IB 104 lectures 1-11

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what is the cell structure of archeabacteria? protista? plantae?: prokaryote, eukaryote, eurkayote
what is the cell structure of eubacteria? fungi? animalia?: single, multi, multi
who was responsible for the 3 domain classification? what are the domains?: carl woese, bacteria, archea, eucarya
what do we call our system of classification of organisms?: systematics
what are the three parts of systematics?: taxonomy (naming and ID), phylogenetic reconstruction (determine ancestry), classification (organization into hierarchal system)
who develeoped the binomial system for taxonomy?: Linnaeus
what is comparative morphology?: the study of structures, including adult anatomy, embryo development, fossils, and behavior
what is comparative biochemistry?: study of the arrangment of molecules in organisms
explain divergence and convergence: divergence- organsims share a common ancestor and are becoming more different over time
convergence- organisms do no share a common ancestor and are becoming more similar over time
define analagous and homologous: analagous- characters from different ancestors that are alike
homologous- characters from related ancestors that are different
what is a cladogram?: branching tree chart that shows ancestry
how are new individuals formed? (molecularly): zygote formed by union of sperm and egg, cleaves into morula, hollows into blastula, gastrulation yields the three primary tissues
how many phyla are there?: 33
what protistans are we likely to be descendants of?: choanoflagellates, protistans that form colonies
what is the one species of Placozoa? descrive: T. adharens, simplest animal, a few thousand cells, top and a bottom, asymmetric
describe the phylum Porifera: sponges, thousands of species, simple cell arrangement, mature=sessile
what are some features of sponges?: choanocytes to trap food particles, defensive armor (carbonate spicules), chemical defenses
describe the Cnidaria: jellyfish, hydras, corals, sea anemones, have radial symmetry, two tissue layers, stinging nematocysts
what are the two body forms of cnidarians?: motile medusa, sessile polyp
explain the structure of a cnidarian: mouth opens into body cavity/gut, lining of gut is gastrodermis (derived from endoderm), outer lining of body is epidermis, acellular material (mesoglea) in between gastrodermis and epidermis to cause buoyancy
describe cnidarian nerves: network of nerves, but no brain, movement is a result of contraction of specialized cells, have no true muscle cells since they have no mesoderm
describe phylum Ctenophera: comb jellies, resemble cnidarians but smaller and never sessile, all swim using cilia, have no nematocysts, have a 3rd payer of tissue that ressembles mesoderm
describle phylum Platyhelminthes: flatworms, bilaterally symmetrical, have mesoderm, nervous system with some cephalization, simple blind gut (no separate anus), respiration takes place across integument, no circulatory system
what are the three major classes of Platyhelminthes?: 1.Turbellarians (reproduce asexually, can regenerate) 2. Tremotoda (aka Flukes) major parasites, cause Schistosomiasis: an epidemic in developing tropical countries 3. Cestoda (tapeworms) also parasites, have simple mouth with hooks
describe phylum Nemertea: ribbonworms, marine predators, use a proboscis to attatch and suck, have complete gut with a mouth and anus
describe phylum Nematoda: roundworms, have a space between ecto and endoderm--> pseudocoelom, have a hard cuticle, found in all habitats, C. elegans,
describe phylum Rotifera: have all features of nematodes including pseudocoelom, however they are tiny, round, and not wormlike, have ring of cilia around mouth
what are the two major divisions of the coelomates?: protostomes and deuterostomes
define protostome and deuterostome: protostome- spiral cleavage, first opening is mouth
deuterostome- radial cleavage, first opening is anus
describe phylum mollusca: unsegmented, coelomate, protostomes, often have hard shell, have muscular foot, visceral mass, and a mantle, scraping radula for food
what are the 4 major classes of Mollusca: Gastropods, chitons, bivalves, cephalopods
describe phylum Annelida: worms, segmented animals
what are the 3 major classes of Annelids?: polychaetes- many bristles (bloodworms)
oligochaetes- a few bristles (earthworms)
Hirudinae-no bristles, leeches, have suckers
describe phylum Onycophora: velvet worms, found in tropics, share features of annelids and arthropods
describe Arthropods: bugs, jointed appendages
what are the 5 major classes of arthropods?: trilobites- extinct marine
