Unit III-Organisms and Organ Systems

Chapters 19, 27, 30, 41, 42, 43, 44, 45, 46, 48, 49, and 50

Pathogens

Agents that cause disease symptoms in their hosts.

Viruses

Small infectious particles that consist of nucleic acid enclosed in a protein coat.

Host range

The number of species and cell types that can be infected by a particular virus or viroid.

Capsid

A protein coat that encloses a nuclear genome consisting of one or more molecules of nucleic acid, whether DNA or RNA.

Viral envelope

A lipid bilayer derived from the plasma membrane of the virus's host cell that is embedded with encoded spike glycoproteins. This layer protects the capsid of a virus.

Bacteriophages

Viruses with more complex protein coats and accessory structures that are used for anchoring and transferring viral nucleic acid to a bacterial host cell.

Viral Genome

The genetic material of a virus, consisting of either DNA or RNA.

1) Attachment
2) Entry
3) Integration
4) Synthesis of Viral Components
5) Viral Assembly
6) Release

What are the six stages of the viral reproductive cycle?

Attachment

The first step of the viral reproductive cycle in which the virus binds to the surface of the host cell. The manner in which this step occurs depends on how viral proteins recognize and bind to specific molecules on the host cell's surface.

Entry

The second step of the viral reproductive cycle in which the viral genome enters the host cell.

From there, one or several viral genes are expressed by host cell enzymes and ribosomes.

Finally, to end this stage, the virus can begin synthesizing viral components or begin the next stage of the cycle.

Integration

The third step of the viral reproductive cycle in which the viral genome is inserted into the host's chromosomal DNA, which is first cut by a viral enzyme called integrase.

Integrase

An enzyme viruses capable of integration carry so that the host's chromosomal DNA can be cut to make room for the viral genome.

Prophage

The phage DNA once integrated into the bacterial host's DNA.

Reverse transcriptase

A viral enzyme that transforms RNA from an RNA virus into a complementary DNA strand that can be transcribed into viral double stranded DNA.

This enables the virus to incorporate its genome into the bacterial genome.

Provirus

Viral DNA that has integrated itself into a chromosome of a eukaryotic host cell.

Retroviruses

An RNA virus that utilizes reverse transcription to produce viral DNA that can be integrated into a chromosome of the host cell.

Synthesis

In the fourth stage of the viral reproductive cycle, host cell enzymes like DNA polymerase make many copies of the phage DNA and transcribes those copies into mRNA.

Assembly

The fifth stage of the viral reproductive cycle in which viruses self-assemble their viral components.

Release

This is the final stage of the viral reproductive cycle in which new viruses are released from the host cell so that they can infect others.

Latency

What occurs when a prophage or provirus is inactive for a period of time after integration into the host's genome.

Lysogenic cycle

A type of viral reproductive cycle in which viral DNA is integrated into that of a bacterium, replicated, and excised.

Lytic Cycle

A type of viral reproductive cycle in which the production and release of new viruses lyses the host cell.

This cycle basically consists of the final three stages of the reproductive cycle: synthesis, assembly, and release.

Episomes

Genetic elements that replicate independently but occasionally integrate into host DNA.

These are also plasmids that can integrate into the bacterial chromosome

Human Immunodeficiency Virus (HIV)

The causative agent of acquired immune deficiency syndrome (AIDS). It destroys T cells, or white blood cells that play an important role in the immune system. With a destroyed immune system, one can develop AIDS.

Viroids

Viruses composed solely of a single-stranded circular RNA molecule a few hundred nucleotides in length, which infect plant cells.

Prions

Viruses composed entirely of protein that converts normal proteins in host cells into their abnormal form.

Nucleoid

A region with a bacterial cell that contains the tightly packed bacterial chromosome.

Loop domains

Chromosomal segments that are folded into loops in order to condense bacterial DNA.

DNA supercoiling

What occurs when topoisomerases twist DNA and control the compaction of DNA.

Plasmids

Small, circular pieces of DNA that exist independently of the bacterial chromosome.

Resistance plasmids (R factors)

Plasmids that confer resistance to antibiotics and other types of toxins.

Degradative plasmids

Plasmids that enable the bacterium to digest and utilize an unusual substance.

Virulence plasmids

Plasmids that turn a bacterium into a pathogenic strain.

Fertility plasmids (F factors)

Plasmids that allow bacterium to mate.

Binary Fission

The means by which bacteria reproduce.

Conjugation

Direct physical interaction transfers genetic material from donor to recipient cell.

Transformation

DNA released from a dead bacterium into the environment is taken up by another bacterium.

Transduction

A virus transfers genetic information from one bacterium to another.

Sex pili

Made by F factor plasmids that connect two cells and draw them closer together so that genetic information can be transferred between the two through conjugation.

Archaea

Prokaryotic organisms who share a common ancestry with eukarya due to common features such as ribosomal proteins, RNA polymerases, and a cytoplasm.

They do, however, have unique lipid membranes that give them resilience to extreme heat, salinity, and pH. Due to this, they can live in moderate conditions or more intense environments.

Extremophiles

Organisms that can occupy extreme conditions, such as high salt content, acidity, high methane levels, and high temperatures.

Bacteria

Prokaryotic organisms that mainly favor moderate conditions and form symbiotic relationships with many eukaryotes.

Cyanobacteria

Abundant, photosynthetic bacteria that are the only prokaryotes who generate oxygen as a result of photosynthesis.

