signal transduction

three stages of cell signaling:

• RECEPTION: signal received
• TRANSDUCTION: signal passes through cell and molecules
• RESPONSE: cell undergoes change based on signal

1. reception

• ligands: signaling molecule
  • polar or non-polar (depends on binding)
    • polar: cell membrane
    • non-polar: cytoplasm
  • once bound, intracellular component changes shape and begins transduction
• g-protein:
  • introduced as:
    • an example receptor used by college board → uses: hormones, neurotransmitters, embryonic development
    • receptors can be disabled by numerous bacterial diseases
  • requires three proteins: receptor, g, and enzyme proteins
  • g-protein: gtp (→ krebs cycle)
    • receptor receives ligand
    • gdp is swapped for gtp
    • g-protein activates third protein (enzyme) that catalyzes transduction and resets
• gated channels
  • receptor proteins possibly → ion channels, open/close based on binded ligand
  • lets ions move inside or stops via facilitated diffusion

2. transduction

• one relay protein can activate multiple molecules at once → AMPLIFIED; METHODS=
  1. phosphorylate
  2. dephosphorylate
  3. second messengers (small polar molecules induce changes)
     • cheaper to induce second messengers vs phosphate groups
• PHOSPHORYLATION / DEPHOSPHORYLATION
  • reversible
  • added or removed by protein kinases / phosphatases; protein → more or less active
• SECOND MESSENGERS
  • fast diffusion within cell
  • CAMP = cyclic AMP = modified ATP
  • Calcium ions (CA^2+)
  • signal amplifies, dozens can be sent and make thousands of changes inside a cell

3. responses

• POSSIBLE RESPONSES: nuclear, cytoplasmic, or additional
  • NUCLEAR: creates transcription factors that turn on/off genes, enter nucleus, bind to DNA + acc. proteins
  • CYTOPLASMIC: existing proteins change in response to transduction
  • OTHER: cell movement, change shape via rearranging cytoskeleton
• responses differ → receptor proteins based on needs of job; only cells that receive signal can change activity
  • different cells may have diff signals or diff responses to the same signals
  • pathways can branch or have one route
  • pathways can influence each other → multiple signals and receptors necessary
• STOPPING A SIGNAL: signal binding is reversible unless caused by a toxin or disease
  • less receptors are bound when molecule concentration drops → relay molecules revert, second messengers break down
  • APOPTOSIS: programmed cell suicide; internal destruction of cell by enzyme
    • cell shrinks and membrane forms lobes ("blebs") that tear cell into vesicles
    • other cells consume and recycle
    • proteins for apoptosis normally inactive
      • autocrine signal sent by:
        • receptor protein in cell membrane
        • nucleus or er (dna damage, misfolded proteins) → activation cascade of apoptosis proteins
    • ROLE: prevent cells from hosting viral infections, regulate+separate developmental stages
    • FAULTY APOPTOSIS: involved in neurological conditions, diseases

summary

Cell signaling has three stages: the reception stage, the signal transduction, and the cell response. In the reception stage, the ligands bind to a protein receptor; then, the receptor's intracellular component changes shape and begins the transduction stage. (At the same time, some of these receptor proteins may be gated channels which open or close based on the ligand bound to them; this controls the movement of ions via facilitated diffusion.) In the transduction stage, proteins activate and change multiple molecules at once. This is achieved through one of three different methods which amplify the signal: phosphorylation and dephosphorylation, where a protein kinases or phosphatase changes the amount of phosphate groups present; or second messengers, where small molecules diffuse through the cell in the dozens. The cell may give a nuclear or cytoplasmic response, or it may respond through other methods (such as the movement of the cell and cytoskeleton.) These responses can differ based on which cells receive the signal given or any influences from the pathways of the ligands. Just as they can be activated, signals can be stopped; additionally, these signals can be used for cell suicide, known as apoptosis, in the case that the cell hosts a viral infection or if development in the cell needs to be regulated.

