Exam 2 (Ch. 11-13)

List three characteristics that differentiate Archaea and Bacteria.

-Archaea lack true peptidoglycan in their cell walls. -Their cytoplasmic membrane lipids have branched or ring form hydrocarbon chains, whereas bacterial membrane lipids have straight chains. -The initial amino acid in their polypeptide chains, coded by the AUG start codon, is methionine (as in eukaryotes and in contrast to the N-formylmethionine used by bacteria).

Describe component of prions and explain how they cause disease.

A prion is composed of abnormally folded protein that causes progressive neurodegenerative conditions, with two of the most notable being mad cow disease and Creutzfeldt-Jakob disease seen in humans. It's a type of protein that can trigger normal proteins in the brain to fold abnormally. Prion diseases can affect both humans and animals and are sometimes spread to humans by infected meat products.

Describe characteristics of a virus that distinguish them from cellular organisms.

A virus is a minuscule, acellular, infectious agent having one or several pieces of nucleic acid - either DNA or RNA. Being acellular, viruses have no cytoplasmic membrane. They also lack cytosol and functional organelles. A virus exists in an extracellular state and an intracellular state.

Describe general characteristics of algae including their type of photosynthesis, why they aren't classified as plants and which alga is the major source of oxygen on Earth.

Algae refers to eukaryotic photoautotrophic organisms that have sexual reproductive structures in which every cell becomes a gamete. Algae can be unicellular or colonial. Historically, taxonomists have used differences in photosynthetic pigments, storage products, and cell wall composition to classify algae into several groups that are named for the colors of their photosynthetic pigments: green algae, red algae, brown algae, golden algae, and yellow-green algae. Cyanobacteria, or blue-green algae, conduct photosynthesis: using sunshine, water and carbon dioxide to produce carbohydrates and oxygen.

Describe the components of a viral nucleocapsid: the possible shape of the capsid and the possible types of genetic material contained within.

All viruses contain the following two components: 1. a nucleic acid genome and 2. a protein capsid that covers the genome. Together this is called the nucleocapsid.

Describe the advantage and disadvantage of naked vs. enveloped virions.

An envelope provides some protection to the virus from the immune system; after all, enveloped viruses are carrying membrane from host cells and thus are more chemically similar to the host. However, membranes are more susceptible to detergents, alcohol, and drying out, so enveloped viruses are more fragile than naked ones. Naked viruses are more stable outside a host than are enveloped viruses, but the naked capsid exposes more viral proteins to the environment and are thus more susceptible to recognition and attack by the immune system once inside a host.

Compare budding vs. lysis processes for viral exit of animal viruses from host cells.

Budding is a method which viruses use to exit the cell. "Budding" through the cell envelope, in effect using the cell's membrane for the virus itself is most effective for viruses that need an envelope in the first place. These include enveloped viruses such as HSV, SARS, or smallpox. Prior to budding, the virus may put its own receptor onto the surface of the cell in preparation for the virus to bud through, forming an envelope with the viral receptors already on it. This process will slowly use up the cell membrane and eventually lead to the demise of the cell. This is also how antiviral responses are able to detect virus infected cells. Lysis releases the virus from the infected cell by bursting its membrane and kills the cell.

Describe the role cancer plays in disrupting the cell cycle, possibly resulting in cancer.

Cancers rob normal cells of space and nutrients; in some kinds of cancers, malignant cells derange the function of the affected tissues, until eventually the body can no longer withstand the loss of normal function and dies. Several theories have been proposed to explain the role viruses play in the development of cancers. These theories revolve around the presence of protooncogenes - genes that promote cell growth and division. As long as protooncogenes are appropriately expressed under controlled conditions, no cancer results. However, activity of oncogenes (name when they are active) or inactivation of oncogene repressors can cause cancer to develop.

Describe the significance of the other Gram-negative bacterial genera: Chlamydia, Treponema, Borrelia, and Bacteroides.

Chlamydias are Gram-negative cocci typified by the genus Chlamydia; they cause neonatal blindness, pneumonia, and a STD. Spirochetes are flexible, helical bacteria that live in diverse environments. The pathogens Treponema (syphilis) and Borrelia (Lyme disease) are important spirochetes. Bacteroids include Bacteroides, an obligate anaerobic rod that inhabits the digestive tract, and Cytophaga, an aerobic rod that degrades wood and raw sewage.

Explain the significance of cyanobacteria in regard to evolution.

Cyanobacteria are Gram-negative phototrophs that vary greatly in shape, size, and method of reproduction. Some filamentous cyanobacteria are motile, moving along surfaces by gliding. Cyanobacteria generally reproduce by binary fission, with some species also reproducing by motile fragments or by thick-walled spores called akinetes.

List three diseases caused by latent viruses.

