The Structure Growth Physiology and Genetics

The structure, growth, physiology, and genetics of prokaryotes and viruses Cell theory (BIO) • • History and development o Robert Hooke observed under a microscope what appeared to be cells. o German botanist Matthias Schleiden looked at all sorts of plants under a microscope and noticed all had the same microscopic structure. o German scientists Theodor Schwann looked all nervous systems of different animals and noticed all had similar structures that were these cells. o German physician and pathologist, Rudolph Virchow observed bacteria that divided and formed two bacteria that were identical = binary fission. o French scientist Louis Pasteur did a famous experiment known as the Swan-Neck Bottle experiment proved that all cells come from preexisting cells. Impact on biology o Proved that cells were the basic structural, functional, and biological unit of life and cells come from preexisting cells. Classification and Structure of Prokaryotic Cells (BIO) • Prokaryotic domains o Archaea ▪ Single-celled organisms that are visually similar to bacteria but contain genes and several metabolic pathways that are more similar to eukaryotes than bacteria. ▪ Considered extremophiles in that they were most commonly isolated from harsh environments with extremely high temperatures, high salinity, or no light. ▪ While some are photosynthetic, many are chemosynthetic and able to generate energy from inorganic compounds, including sulfur- and nitrogen-based compounds, such as ammonia ▪ Due to similarities to eukaryotes, it is hypothesized that eukaryotes and domain Archaea share a common origin. Both start translation with methionine, contain similar RNA polymerases, and associate their DNA with histones. However, Archaea contain a single circular chromosome, divide by binary fission or budding, and overall share a similar structure to bacteria. Interestingly, Archaea are resistant to many antibiotics. o Bacteria ▪ All bacteria contain a cell membrane and cytoplasm, and some have flagella or fimbriae (similar to cilia). Because bacteria and eukaryotes often share analogous structures, it can be difficult to develop medicines that target only bacteria. ▪ Bacterial flagella and eukaryotic flagella are distinct enough that scientists are able to develop antibacterial vaccines that specifically target bacterial flagella. Also, many antibiotics target the bacterial ribosome, which is significantly smaller than the eukaryotic ribosome. • Major classifications of bacteria by shape o Bacilli (rod-shaped) o Spirilli (spiral-shaped) o Cocci (spherical) • Lack of nuclear membrane and mitotic apparatus o Bacteria do not have a membrane-enclosed nucleus. Their genetic material is located in an irregular region called the nucleoid. Bacteria do not have spindles and asters that make up the eukaryotic mitotic apparatus. Instead, the prokaryotic cytoskeleton helps pull the replicated DNA apart. • Lack of typical eukaryotic organelles o Bacteria don’t have Golgi, ER, mitochondria, chloroplasts • • Presence of cell wall in bacteria o Bacterial cell wall is made of peptidoglycan, a polysaccharide-protein molecule. In contrast, plant cell wall is made of cellulose and fungi cell wall is made of chitin. Flagellar propulsion, mechanism o Bacterial flagella is made of flagellin. In contrast, eukaryotic flagella is made of microtubules. o The mechanism of the bacterial flagella is rotation. A rotor at the base of the flagella drives the rotation, powered by a proton or sodium gradient. (Compare this to eukaryotic flagella, which is powered directly by ATP) Growth and Physiology of Prokaryotic Cells (BIO) • Reproduction by fission o DNA replicates o Replicated DNAs separate by attached to the cell membrane as the cell elongates (in contrast to mitosis, no spindle fibers needed) o Cytokinesis divides the parent cell into two daughter cells • High degree of genetic adaptability, acquisition of antibiotic resistance o Mutation o Transformation: bacteria take in plasmids and DNA fragments and integrates them into the genome o Transduction: bacteriophages undergoing lysogenic life cycle incorporate the viral DNA into the bacterial genome o Conjugation: bacteria transfer DNA between one another through the sex pilus • Exponential growth o Bacterial growth starts off being exponential because of the nature of binary fission. Later, when food becomes short, and it gets crowded, growth slows and eventually plateaus • Existence of anaerobic and aerobic variants o Obligate aerobe = must have oxygen for growth o Obligate anaerobe = dies when oxygen is present o Facultative anaerobe = doesn’t need oxygen for growth, but grows better with oxygen • Parasitic and symbiotic o Parasitic = bacteria benefits at the expense of the host. Disease causing bacteria are examples of parasitic relationships. o Mutualistic = both bacteria and host benefits. For example, the E. coli in your gut; the natural flora on your skin o Commensalistic = one benefits while the other has no effect • Chemotaxis o Movement in a direction corresponding to a gradient of increasing or decreasing concentration of a particular substance/chemical Genetics of Prokaryotic Cells (BIO) • Existence of plasmids, extragenomic DNA o Plasmids are double stranded DNA o A plasmid can exist and replicate independently of the genomic DNA, or be integrated into it o Plasmids are inherited o Plasmids are not essential for