chelicerates- spiders, scorpions, named for stining mouth parts, have book lungs
Crustaceans-crabs, etc
Miriapods- centipedes, millipedes
insects-six legs, 3 body regions (head, thorax, abdomen)
what are the 6 major features of insects: 1. specialized body segments
2. protective exoskeleton
3. jointed appendages
4. specialized sensory capabilities
5. division of labor
6. respiratory structures
(also only invertebrates to evolve flight and metamorphosis)
what are the major Orders of insecta?: Coleoptera- beetles
Dipera- flies
Lepidoptera- moths and butterflies
Hymenoptera- wasps, bees, ants
Hemiptera, Homoptera- bugs with sucking mouthparts
Odonata- dragonflies
describe phylum Echinodermata: sea urchins, sand dollars, sea stars, brittle stars, entirely marine, deuterostomes, penta-radial symmetrym mineralization, tube feet, NOT cephalized
what are the four major features of Phylum Chordata?: 1. notochord
2.tubular dorsal nerve cord
3. pharynx
4. tail that extends past anus
what are the 3 SUBphyla of Chordates?: tunicates- sea squirts
cephalochordates- lancelets, maintain all 4 features to adulthood
vertebrates
what are the 2 additional features vertebrates have?: spine, skull
what is the name of the single set of "mater control"/ regulatory genes?: homeobox or HOX genes
describe Class Agnatha: jawless fish, cartilaginous skeletons, hagfish, lamprey
describe Class Placodermi: jawed armored fish, jaws evolved from specialized gill slits, now extinct
describe class Condrichthyes: cartilaginous fishes, sharks, rays, chimaeras, fins and well developed jaws,
descrive class Osteichthyes: bony fishes
what are the three groups of Osteichthyes: ray finned fishes (like normal fish), lobe-finned fishes (coelacanth), lungfish
describe class Amphibia: evolved from fish, lungs, closed circulatory system, frogs, toads, salamanders, newts, caecilians
describe class Reptilia: first fully terestrial, leathery eggs (additional membrane called AMNION), thick scaly skins, internal fertilization, efficient kidneys, single bone skull, extensive teeth
describe class Aves: birds, descendants of reptiles, feathers, loss of teeth--> beak, egg shell, well developed sternum to which flight muscles are attatched
describe class Mammalia: descendants of reptiles, feed young with milk, have hair, teeth with different shapes
what are the 3 SUBclasses of mammals?: Prototheria/monotremes- egg laying, platypus and echidna (spiny anteater)
Metatheria/marsupials- pouch animals, possum, kangaroo
Eutheria/placental
what are the basic energy sources and stores for all organisms that also are commonly structural?: carbohydrates
what are the monomers of carbohydrates?: sugars/monosaccharides ex: glucose, fructose
monomers linked together in chains are.. for carbohydrates?: polymers, polysaccharides
how are polymers made?: condensation/synthesis/dehydration
what is the reverse of condensation/synthesis/dehyration?: hydrolysis
what is the major polymer in animals? plants?: glycogen, starch
what is the major structural material in plants? animals?: cellulose, chitin
what is primarily involved in energy storage and membrane structure?: lipids
what can lipids also be?: hormones, waxes
what are the monomers of lipids?: fatty acids (ex: linoleic acid)
what are the polymers of lipids?: triglycerides- saturated or unsaturated (refers to presence of double bonds)
what are phospholipids>: triglycerides with one fatty acid replaced by a phosphate group, one side polar and one nonpolar, MAKE UP MEMBRANES
what are the building blocks of cells and the enzymes that facillitate all cellular activites?: proteins
what are the monomers of proteins? how many involved in most life?: amino acids, 20
what are the polymers of proteins?: polypeptides
describe structure of protein: primary- long strings
secondary- coiled chains or pleated sheets
tertiary-disulfide bridges and cysteins
quaternary- 2 alpha and 2 beta hemoglobin polypeptide chains
what are the monomers of nucleic acids?: nucleotides
differentiate pyrimidines and purines: pyrimidines-single ring
purines- double ring
what is the major nucleotide in the body?: ATP (adenosine triphosphate)
what is chromatin?: complex of long DNA strands wrapped around proteins
what surrounds the nucleus of a cell?: double membrane with large pores
what is a nucleolus, where?: in the nucleus. assembles ribosomes
what is the other major organelle of an animal cell?: mitochondrion, cell within a cell, dounble membrane