HIV, AIDS, herpes virus, hepatitis B, chicken pox

Define haploid, diploid, mitosis, cytokinesis, coenocyte, and schizogony.

Haploid - having a single copy of each chromosome. Diploid - having two copies of each chromosome. Mitosis - type of nuclear division. Begins after the cell has duplicated its DNA such that there are two exact DNA copies , the cell partitions its replicated DNA equally between two nuclei. Cytokinesis - cytoplasmic division, typically occurs either during or after nuclear divison. Coenocyte - multinucleate cells resulting from repeated mitoses but postponed or no cytokinesis. Schizogony - some microbes undergo multiple mitoses by schizogony to form a multinucleate schizont, which then undergoes cytokinesis to produce numerous daughter cells.

Differentiate between mitosis and meiosis including stages at which: DNA replication occurs, homologous chromosomes line up, crossing over occurs, and sister chromatids separate.

In contrast to mitosis, meiosis is nuclear division that involves the partitioning of chromatids into four nuclei such that each nucleus receives only half the original amount of DNA. Meiosis occurs in two stages known as meiosis I and meiosis II. As with mitosis, DNA replication during interphase results in pairs of identical chromatids joined at centromeres, forming chromosomes. But in meiosis I, additional pairing occurs: homologous chromosomes. Once tetrads have formed, the homologous chromosomes exchange sections of DNA in a random fashion via a process called crossing over. In the anaphase of mitosis, the sister chromatids separate and crawl along the microtubules toward opposite poles of the spindle. In contrast to mitotic anaphase, sister chromatids remain attached to one another.

Describe medical and environmental significance of fungi.

In response to environmental conditions such as temp. or carbon dioxide concentration, some fungi produce both yeastlike and moldlike shapes; fungi that produce two types of body shapes are said to be dimorphic (two shaped). Many medically important fungi are thermally dimorphic; that is, they change growth habits in response to the temp. in their immediate vicinity. Such fungi include Histoplasma capsulatum (causes a respiratory disease called histoplasmosis), and Coccidioides immitis which causes a flulike disease called coccidioidomycosis.

Describe three ways to evaluate virus cultures: plaque assay, chicken egg culture, cell (tissue) culture.

In the laboratory, viruses must be cultured inside mature organisms, in embryonated chicken eggs, or in cell cultures because viruses can't metabolize or replicate alone. When a mixture of bacteria and phages is grown on an agar plate, bacteria infected with phages lyse, producing clear areas called plaques on the bacterial lawn. A technique called plaque assay is used to estimate phage numbers. Viruses can be grown in two types of cell cultures. Whereas diploid cell cultures last about 100 generations, continuous cell cultures, derived from cancer cells, last longer. Chicken eggs that have been fertilized and contain a developing embryo are most suitable for culturing viruses. Embryonic tissues (called membranes, shouldn't be confused with cellular membranes) provide ideal inoculation sites for growing viruses.

List four types of insect vectors and a disease transmitted by a flea.

Insect vectors include: fleas; lice, bloodsucking flies, including mosquitoes; and kissing bugs. The most significant microbial disease transmitted by fleas is plague, carried by rat fleas.

Describe lichens; explain their environmental and evolutionary significance.

Lichens are economically and environmentally important organisms composed of fungi living in partnerships and photosynthetic microbes, either green algae or cyanobacteria. Lichens create soil from weathered rocks and lichens containing nitrogen-fixing cyanobacteria provide significant amounts of usable nitrogen to nutrient poor environments. Many animals eat lichens (reindeer and caribou) Birds use lichens for nesting materials, and some insects camouflage themselves with bits of living lichen.

Differentiate between the three domains of living things.

Living things are now classified into three domains - Archaea, Bacteria, and Eukarya - based largely on genetic similarities.

Differentiate between low G+C and high G+C gram positive bacteria including significance of the following bacterial genera: Clostridium, Mycoplasma, Bacillus, Listeria, Lactobacillus, Streptococcus, Corynebacterium, and Mycobacterium.

Low G + C Gram-positive bacilli and cocci important to human health and industry include Bacillus (which contains species that cause anthrax and food poisoning and includes beneficial bacteria that produce Bt toxin), Listeria (which causes bacteremia and meningitis), Lactobacillus (used to produce yogurt and pickles), Streptococcus, Enterococcus, and Staphylococcus, each of which causes a number of human diseases. High G +C Gram-positive bacteria (Corynebacterium, Mycobacterium, and actinomycetes) are classified in phylum Actinobacteria.

Differentiate between molds and yeasts.

Molds are multicellular with long filaments, reproduce sexually and asexually. Yeasts are unicellular and reproduce asexually by budding.

Define neoplasia, metastasis, tumor, and cancer.

