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112 Cards in this Set
- Front
- Back
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Biogenesis |
The idea that every living organism comes from a pre-existing living organism (vertical transmission). Implies one root for the tree of life. |
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Heterogenesis |
Some life forms can arise spontaneously from non-living matter (decaying matter, broth). Implies many roots for the tree of life |
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Things good experiments have (6) |
Predictive and descriptive hypothesis Novelty Impact: universality- simplicity. Want it to be representative Objectivity- validity of the interpretation Quality of data and controls Reproducibility |
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T/F: The tree of life contains only organisms currently living |
F- includes all extant and extinct organisms. |
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Taxonomy |
ordered division and naming of organisms |
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Taxon (taxa, plural) |
taxonomic unit at any level (species, genus, order, etc) |
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Systematics |
branch of biology that classifies organisms and determines their evolutionary relationships |
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Linnaeus' concepts still used (2) |
hierarchical organization binomial nomenclature |
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specific epithet |
unique name for each species within a genus |
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Hierarchical organization (acronym) |
Domain Kingdom Phylum Class Order Family Genus Species |
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Phylogeny |
evolutionary history of species or group of related species. Represented by phylogenetic tree. |
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Homology |
similarity due to shared ancestry |
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analogy |
similarity due to convergent evolution (be careful with morphologies) |
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Convergent evolution |
similar environmental pressures and natural selection produce analogous adaptations in organisms from different evolutionary lineages |
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Homoplasies |
Analogous structures that evolved independently |
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What kind of gene do we use when constructing a phylogenetic tree? 3 |
Ubiquitous (present in every organism) Short enough to code easily Long enough to have significant ratios ex: 16S rRNA (ribosomal RNA). |
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orthologous genes |
different species, common functionality and ancestry. 2 genes are homologous in different species and come from same common ancestor. |
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paralogous genes |
same species, gene duplication and divergence Also homologous trait, but then they diverge. There was 1, then it duplicates, and the 2 evolve separately. |
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During which time period did he colonization of land happen? |
Paleozoic |
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During which period did humans emerge? |
Cenozoic |
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Oparin-Haldane Hypothesis |
Spontaneous generation of life occurred once with the primordial soup (tested with Miler-Urey experiment) |
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Oxygen revolution (great oxidation event) |
Atmospheric oxygen increased 2.7 bya. Most O2 is from organisms similar to modern cyanobacteria. |
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Obligate aerobes |
cannot grow without O2 (cellular respiration is essential) |
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Facultative anaerobes |
Use O2 if present or use different electron acceptor for respiration (doesn't matter) |
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Obligate Anaerobes |
grow exclusively by fermentation (O2 is poisonous) |
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epidemiology |
study of disease in populations |
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epidemic |
occurrence of a disease in unusually high numbers in a localized population |
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pandemic |
worldwide epidemic |
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endemic |
disease is constantly present (usually in low numbers) ex: malaria |
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Most dangerous pathogens to humans are (2) |
emerging pathogens Pathogens not dependent on the human host for survival |
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Water treatment (4) |
sedimentation Coagulation (insoluble stuff and microorganisms) Filtration Chlorination |
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Tobacco Mosaic Virus |
Discovery of viruses Showed that viruses are much smaller than bacteria (passed through filter) |
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structure of viruses |
Nuelcid acid, protein capsid, sometimes envelope (membrane) |
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Virus Reproduction |
only within a host cell Disassemble during reproductive cycle Host range- number of hosts a virus can infect, broad vs wide Viral proteins made by host cell (hijacking) Spontaneous self-assembly into new particles |
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capsid |
Very symmetrical (rod shaped, spherical) Protein shell that encloses viral genome Some are only made from a single protein, others are made of different types of proteins |
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Icosahedral viruses |
5-3-2 symmetry.. HPV Relatively easy to design vaccine because the capsid is exposed (no membrane). |
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Membranous envelope |
comes from host, contains proteins from host. Shields virus and facilitates fusion for spreading |
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Influenza |
Rod shaped capsid RNA genome is found in 8 segments that can recombine- why it's variable 2 proteins in membrane (Hemagglutinin, Neuraminidase) |