growth and reproduction in the wild • Transformation: incorporation into bacterial genome of DNA fragments from external medium o When a bacterium dies, it lyses and spills many DNA fragments into the environment o Another bacteria encounters these DNA fragments, takes them in, and integrates them into its own genome o If the DNA fragments contained an antibiotic resistant gene, then the transformation just made the bacteria antibiotic resistant • • Conjugation o Transfers genetic material between bacteria via a pillus o A bacterium able to make the pillus (F+) has a plasmid that contains the pillus genes o F+ bacteria can transfer the plasmid to an F-bacteria o Conjugation can also transfer some genomic DNA (because F+ plasmid can integrate into the chromosome) Transposons (also present in eukaryotic cells) o They are a heterogeneous class of genetic elements that can insert at new locations on chromosomes. Classified into three major groups: ▪ Class I, retrotransposons; Class II, DNA transposons; Class III, miniature inverted-repeat transposable elements o Transposons have direct repeat flanking sequences that are not part of the transposons, and terminal inverted repeats that are part of the transposons. DNA transposons translocate via a cutand-paste mechanism, retrotransposons translocate via a copy-and-paste mechanism. o Transposons cause significant changes in genome organization and gene sequence. They can give insertion/deletion mutant and chromosomal inversion mutant. They are used as tools in gene delivery or targeted mutation. Virus Structure (BIO) • General structural characteristics (nucleic acid and protein, enveloped and non-enveloped) o Nucleic acid can be DNA or RNA, single stranded or double stranded o Protein coat covers the nucleic acid o Some viruses have an envelope derived from the host’s cell membrane, while others lack it (nonenveloped) ▪ Enveloped viruses bud off the host’s membrane ▪ Non-enveloped viruses cause the host to burst to release viral particles o Smaller than bacteria • Lack organelles and nucleus o Viruses don’t have any organelles or a nucleus. The genetic material is simply packed inside a protein coat. • Structural aspects of typical bacteriophage o Head stores genetic material o Sheath provides a passageway for genetic material to be injected into the host bacteria o Tail fibers attach to the host bacteria • Genomic content - RNA or DNA o Viruses can contain either RNA or DNA as their genomic content o Out of the RNA viruses, those that convert their genome into DNA inside their host are called retroviruses • Size relative to bacteria and eukaryotic cells o Viruses are roughly 100 times smaller than bacteria, and 1000 times smaller than eukaryotic cells Viral Life Cycle (BIO) • Self-replicating biological units that must reproduce within specific host cell o Viruses cannot replicate by themselves. They depend on the host’s replication organelles to replicate. The host’s ribosomes will make the necessary protein coats and polymerases that replicate the viral genetic material. Retroviruses contain their own reverse polymerase to convert RNA to DNA before the host’s polymerases take over • Generalized phage and animal virus life cycles o Attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic material o Use of host synthetic mechanism to replicate viral components ▪ • • • Host’s ribosomes synthesize the necessary enzymes. Host’s ATP provides necessary energy. The host also provides the raw materials such as nucleotides and amino acids. o Self-assembly and release of new viral particles ▪ The coat proteins and viral genetic material will assemble into viral particles by themselves Transduction: transfer of genetic material by viruses o 1. Virus infects cell: host DNA degraded into fragments, viral DNA takes over control o 2. Host DNA fragment gets packed into virus progeny by accide nt o 3. Virus progeny infects another cell, injects previous host’s DNA fragment o 4. Fragment enters cell, finds its homologous counterpart, and crossover Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV o 1. Retrovirus enters the host o 2. Viral reverse transcriptase converts viral RNA genome into double-stranded DNA o 3. Virally encoded enzyme, called integrase, adds in viral DNA into the host’s genome at a random place o 4. When the host replicates, the viral DNA gets replicated also Prions and viroids: subviral particles o Viroids are smaller than viruses because they’re only made of a single strand of circular RNA. Before, they were only found to infect plants. Today, they have been found in humans, in the case of Hepatitis D. ▪ It’s thought to be catalytic RNA, meaning it can make or break covalent bonds. It can self-cleave to create more viroids. Don’t confuse with virions which are whole viruses. o Prions have no genetic material, no DNA or RNA. They are only made of proteins. A prion protein tends to be in a beta-sheet conformation (normal protein generally in shape of an alpha helix). It’s thought that because prion protein and normal protein made of same amino acids, they are the same protein but in a different shape. When the beta-sheet comes in contact with the alpha-helix, it will change the α-helix to a β-sheet. As more and more become β-sheets, this creates protein deposits. This happens somewhere in the brain, normal cleanup still happens. This leaves huge holes in your brain as the proteins are removed, causing disease.