Neoplasia - uncontrolled cellular reproduction in a multicellular animal. Metastasis - describes the spreading of malignant tumors. Environmental factors or oncogenic viruses may cause neoplasia. Tumor - A mass of neoplastic cells. May be relatively harmless (benign tumor) or invasive (malignant tumor). Cancer - Malignant tumors are also called cancer.

Describe the significance of the following genera of Proteobacteria: Betaproteobacteria - Neisseria, Bordetella, and Burkholderia; gamma-Enterobacteriacea and Pseudomonas; and epsilon-Campylobacter and Heliobacter.

Phylum Proteobacteria is a very large group of Gram-negative bacteria divided into five classes - the alpha-, beta-, gamma-, delta-, and epsilonproteobacteria. The betaproteobacteria include the nitrifying Nitrosomonas and pathogenic species such as Neisseria (gonorrhea), Bordetella (whooping cough), and Burkholderia (which colonizes the lungs of cystic fibrosis patients) The gammaproteobacteria constitute the largest class of proteobacteria; they include purple sulfur bacteria, intracellular pathogens, methane oxidizers, facultative anaerobes that utilize glycolysis and the pentose phosphate pathway, and pseudomonads. Pseudomonads utilize the Entner-Doudoroff and pentose phosphate pathways for catabolism of glucose. The epsilonproteobacteria include some important human pathogens, including Campylobacter and Heliobacter.

Describe four strategies used by RNA viruses to direct the host cell to synthesize viral proteins and produce viral RNA.

Positive-sense ssRNA Viruses - some ssRNA viruses have positive-sense single stranded RNA (+ssRNA), which can be directly translated by ribosomes to synthesize protein. From the +ssRNA, complementary negative-sense single stranded RNA (-ssRNA) is transcribed to serve as a template for more +ssRNA. Retroviruses - such as HIV, are +ssRNA viruses that carry reverse transcriptase, which transcribes DNA from RNA. This reverse process (DNA transcribed from RNA) is reflected in the name retrovirus. Negative-sense single stranded RNA (-ssRNA) viruses carry an RNA-dependent RNA transcriptase for transcribing mRNA from the -ssRNA genome, and the mRNA is translated to protein. Transcription of RNA from RNA does not occur in cells. dsRNA viruses - the positive strand of RNA functions as mRNA, and each strand functions as a template for an RNA complement.

Describe common types of reproduction in prokaryotic cells.

Prokaryotes reproduce asexually by binary fission, snapping division (a type of binary fission), spore formation, and budding.

Describe characteristics of protozoa that differentiate the group from other eukaryotes; differentiate the trophozooite and cyst stages.

Protozoa are eukaryotic, unicellular organisms that lack cell walls. Most protozoa are chemoheterotrophs , getting their energy from chemicals and their carbon from other organisms. A mobile trophozoite is the feeding stage of a typical protozoan. Some protozoa form a cyst, a resting stage that is resilient to environmental changes.

Describe significance of the following protozoan genera: parabasala— Trichomonas, diplomonadida— Giardia, euglenozoa— Trypanosoma, and Leishmania, alveolates— Plasmodium, Cryptosporidium, Toxoplasma (apicomplexans), Dinoflagellates, and amoebozoa- Naegleria and Acanthamoeba and Entamoeba

Protozoa may be classified into six groups: parabasalids, diplomonads, euglenozoa, alveolates, rhizaria, and amoebozoa. Parabasalids (Trichomonas) are characterized by a Golgi body-like structure called a parabasal body. Members of the Diplomonadida lack mitochondria, Golgi bodies, and peroxisomes. Unicellular flagellated euglenids are euglenozoa that store food as paramylon, lack cell walls, and have eyespots used in positive phototaxis. Because they exhibit characteristics of both animals and plants, euglenids are a taxonomic problem. A kinetoplastid is a euglenozoan with a single, large, apical mitochondrion that contains a kinetoplast. Alveolates, with cavities called alveoli beneath their cell surfaces, include ciliate alveolates (characterized by cilia) , apicomplexans (all of which are pathogenic) and dinoflagellates (responsible for red tides). Protozoa that move and feed with pseudopods are amoebas, which are classified into two kingdoms: Rhizaria and Amoebozoa.

Describe the role of endospores and list two genera of bacteria that produce endospores.

The Gram-positive bacteria Bacillus and Clostridium produce endospores, which are important for several reasons, including their durability and potential pathogenicity. Endospores constitute a defensive strategy: They are stable resting stages that barely metabolize in hostile or unfavorable conditions, and they germinate when conditions improve.

Explain the significance of the term "deeply branching bacteria".

The deeply branching bacteria are so named because their rRNA sequences and growth characteristics lead scientists to conclude that these organisms are similar to the earliest bacteria, that is, they appear to have branched off the "tree of life" at an early stage. For example, the deeply branching bacteria are autotrophic, and early organisms must have been autotrophs because heterotrophs by definition must derive their carbon from autotrophs.