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Retroviruses |
HIV is one of these they have RNA genomes and copy the RNA into DNA with reverse transcriptase, then this DNA is integrated into the host genome (provirus) |
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HIV |
2 identical strands of RNA with reverse transcriptase inside capsid Reproductive cycle: releases RNA, DNA is made and inserted into genome, makes viral proteins, they spread and RNA, reassembly, spread. |
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Nucleoside analog |
AZT- inhibit reverse transcription with analog of nucleotide to stop the development of the DNA. Genome of virus can't be fully replicated. |
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Antiviral drugs |
treat viral infections |
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Antibiotics |
natural compounds that only work against bacteria |
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Vaccine |
prevent certain viral and bacterial infections. Harmless derivatives of pathogens that stimulate the immune system. |
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Inoculation vs Attenuation |
Inoculation introduces a live organism to a person to minimize the severity of another infection while attenuation introduces a dead/weakened virus so the body can create antibodies to fight it. The virus is altered before being introduced. |
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Viroids |
More simple than viruses. Circular RNA molecules that infect plants and disrupt growth. No capsid, inactivated with enzyme that cuts RNA. |
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Prions |
infectious proteins that cause brain disease in mammals (also more simple than viruses). Can exist in normal (in the brain) and prion versions (makes aggregates of protein which accumulate win brain and affect function). |
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Bacteriophages |
look like little robots. Icosahedral capsid head. Viruses that infect bacteria. DNA is injected in cytoplasm of bacteria. Double stranded DNA. Tail attaches to host cell and injects phage DNA. Form plaques on bacterial lawns |
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Lytic vs Lysogenic cycles |
Lytic is the typical pathway and kills the cell. Makes a lot of viral proteins and the virus spreads. Lysogenic cycle integrates DNA into genome (lysogeny) making a prophage. Spreads through reproduction to progeny. In stress, the phase will emerge from the dormant state and enter the lytic pathway. |
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Horizontal Gene Transfer |
Transferred from one bacterium to another through the virus. |
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Modes of HGT |
Conjugation Transduction Transformation |
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Conjugation |
2 auxotrophic bacteria have different supplement requirements to function and can make different proteins. Progeny can make all 5 compounds. Requires physical contact! Done through tube. Tube made from F plasmid. |
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Transduction |
Phage infects bacterium but may incorporate bacterial DNA into the phage's head. Transfers this new DNA into new recipient, recombination happens |
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Transformation |
Donor bacterium doesn't need to be alive, recipient needs to be in a competent state (can pick up DNA from environment), take into cytoplasm, and then recombine. Competence can be natural or induced. |
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Innate Immunity |
Present before exposure, nonspecific responses. First, rapid response to infection. Components: barrier defenses (mucus), chemical defenses (antimicrobial peptides), cellular defenses (phagocytosis) |
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Pathogens |
Agents that cause disease (usually microbes or toxins) |
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Innate Immunity triggers |
MAMPs- microbe-associated molecular patterns PAMPs- pathogen-associated molecular patterns Peptidoglycan, LPS, and Flagellin are recognized by PRMs (pattern-recognition molecules), aka PRRs (pattern recognition receptors) |
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TLRs |
Toll-like receptors homologous proteins in mammals. Not a lot of them exist Recognize certain receptors Each TLR recognizes different things (peptidoglycan, LPS, flagella, etc) |
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PRRs |
Pattern recognition receptors. TLRs are PRRs |
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Cytokines |
signaling molecules of the immune response (particularly inflammatory response). They cause the inflammatory response. |
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Histamine |
triggers dilation of blood vessels so permeability increases. produced by mast cells |
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Types of phagocytic cells (2) |
Macrophages- found everywhere in organs and tissues Neutrophils- found only in blood, attracted by signals from infected tissues (cytokines) |
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Phagolysosome |
contains lysozyme, proteases, phosphatases, nucleases, lipases, oxidases. |
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Process of Phagocytosis |
Pseudopod engulfs microbe Phagosome transports microbe and then fuses with lysosome, creating the phagolysosomal vesicle. Microbe is then killed and digested by lysosomal enzymes in the vesicle. |
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tissues |
collections of specialized cells isolated from other tissues by membranes. 2-3 germ layers give rise to tissues and embryonic organs |
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embryonic development
(3) |
cleavage, blastula, gastrula
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How does penicillin work? |
inhibits transpeptidation |
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eukaryotic vs prokaryotic flagella |
eukaryotic: circular microtubules, made of tubulin. whip-like Prokaryotic: made of flagellin (protein), propeller motion |
