase molecules are release into the cytoplasm and catalyze the synthesis of viral DNA, which then enters the cell's nucleus and integrates into the DNA of a chromosome, becoming a provirus. The host's RNA polymerase transcribes the proviral DNA into RNA, which can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell. Envelope glycoproteins are made in the ER.

Back

Viral Envelopes

Front

Membranous envelopes that surround the capsids of some viruses. Derived from the membrane of the host cell and contain host cell phospholipids and membrane proteins but also contain proteins and glycoproteins of viral origin.

Back

Phage Lambda

Front

A temperate phage widely used in biological research. Resembles a T4 phage but its tail has only one short tail fiber.

Back

Vaccines

Front

Harmless variants or derivative of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen. The immune system is the basis for this major medical tool that prevents viral infections.

Back

Virus (general concept)

Front

Obligate intracellular parasites: they can only reproduce within a host cell. Lack metabolic enzymes, ribosomes, and other equipment for making proteins; are merely packaged sets of genes in transit from one host to another. All have a host range. After a virus has its host cell assemble the viral nucleic acids and capsomeres, their assembly into new viruses is usually spontaneous.

Back

Virulent Phage

Front

A phage that reproduces only by a lytic cycle.

Back

Capsid

Front

The protein shell that encloses a virus. Depending on the virus, it may be rod-shaped, polyhedral, or more complex such as a polyhedral head and a tail apparatus. Built from large numbers of protein subunits called capsomeres.

Back

Temperate Phages

Front

Phages capable of using both the lysogenic cycle and lytic cycle within a host.

Back

How T-even Phages Infect a Cell

Front

Use their elaborate tail apparatus to inject DNA into a bacterium. Once inside, the viral genome can commandeer its host, reprogramming the cell to copy the viral nucleic acid and manufacture viral proteins. The host provides the nucleotides, enzymes, ribosomes, tRNAs, amino acids, ATP, and other components needed for making the viral proteins provided by the viral DNA.

Back

Conjunction

Front

A process that brings together bacterial DNA from different individuals. The direct transfer of genetic material between two bacterial cells that are temporarily joined. The transfer is one way: one cell donates DNA and its mate receives the DNA. The donor uses appendages called sex pili to attach to the recipient, which retract once they've made contact, bringing the two bacteria together. A temporary cytoplasmic mating bridge then forms between the two cells, providing an avenue for DNA transfer. Process involves a special type of DNA replication so that each bacteria has a copy of the shared genome.

Back

3 Processes Contributing to the Emergence of Viral Diseases

Front

1. The mutation of existing viruses; RNA viruses ten to have an unusually high rate of mutation because errors in replicating their RNA genomes are not corrected by proofreading. 2. The spread of existing viruses from one host species to another. 3. The spread of a viral disease from a small, isolated population can leave to widespread epidemics.

Back

Provirus

Front

The integrated retrovirus DNA into an animal host cell's DNA in the nucleus. Never leaves the host's genome, remaining a permanent resident.

Back

Section 2

(20 cards)

Insertion Sequences

Front

The simplest transposable element which contains a single gene that codes for transposase. Don't seem to benefit the bacteria in any way.

Back

Operon

Front

Constitutes the operator, the promoter, and the genes they control--the entire stretch of DNA required for enzyme production of a certain pathway.

Back

Hfr Cell

Front

A cell with the F factor built into its chromosome. (High frequency of recombination).

Back

Corepressor

Front

A small molecule that cooperates with a repressor protein to switch an operon off. Usually the molecule that is being regulated (in E. coli: tryptophan).

Back

R Plasmids

Front

Plasmids that confer a type of antibiotic resistance.

Back

CAP (catabolite activator protein)

Front

Is inactive until cAMP concentrations increase in response to decrease in glucose concentration. Activation of CAP allows it to bind to a promotor and stimulate gene expression.

Back

Transposition

Front

The movement of transposable elements. In this, the elements move from one site in a cell's DNA to another--the target site-by a recombination process. Can move from plasmid to chromosome and vice versa as well as from one DNA location to another by a "cut and paste" mechanism or a "copy and paste" mechanism in which they replicate and the copy gets inserted elsewhere.

Back

Bacterial Metabolic Control (e.g. E. coli)

Front

If an bacteria's environment is lacking in something it needs for survival, e.g. the amino acid tryptophan for E. coli, the cell respond by activating a metabolic pathway that makes tryptophan from another compound. Later, if the environment (human intestines) is rich in tryptophan, the bacteria can stop producing it, saving itself from depleting its own resources. This example shows how cells can adjust the activity of enzymes already present, which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity. The cell can also adjust the amount being made of a certain enzyme, regulating the expressing of the genes encoding that enzyme.

Back

F Factor

Front

A special piece of DNA in bacteria that, in most cases, gives the bacteria the ability to form sex pili and donate DNA during conjunction. Can exist as either a segment of DNA within the chromosome or as a plasmid (which can undergo reversible integration into the cell's chromosome).

Back

Transposase

Front

Coded for by the single gene of an insertion sequence. An enzyme that catalyzes movement of the insertion sequence from one site to another within the genome. Bracketed by a pair of inverted repeats and recognizes these as the boundaries of the insertion sequence.

Back

Transposable (genetic) Elements

Front

A way in which the DNA of a single cell can undergo recombination by movement of these elements within the cell's genome. Always exist as part of chromosomal or plasmid DNA, never independently.

Back

Transposons

Front

Transposable elements that are longer and more complex than insertion sequences. Move about in the bacterial genome. In addition to the DNA required for transposition, they also have extra genes that go along for the ride, such as genes for antibiotic resistance; sometimes these extra genes are sandwiched between two insertion sequences. As though two insertion sequence happened to land relatively close together and now travel together, along with all the DNA between them, as a single transposable element. May help bacteria adapt to new environments. Not unique to bacteria and actually show up in the eukaryotic genome as well.

Back

Operator

Front

Part of the operon. A segment of DNA that acts as a switch--a key advantage of grouping genes of related function into one transcription unit is that a single on-off "switch can control the whole cluster of functionally related genes. Positioned within in the promoter or between the promoter and the enzyme-coding genes and controls the access of RNA polymerase to the genes. By itself, it is left on and is switched off by a repressor.

Back

Regulatory Gene

Front

Controls operons and codes for the repressor. Has its own promoter.

Back

Inverted Repeats

Front

A pair of noncoding DNA sequences. Bracket the transposase gene; the base sequence at one end of the insertion sequence is repeated upside down and backward at the other end.

Back

Episome

Front

A genetic element that can replicate either as part of the bacterial chromosome or independently. Some plasmids, temperate viruses (like phage lambda) qualify as this.

Back

F Plasmid

Front

The plasmid form of the F factor.

Back

Repressor

Front

A protein that switches off an operator. Binds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of those genes. Specific (i.e. it recognizes and binds only the operator of a particular operon. Binding to operators is reversible.

Back

Mating Bridge

Front

Results from the connection of two bacterium via sex pili during conjunction. Provides an avenue for DNA transfer.

Back

Cyclic AMP (cAMP) in E. coli

Front

A small organic molecule that accumulates when glucose is scarce in E. coli cells. Can bind to CAP, causing it to assume its active shape and allows it to bind to a specific site at the upstream end of the promotor, which directly stimulates gene expression--positive gene regulation.

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