List the significant characteristics of extremophiles and methanogens.

The domain Archaea includes extremophiles, microbes that require extreme conditions of temperature, pH, pressure, and/or salinity to survive. Methanogens (phylum Euryarchaeota) are obligate anaerobes that produce methane gas and are useful in sewage treatment.

Describe general components of a virus; describe the function and source of a viral envelope, if one is present.

The genomes of viruses include either DNA or RNA. Viral genomes may be dsDNA, ssDNA, dsRNA, or ssRNA. They may exist as linear or circular and singular or multiple molecules of nucleic acid, depending on the type of virus. Viruses are specific for their hosts' cells because viral attachment molecules are complementary in shape to specific receptor molecules on the host's cells.

Describe the steps and advantages/disadvantages of lytic vs. lysogenic replication of bacteriophages.

The replication cycle of a virus usually results in the death and lysis of the host cell. Because the cell undergoes lysis near the end of the cycle, this type of replication is called a lytic replication cycle. The lytic replication cycle consists of the following five stages: -Attachment of the virion to the host cell. -Entry of the virion or its genome into the host cell. -Synthesis of new nucleic acids and viral proteins by the host cell's enzymes and ribosomes. -Assembly of new virions within the host cell. -Release of the new virions from the host cell. Not all viruses follow the lytic pattern of phage T4, some bacteriophages have a modified replication cycle in which infected host cells grow and reproduce normally for many generations before they lyse. Such a replication cycle is called a lysogenic replication cycle or lysogeny and the phages are called temperate phages. Another difference between a lysogenic cycle and a lytic cycle is that the prophage inserts into the DNA of the bacterium, becoming a physical part of the bacterial chromosome.

Describe three basic shapes of prokaryotic cells and list three other variations in cell shape; describe possible arrangement of bacterial cells

Three basic shapes of prokaryotic cells are spherical cocci, rod-shaped bacilli, and spirals. Spirals may be stiff (spirilla) or flexible (spirochetes). Other variations in shapes include vibrios (slightly curved rods), coccobacilli (intermediate to cocci and bacilli) and pleomorphic (variable shape and size). There are three basic shapes of bacteria: coccus, bacillus, and spiral. Based on planes of division, the coccus shape can appear in several distinct arrangements: diplococcus, streptococcus, tetrad, sarcina, and staphylococcus. The bacillus shape can appear as a single bacillus, a streptobacillus, or a coccobacillus.

List two types of arachnid vectors and name a disease transmitted by a tick.

Ticks and mites are arachnids - eight legged arthropods. Lyme disease is transmitted by a tick.

Describe three types of viral entry and uncoating in an animal cell.

Viral entry: Direct penetration - a process in which the viral capsid attaches and sinks into the cytoplasmic membrane, creating a pore through which the genome enters the cell, leaving the empty capsid on the surface. Membrane fusion - the viral envelope and the host's cytoplasmic membrane fuse, releasing the capsid into the cell's cytoplasm while leaving the envelope glycoproteins as part of the cell membrane. Endocytosis - most enveloped viruses and some naked viruses enter host cells by triggering endocytosis. Attachment of the virus to receptor molecules on the cell's surface stimulates the cell to endocytize the entire virus. Uncoating - a virus that penetrates a host cell with its capsid intact, the capsid must be removed to release the genome before replication of the virus can continue. Uncoating occurs by different means in different viruses; some viruses are uncoated within vesicles by cellular enzymes, whereas others are uncoated by enzymes within the cell's cytosol.

Describe viroids.

Viroids are small circular pieces of RNA with no capsid that infect and cause disease in plants. Similar pathogenic RNA molecules have been found in fungi.

Explain why viruses are usually host specific.

Viruses are host specific because they only can attach to and infect cells of certain organisms. The virus attacks the host cell by first attaching to a specific receptor site on the membrane of the host cell.

Describe two strategies used by DNA viruses to direct the host cell to synthesize viral proteins and produce viral DNA.

dsDNA viruses - the genome of most dsDNA viruses enters the nucleus of the host cell, where cellular enzymes replicate the viral genome in the same manner as they replicate the host DNA - using each strand of viral DNA as a template for its complement. Messenger RNA is transcribed from viral DNA in the nucleus and exported into the cytoplasm, where host ribosomes make capsomere proteins. Capsomeres then enter the nucleus, where new virions spontaneously assemble. ssDNA viruses - a human virus with a genome composed of single stranded DNA is a parvovirus. Cellular RNA polymerase synthesizes mRNA complementary to the viral ssDNA, and cellular ribosomes can then translate viral proteins. Cells don't have ssDNA, so synthesizing ssDNA viruses requires a unique form of DNA replication. This single stranded DNA is packaged into a viral capsid.