what is the cytomembrane system? path?: series of membranous vesicles involved in coordinating protein production and secretion. have signal sequence that admits to endoplasmic reticulum, then the go to golgi complex via transport vesicle, leave via secretory vesicle to the cell surface where exocytosis takes place
how is the structure of the cytoskeleton maintained? (by what? define): microtubules- large, composed of tubulin, stack into long filaments
microfilaments-narrow, made of actin, inolved in movement
the phospholipid bilayer is permeable to what? not permeable to?: perm- CO2, O2
imperm- charged ions H+ etc, larges molecules
what allows water to cross the membrane?: aquaporins (water channels)
what is osmosis?: water crossing the membrane to make up for the concentration difference when ions can't cross
what is involved in facilitated diffusion/passive transport?: sodium and potassium channels
how do cells return t resting condition of concentrations? requires what?: active transport, energy
what is our light receptor protein?: rhodopsin
what are the kind of receptors in our noses and mouths>: chemoreceptors
what is endocytosis?: bring messangers into the cell from outside
what is it called when amoebae and leukocytes deed by ingesting bacteria or other foreign particles to form vaculous where the food is digested?: phagocytosis
what are the two laws of thermodynamics?: 1. energy can't be created or destroyed
2. left alone everything tends toward a lower state of organization
what is metabolism?: the way we convert one molecule into another
what are enzymes? what do they do?: devices that facillitate reactions, generally proteins, INCREASE the rates of reaction
Other than ATP what are the coupling agents/co-factors?: NAD and FAD
how many ATP does glycolosis yield?: 2 (and 2 NADH)
how many ATP does aerobic respiration yield?: 36 ATP
what are the major parts of aerobic respiration?: krebs cycle and electron transport chain/oxidative phosphorylation
when was DNA first isolated? by whom? called it what?: 1870, Johann Miescher, nuclein
what did Fred Griffith study in 1928?: transformation experiment, heat-killed virses and mice
who discovered the structure of DNA?: James Watson and Francis Crick
what is the shape of DNA?: right-handed double helix, antiparallel
what catalyzed replication of DNA?: DNA polymerase
what is coping DNA to RNA called?: transcription
what is it called when info in the RNA is decoded by proteins?: translation
what does it mean to delimit genes?: tell where to transcribe along the DNA
what are the three parts of transcription?: initiation (promoter sequence tells where to start), elongation (RNA polymerase releases RNA), termination (reaches second signal and stops copying)
what are the two features added to RNA in post-transcriptional modification?: G-cap, poly-a tail
splicing machinery in nuclei of eukaryotes cuts out...?: introns
what does transcription yield?: a particular gene encoding a particular protein
what is the codon for start?: methionine, AUG
how many stop codons are there?: 3 (except in mitochondria where UGA means tryptophan)
where is mRNA translated?: on the ribsomes with the help of transfer RNA
what are the 3 stages of translation?: initiation (finds start codon)
elongation
termination (at stop codon)
what is the central dogma of molecular biology?: while info is STORED in DNA and replicated ny DNA replication, it is transmitted via RNA to protein
what are the 5 kinds of viruses?: DNA viruses (herpes), RNA viruses (influenza), retroviruses (star with an RNA genome and copy in into DNA with reverse transcriptase), viroids (in plants, contain single stranded RNA molelcules), prions (Creutzfeld-Jakob disease)
what percent of the genome is junk DNA?: 97%
what do bacterial operons do>: control levels of expressions of genes (only transcriptional regulation)
what do histones do?: they are the fundamental proteins involved in binginf DNA into nucleosome
what do you call the genes that cause cancer? normal version?: oncogenes, proto-oncogenes
what is it called when a tumor loses cells which then spread through the body via lymph and blood and form additional tumors?: metastasis
what are plasmids? what are the two types?: circular, double strand DNA molecules which propagate themselves semi-autonomously in bacteria, F (fertility) and R (resistance)
who discovered cloning? when?: Herbert Boyer and Stanley Cohen, 1970's
since plasmids only work in bacteria, what do we use in insects, plants, and humans?: insects: transposon plants:ti plasmid humans: retro viruses, adenoviruses, cell cultures
define exocrine glands: glands with ducts
define endocrine glands: glands without ducts
what should be considered as signaling molecules?: hormones