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conidia |
asexual spores formed @ tip of specialized hyphae (ascomycetes) |
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cambrian explosion |
sudden increase in diversity, explosion of life. early paleozoic era |
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trilobites |
early arthropods, extensive segmentation |
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hox genes |
provide positional information (type of homeotic gene) |
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homeotic genes |
control placement and organization of body plan |
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exoskeleton |
layers of proteins and chitin |
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notochord |
longitudinal and flexible rod between digestive tube and nerve cord. Provides skeletal support
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Nerve cord |
dorsal, hollow (solid and ventral in invertebrates) |
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origin of teeth |
mineralization of body began in mouth. Transition in feeding mechanisms, allows ingestion of larger prey |
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Modes of embryo development (3) |
Oviparous- eggs hatch outside mother, fertilization is internal or external Ovoviviparous- embryo is in an egg and develops within the mothers or father's body viviparous- embryo develops within mother's uterus |
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Tiktaalik |
fish characteristics: scales, fins, gills Tetrapod characteristics: neck, ribs, fin skeleton, flat skyll, eyes on top of skull, lungs |
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adaptions of terrestrial amniotic egg |
inflexible shell permeable to O2 and CO2. Extraembryonic membranes- specialized membranes protecting embryo |
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Allantois |
disposal sac in embryo |
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yolk sac |
nutrient sac for embryo |
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Mesozoic era |
time of dinosaurs |
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Archeopteryx |
early bird. Had feathers, wings, teeth, claws on wings, tail |
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cenozoic era |
mammals. Mass extinction happened, mammals filled niches. |
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nucleoid |
bacterial chromosome. single, circular |
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plasma membrane |
barrier, transport, protein secretion. |
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Mycoplasmas |
bacteria without cell walls |
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Gram positive |
1 thick peptidoglycan wall, allows purple to be trapped and stay. |
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Gram negative |
1 thin peptidoglycan membrane and an outer membrane with LPS. red washes away purple. |
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peptidoglycan |
glycan- modified sugar polymer cross linked by short peptides |
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sporulation |
triggered by starvation. Spores are dormant cells with protective layers |
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endospore |
formed within mother cell. |
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structure of bacterial cell |
pili capsule flagella |
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adaptive immunity |
develops after exposure very specific response large repertoire of receptors memory |
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antigens
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foreign molecules recognized by antigen receptors found on lymphocytes |
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epitope |
small part of an antigen that binds to receptor |
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Myeloid precursor |
creates monocyte which then turns into dendritic cell or macrophage. Can also turn directly into neutrophil or mast cell |
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Lymphoid precursor |
can make natural killer cell, T cell, or B cell (then plasma) |
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T cells vs B cells |
B cells have double pronged antigen receptors B cells mature in bone marrow, t cells mature in thymus |
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How do B cells work? |
They secrete antibodies (the y shaped molecule) which tag cells for phagocytosis |
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antibody function |
neutralization of toxins and viruses activation of complement system favoring opsonization of microbial cells |
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Membrane attack complex( (MAC) |
peptides promoting cell lysis by forming holes in the membranes. |
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Opsonization |
efficient phagocytosis. zipper-like interaction |
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Bacterial strategies against complement (2) |
use of capsules Production of surface components inhibiting MAC |
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Major histocompatibility complex (MHC) |
host proteins that display the antigen fragments on the cell surface. T cell binds both. I: cytotoxic t cells, II: helper t cells |
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Origin of self-tolerance |
lymphocytes that react against host molecules are destroyed (T cells!) |
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Humoral immunity |
type of adaptive. B cells are activated by helper T cells and differentiate into memory B cells or plasma cells (antibody secreting) |
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Cell-mediated immune response |
type of adaptive. Antigen receptors bind to class I MHC which call cytotoxic cells. They secrete proteins (performs and granzymes) that disrupt membranes by pore formation |
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allergies |
exaggerated response to antigens |
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sleeping sickness |
kinetoplastid has kinetoplast |
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malaria |
apicomplexa apicoplast and apex |