They are named for their blue-green color, which is easily seen when large blooms of this bacteria form on the surface of lakes.

Proteobacteria

Bacteria possessing amazing diversity of form and metabolism.

There are five major subgroups of this bacteria.

1) α-proteobacteria
2) β-proteobacteria
3) γ-proteobacteria
4) δ -proteobacteria
5) ε –proteobacteria

What are the five major subgroups of proteobacteria?

Horizontal gene transfer

The process in which an organism receives genetic material from another organism without being the offspring of that organism.

About 17% of the genes in human gut bacteria E.coli were transferred using this method, while 80% of prokaryotic genes have been involved in this process at some time or another.

Mitochondria and plastids

What two structures arose from proteobacteria and cyanobacteria?

1-5 μm

What is the average diameter of bacteria and archaea?

This small diameter means less can fit in the cell, but accounts for faster cell division.

Thylakoids

Ingrowths of plasma membrane that increase surface area for photosynthesis.

Magnetosomes

Magnetite crystals that when lined up, act like a compass for bacteria and archaea living in low-oxygen habitats

Gas Vesicles

Adjust buoyancy of bacteria and archaea.

Nucleus-like bodies

Result from plasma membrane invaginations.

Cocci

Spherical shaped bacteria

Bacilli

Rod-shaped bacteria

Vibrios

Comma-shaped bacteria

Spirochaetes

Flexible, spiral-shaped bacteria

Spirilli

Rigid, spiral-shaped bacteria.

Glycocalyx

Slimy mucilage composed of polysaccharides and/or proteins that is secreted by cells to fold bacterial colonies together and evade host defenses.

Cell wall

Most bacteria have a ( ) in addition to their plasma membrane to protect against attack, maintain their shape, and avoid lysis

Gram-positive bacteria

Bacteria with a relatively thick peptidoglycan layer.

More vulnerable to antibiotics like penicillin.

Gram-negative bacteria

Bacteria with a thinner peptidoglycan layer and a thin outer envelope of lipopolysaccharides.

More resistant to antibiotics like penicillin.

Bacterial Flagella

Basically serves as a motor attached to the bacteria that enables it to "swim" through its environment.

Pili

Threadlike structures on the surface of a bacterial cell that twitch or glide across surfaces.

Akinetes

These thick-walled, food-filled structures develop when winter approaches for aquatic filamentous cyanobacteria to survive the winter and produce new filaments in the spring.

Endospores

A structure with a touch protein coat and long dormant span that stores DNA and carries it along to be taken up by another bacterium when the original bacterium dies.

Autotrophs

Produce all or most of their own organic compounds from inorganic sources.

Photoautotroph

Uses light as an energy source for the synthesis of organic compounds from CO2 or H2S.

Chemoautotroph

Use energy obtained from chemical modification of inorganic compounds to synthesize organic compounds.

Heterotrophs

Organisms that require at least one organic compound.

Photoheterotroph

Able to use light energy to make ATP but they must take in organic compounds from the environment.

Chemoheterotroph

Must obtain organic molecules for both energy and carbon source.

Obligate Aerobes

Require oxygen

Facultative Aerobes

Can use oxygen or not.

Obligate anaerobes

Cannot tolerate oxygen

Aerotolerant anaerobes

Do not use oxygen but are not poisoned by it.

Diazotrophs

Conduct nitrogen fixation.

Heterocysts

Specialized cells for nitrogen fixation in cyanobacteria.

Koch's Postulates

A set of criteria used in identifying whether an organism is the cause of a particular disease.

Microbes

Millions of species of archaea, bacteria, protists, and fungi that play important ecological roles worldwide.

Biomes

Major types of habitat characterized by distinctive life forms.

Microbiomes

A particular assemblage of microbes and genes that occurs in a defined environment.

Amplicon analysis

A method in which scientists can identify unknown microbial species from a database of known microbial organisms.

You first extract DNA from a sample and use polymerase chain reaction to create amplicons of rDNA regions. After DNA sequencing, you can compare those sequences to references of known species in a database to identify new species.

Metagenome

The genomes of all the organisms present in a sample

Whole Metagenomic Sequencing (WMS)

In this process, you obtain the base sequences of all the DNA present in a sample. A computer is used to identify place where the ends of DNA fragments have the same DNA sequences. The overlapping regions are then used to align the DNA fragments into contiguous sequences, or contigs.

Metatranscriptome

Collection of all the mRNAs present in an environmental sample.

Metaproteome

All the proteins produced by the members of a microbiome

Meta-metabolome

Collections of information about all the types and abundances of molecules produced by metabolism of the organisms in a microbiome.

Cryosphere

Includes sea ice, glaciers, and snow.

Holobiont

Combination of host organism and its microbiome

Hologenome

The host and microbiome genomes together

Lichen structure

Photosynthetic green algae or cyanobacteria typically covers up the rest of the lichen, known as the fungal hyphae, in a distinct layer close to the lichen's surface.

Crustose Lichen

Flat lichen that adhere tightly to an underlying surface.

Fruticose Lichen

Lichen that grows upright or hangs down from tree branches

Microbiota

The organisms in a microbiome

Mutualism

Both organisms benefit

Symbiosis

The relationships between organisms that live together.

Commensalism

One organism benefits, while the other is not harmed

Parasitism

One organism benefits and the other is harmed.

Probiotics

Live microorganisms that are believed to provide health benefits when consumed.

Tissue

An association of many cells that have a similar structure and function.