where is the hypothalamus? what does it secrete? what does it do?: near the base of the brain, secrets neurohormones for special neurns that control secretions of hormones by the pituitary, it's the central control center for homeostasis
where is the pituitary? what does it do?: on a stalk below the hypthalamus, secrets hormones that are carried by blood around the body and only target cells that express the appropriate receptor
what is one of the hormones secreted by the pituitary?: growth hormone/somatropin ( a peptide hormone that works in tiny quantities), or antiduiretic hormone that regulates water and salt levels in the kidney
what does the pineal gland release?: melatonin, regulates circadian and seasonal cycles
where is the thyroid gland? what does it secrete?: the neck, thyroxine that controls metabolism and well being levels
where is the adrenal gland? what does it secrete?: on top of the kidneys, secretes cortisol from it's cortex which decreases inflammation, and adrenaline (epinephrine) from it's medulla that creates the fight or flight reflex
what do the testes secrete?: testosterone
what are nervous systems constructed out of?: neurons
what are the two major parts of all neurons?: dendrites- small projections at one end
axon- long extension
what is the basic resting state of all neurons?: -70 mV
what are action potentials?: all or nothing spikes of depolarization
what are action potentials the result of?: voltage sensitive gated sodium channels opening with sodium rushing into the cell and then potassium channels opening and potassium leaving the cell
what are the two features additional to our own axons that differentiate them from the giant squid the nervous system was originally demonstrated on?: wrapped in myelin sheaths of schwann cells, leaves periodical; nodes of exposed axon membrane from which action potentials jump
what happens at the end of an axon?: electrical signal changed into a chemical signal to cross the synaptic junction, opens special sensitive calciu channels which causes vesicles packed with neurotransmitters to fuse with the cell membrane, releasing neurotransmitters into the synaptic gap
what are the three major kinds of neurons?: sensory: bipolar
interneurons- in the brain
motor neurons- also bipolar, in muscle cells
where are the three additional opsins for trichromatic color vision expressed?: cone cells
how many receptors are associated with olfaction in mammals? how many do we have functional?: 1000, 300
what are the two main parts of the central nervous system?: brain and spinal cord
what are the two kinds of matter in vertebrate brains?: gray matter- consists of cell bodies, on surface of cortex
white matter- consisting of myelin-sheathed axons, internal to the gray matter
what are the major divisions of the brain?: hindbrain (medulla and cerebellum), midbrain, forebrain (includes cerebrum, thalamus, hypothalamus, and limbic system)
what are the 4 lobes of the cerebrum?: frontal (memory and planning, inhibits inappropriate responses, voluntary muscles), parietal (in the middle, integrate sensory input from skin and internal body), occipital (posterior, integrate vision), temporal lobes (sides, integrate hearing)
what is the corpus callosum?: band of nerves that is the only connections between the right and left cerebral hemispheres
what are the 3 parts of the limbic system and what do they do?: thalamus (cordinates sensory input), hypothalamus (maintains homeostasis), amygdala (memory formation)
what are the three lines of defense against pathogens and parasites?: 1. integument
2. innate immune system
3. adaptive immune system
what are the two layers of our skin?: epidermal/stratified epithelium- has keratinocytes, produces melanin, outer
dermis- inner, connective tissue layer, capilaries, sensory nerves, sweat glands, and hair follicles
what does the innate immune system do?: various proteins such as defensins and ceropins in insects, complement proteins in vertebrates form pores in the cell membranes of foreign cells causing cell death
what is a further specialization of insects in response to foreign objects?: hemocytes-encapsulate foreign objects by coating them in many layers of melanin, killing them
what happens in the inflammation response?: basophil white blood cells secreting histamine which causes vasodilation and loosening of the connections of the endothelial cells of capillaries. Plasma carrying defensive proteins leaks out and neutrophils followed by monocytes (that mature into macrophages) go into the surrounding tissue and phagocytose (eat) foregin cells and damaged host cells.
