Unit 1

• The four forms of viral genomes are double-stranded DNA, single-stranded DNA, double-stranded RNA, and single-stranded RNA
• Viruses vary in shape, genome composition, and whether they have an envelope or not. All viruses have a capsid(protein shell) that surrounds genetic material(DNA and RNA)
• The protein shell enclosing the viral genome is called a capsid. Depending on the type of virus, the capsid may be rod-shaped, polyhedral, or more complex in shape. Capsids are built from a large number of protein subunits called capsomeres
• The envelopes help the virus infect their host
• Viruses usually identify host cells by a "lock-and-key" fit between viral surface glycoproteins and specific receptor molecules on the outside of host cells
• Viruses are obligate intracellular parasites. Viruses can replicate only within a host cell
• Host range refers to the number of species that a virus can infect. Viruses with broad host ranges are generalists and infect numerous species. Viruses with narrow host ranges are specialist and only infect one or two species. They may also only infect a particular tissue type within a single species(HIV). The correct match (lock and key) of the viral glycoproteins on the surface of the virus and the receptor proteins of the host cell.
• The host cell provides the nucleotides for making viral nucleic acids, as well as enzymes, ribosomes, tRNAs, amino acids, ATP, and other components needed for making the viral proteins
• Once the capsid proteins(capsomeres) and the genetic material has been made, new viruses are assembled by the proteins self-assembling spontaneously.
• The phage DNA enters the host cell. After the bacteriophage binds to a specific receptor on the outer surface of the host cell, the sheath of the tail contracts, injecting the DNA into the cell and leaving an empty capsid outside
• The lytic mode of bacteriophage reproduction results in the release of new phages by lysis(and death) of the host cell
• The lysogenic mode of bacteriophage reproduction, the viral genome becomes incorporated into the bacterial host chromosome as a prophage, is replicated along with the chromosome, and does not kill the host
• A retrovirus is an RNA virus that replicates by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses
• Vaccines are a harmless variant or derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen. They prompt the body to develop an immune response to a weakened form of the virus, which prepares you to fight off the full virus if/when you are exposed
• Most antiviral drugs resemble nucleosides and as a result interfere with viral nucleic acid synthesis
• Mad cow disease and chronic wasting disease are both caused by prions. Prions are infectious proteins that appear to cause a number of degenerative brain diseases in various animal species. Prions are most likely transmitted in food. They cause misfolding of proteins, particularly in the brain. The infection results in slow damage, but ultimately leads to death.
• The incubation period of prions can last for decades. They infect the animal brain, causing diseases such as mad cow. There are no known cures for prion-caused diseases. Since prions are not living removing or managing them is very difficult
• Viruses are not considered to be alive by scientists because they cannot replicate or transcribe DNA without a host cell. They do not contain many of the components of living cells, like cytoplasm or a membrane. They do not exhibit some of the characteristics of living things, such as energy processing or homeostasis.
• Smallpox has been eradicated due to vaccines
• The chemical reactions necessary to support life require small molecules that contain carbon and hydrogen. The abiotic synthesis of small organic molecules, such as amino acids and nitrogenous bases, could occur within the environment of earth before life
• The abiotic synthesis of small organic molecules, such as amino acids and nitrogenous bases. The joining of these small molecules into macromolecules, such as proteins and nucleic acids. The packaging of these molecules into protocells, droplets with membranes that maintained an internal chemistry different from that of their surroundings. The origin of self-replicating molecules that eventually made inheritance possible.
• The first organisms on earth were bacteria. Life began ~3.5 billion years ago
• Bacteria and archaea are examples of prokaryotes
• Bacteria that cause disease are known as pathogens. They produce toxins called endotoxins and exotoxins. Endotoxins are found in gram-negative bacteria. Endotoxins are lipopolysaccharides and thus structurally integral to the bacterium, whereas exotoxins are proteins secreted by living bacteria
• The first atmosphere had little oxygen and was likely thick with water vapor, along with compounds released by volcanic eruptions, such as nitrogen and its oxides, carbon dioxide, methane, ammonia and hydrogen. As Earth cooled, the water vapor condensed into oceans, and much of the hydrogen escaped into space
• Eukaryotes have organelles and prokaryotes do not
• The RNA world hypothesis says the first genetic material was RNA not DNA. Scientists think this because RNA molecules can self-replicate. RNA molecules can fold into several distinct 3D shapes which help their enzymatic activity. RNA has catalytic properties
• In general, bacteria come in three shapes: cocci(spherical), bacilli(rod-shaped), and spiral
• Prokaryotes are probably the most abundant organisms on the planet. Prokaryotes are the primary decomposers on earth. They recycle soil nutrients and break down organic matter which can then be used again by plants. If prokaryotes went extinct, dead organic material would build up and nothing would decompose. Most of life would eventually go extinct
• Bacteria and Archaea are genetically diverse. They have short generation times. So even with rare mutations, they accumulate quickly in the population. They can also share DNA
• Some bacteria have additional loops of DNA called plasmids. In the process of conjugation, the donor cell extends a pilus that attaches to a recipient cell, a key first step in the transfer of DNA. The pilus then retracts, pulling the two cells together. The cells then form a "mating bridge", through which the donor may transfer DNA to the recipient.
• The sex pilus is a flexible tube of protein subunits that attaches from a donor cell to a recipient cell and retracts, pulling the cells together during conjugation.
• The F factor is the DNA segment that confers the ability to form pili for conjugation and associated functions required for the transfer of DNA from donor to recipient. The F factor may exist as a plasmid or be integrated into the bacterial chromosomed. The F Factor is necessary for the formation of the sex pilus. R plasmids are bacterial plasmids carrying genes that confer resistance to certain antibiotics
• Conjugation involving plasmids with R and F factors, can result in rapid spread of antibiotic resistance in bacteria
• Cyanobacteria first evolved oxygenic photosynthesis. The accumulating oxygen gas (O2 ) probably doomed many prokaryotic groups by attacking chemical bonds and damaging cells. Bacteria were anaerobic at the time. It also may have resulted in snowball earth
• Extreme halophiles are found in very salty environments
• Extreme thermophiles are found in very hot environments such as volcanic springs
• Methanogens are archaea that release methane as a by-product of their unique ways of obtaining energy
• Archaea are more closely related to eukaryotes than bacteria
• The structures of plasma membrane, cytoplasm, DNA and ribosomes are common among bacteria, archaea, and eukaryote