phylogenetics and speciation

• phylogenetics: classifying organisms based on evolutionary relationships via fossil, anatomical, molecular, genetic data
  • phylogenetic trees are hypotheses and change based on data
• cladogram: brancing points are "nodes", common ancestor
  • cladograms aren't scaled to time, phylogenetic trees are
• monophyletic group: all desc. of common ancestor → clade → ex. primates
• paraphyletic group: some but not all → reptiles (includes dinosaurs except birds)
• polyphetic group: no recent common ancestor → shellfish: molluscs and edible crustaceans
  • traditional groups are paraphyletic vs. monophyletic: ex. fish, where many fish are in different groups and "some" are excluded (tetrapods, monophyletic sarcopterygia that don't look like fish)
• cladograms are made via studying homology: the more traits shared, the closer related they are → traits called synapomorphies
  • homologous traits can be lost or confused by analogous traits (independent evolution, similar) so dna similarities considered reliable vs. anatomy
  • both used in conjuction: dna lost from ancient fossils, dna time consuming
• in and out groups: out groups have few shared traits, odd ones out vs. in group; polytomy
• speciation: cladogram nodes theoretically represent speciation points
  • several concepts
    • biological species concept: sex → biol species can not breed with each other and form viable, fertile offspring, called reproductive isolation
      • problems: asexual species exist; fertile hybrids are more common than believed in concept; extinct organisms cannot be tested
    • most scientists just use concepts useful for the current study
• reproductive isolation: prezygotic (4), postzygotic (3)
  • temporal: active and mating at different times
  • geographic: too far away
  • behavioral: don't recognize mating signals
  • mechanical: physical inability
  • hybrid inviability: genetic incompatibility → can't be brought to term (less chromosomes)
  • hybrid sterility: hybrid cannot reproduce (mules)
  • hybrid fitness: less fit hybrid is outcompeted by both parent species (liger)
• speciation occurs —
  • allopatric speciation: via geographic isolation
  • or sympatric speciation: population isolated by behavior or ecology in the same habitat

summary:

Phylogenetics is the classification of organisms based on their evolutionary relationships as studied through data found by studying fossils, anatomy, molecules, or genes. These result in phylogenetic trees and cladograms, which depict common ancestors and the evolution of modern species—although cladograms do not show time like phylogenetic trees do. There are three different groups found on phylogenetic trees: monophyletic (all descendants of one common ancestor, known as a clade;) paraphyletic (which excludes some descendants;) or polyphyletic (animals without a recent common ancestor) groups. Cladograms are created by studying homology, or shared traits called synapomorphies, which are found in anatomical and genetic data. They have in groups and out groups: out groups have few shared groups to the rest of the “in group” and branch out earlier than the rest of the cladogram. The nodes of the tree represent “speciation” points, an idea represented through different concepts of speciation. One concept in particular is the biological species concept, which says speciation occurs if two species cannot breed with each other and form viable, fertile offspring. This occurrence, called reproductive isolation, may occur because of several factors: it may be for temporal, geographic, behavioral, or mechanical reasons, or it may result from hybrid inviability, sterility, or hybrid fitness. Speciation can be allopatric or sympatric: it can occur through either geographic isolation or because the population has been isolated by behavior or the ecology, even if it is in the same habitat.

biodiversity

• biodiversity: diversity of species within an ecosystem
• all things respond to stimuli in their environment — environmental response ie hibernation: behavioral and/or physiological changes ie slower metabolism, diff behavior
• all things communicate to change others' behavior and suit their needs: signaling mechanisms via visual, auditory, tactile, electrical, or chemical cues
  • aposematic coloration, birdsongs warnings, mating: visual, auditory
  • electrical: elephantfish (snoot organ generates and senses electrical signals, cannot see in water)
  • chemical: plant roots and fungi
• evolution shapes communication over time to increase survival and reproduction
  • crypsis: resembles background
  • mimicry: resembles specific object or creature
  • parasitism
  • cooperative behavior can increase group fitness vs. individual performance
• community interactions: 1 of 3 outcomes, positive neutral or negative
  • symbiosis interaction: orgs that live with each other, closely associated, one requires the other to survive; not always beneficial to both parties
    
• energy drains from competition: costs both organisms, less chances to survive and reproduce because they struggle
  • competitive exclusion principle: two organisms using same resource in same way wipes out one bc one is slightly better
  • avoided by niche partitioning, differences between competing species
• antagonism: positive and negative → predation and herbivory and symbioses
  • evolutionary arms' race is race between predator and prey tactics evolving
  • herbivory is the defense of plants being eaten by another organism ie chemical warfare
  • symbioses: parasitism, mutualism, and commensalism; parasitism incl. endo/ectoparasites, mutualism both species benefit (shades into parasitism by exploitation ie bees), commensalism one species benefits from unimpacted species (phoresy)
• keystone species impact community structure in few numbers like sea otters (eat urchins, kelp can grow)
  • ecosystem engineers cause physical changes to their environment (beavers, dams, rivers turn into ponds, beaver meadows)
• disruptions to ecosystems: change conditions, affect adaptations (t. rex and asteroid: extinct because needed to hibernate, needed food, t-rex top predator before but too large after and size couldn't be achieved because didn't have enough food)
  • disruptions include geological or meteorological (extreme weather, volcanic/earthquake disruptions, asteroids,) human influence (habitat loss as a result of human use, pollution, global warming,) introduced species (invasive species disrupting native species — 40% of extinctions since 1750 caused by goats, pigs, cats, rats [human influence,]) overexploitation (marine ecosystems)