secretion of interleukins by macrophages furing a prolonged fight leads to?: fever
after leaked plasma is done doing it's job, what happens?: it goes back to the bloodsteam after it is checked by the lymphatic system
when does the adaptive immune system kick in?: only after the first two defenses fail and and infection is established
what are the two major features of the adaptive immune system?: memory and specificity
how does an immune response start?: macrophages cut up proteins of foreign cells (antigens) and display them on their surfaces in conjunction with MHC proteins, these are recognized by special receptors on one kind of lymphocyte (T-cells) and the T-cells are activated and divide to form huge clones that respond
what are the two types of t-cells?: cytotoxic-attackers
helper-secrete interleukins that activate more t-cells, also sequestered in lymph nodes as memory cells
what is the other kind of lymphocyte? (besides t-cells): b-cells: produced from stem cells in bone marrow, with a unique antibody on their surface
what is immunization?: intentional exposure of a weakened or killed pathogen to produce memory T and V cells to provide a swift response to later infections
what are autoimmune diseases?: diseases with faulure of screening for self-antigens, causes immune system to attack a particular part of our body (ex:arthritis)
what is the % of oxygen in the atmosphere? carbon dioxide? what does this mean?: 20%, .04%, O has a high partial pressure, CO2 has a low partial pressure
what do birds and fish have to get oxygen?: countercurrent system
what does digestion rely on?: enzymes
where does absorption occur?: second part of small intestine
how are monosaccharides, amino acids, nucleotides absorbed? fatty acids?: active transport, simply diffuse
what does the large intestine absorb?: water and salts
what are the four fat soluble vitamins? are they toxic in large quantities?: A, D, E, K, yes
what is the objective of excretion?: to remove metabolic wastes generated through degredation of various biochemicals, particularly amino groups
what do aquatic animals excrete? terrestrial animals? mammals?: ammonia, uric acid, urea
what are the steps of excretion? occuring where?: 1. filtration- in bownmans capsule in the cortex of the kidney, forces out blood plasma including anything the size of glucose or smaller
2. fluid collected in tubule foes down into the medulla and back out into the cortex via the loop of henle, filtered sodium is reabsobed by capillaries surrounding it and water by osmosis and active transport or aquaporins
3. other chemicals secreted from blood INTO tubules
4. result is urine, collected in the ureter, stored in the urinary bladder, released via the urethra
what do you call the process of the division of somatic cells?: mitosis
how many chromosomes do we have? drosophila?: 23, 4
what are the 4 parts of the cell cycle?: growth (G1), synthesis (S), preparation for divison (G2), mitosis
what happens in mitosis?: sister chromatids must be reliably segregated into two daughter cells so each is identical to the other.
what does totipotent mean?: all cells carry all info for the species
what do you call the division of germline cells?: meiosis
what is special to meiosis?: homologs are separated in prophase 1, crossing over (causing recombination), 2 divisions (only one replication)
what is oogenesis?: process of meiosis in the female germline, produces one egg and 3 polar bodies
what is parthenogenetic reproduction?: reproduction without sex --> no mixing, creates clones

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