* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Biology Notes - askmrspierce
Survey
Document related concepts
Cell culture wikipedia , lookup
Genetic engineering wikipedia , lookup
Organ-on-a-chip wikipedia , lookup
Cell theory wikipedia , lookup
Cell (biology) wikipedia , lookup
Drosophila melanogaster wikipedia , lookup
Human genetic resistance to malaria wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Evolutionary history of life wikipedia , lookup
Neurogenetics wikipedia , lookup
Microbial cooperation wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Neuronal lineage marker wikipedia , lookup
Symbiogenesis wikipedia , lookup
State switching wikipedia , lookup
Sexual reproduction wikipedia , lookup
Transcript
Biology Notes: Chapter 1 – Class objectives Rules and policies What is biology? Scientific theories Energy mater and organization: Chemistry of life: Atoms Molecules Compounds Water, hydrogen gas, oxygen gas Structure of atoms PEN Chemical reactions in living cells Types of bonds review: covalent, polar covalent, ionic Balancing equations review: 2H2O = 2H2 + O2 Ions and living cells – salt and pH Organic compounds – Carbohydrates Monosaccharide Disaccharide Polysaccharide Lipids Proteins Amino acids Peptide bonds Polypeptide Primary structure Secondary structure Tertiary structure Hydrophobicity Nucleic acids Nucleotides DNA RNA C T A G Phosphate Sugar The double helix The function of DNA – genes Types of microscopes (?) __________________________________________________________________________________________________ Chapter 2 – Organisms and energy Chapter 3 – __________________________________________________________________________________________________ Chapter 4 – Chapter 5 – __________________________________________________________________________________________________ Chapter 6 – Chapter 7 – __________________________________________________________________________________________________ Chapter 8 – Cell cycle Asexual Sexual Very similar in all eukaryotes Cell splits into 2 daughter cells Mitosis = splitting process Interphase = time between divisions G1 = prereplication, grows, produces proteins S = DNA synthesis G2 = premitosis M = mitosis G0 = nonreplicating cells R = restriction point at end of G1, cell is committed to mitosis DNA Structure Depends on molecular shapes of DNA and its bases Base pairing depends on how many hydrogen bonds each nitrogenous base can form Adenine and Thymine = 2 hydrogen bonds Guanine and cytosince = 3 hydrogen bonds Strands are parallel, but twisted into double helix Sugar, phosphate backbones 3 major parts of DNA synthesis - binding of enzymes to existing DNA - unwinding the double helix - synthesis of a new matching strand for each existing strand enzymes and other proteins bind to specific regions called replication origins one of these unwinds helix DNA polymerase catalyzes the formation of the new DNA strand The combination of the DNA and proteins is called a replisome Prokaryotes have one origin Eukaryotes have multiple DNA polymerase can add nucleotides only at the end of an existing nuclein acid strand Synthesis of new strand is continuous only on leading strand Lagging strand builds in pieces Semiconservative = each new strand has half of the original strand Proteins wrap DNA in tightly wound structure called a chromosome Mutation = change in sequence of cell’s DNA Can be silent, harmful, or lethal to the cell Mutations can be passed to daughter cells Mutagenic chemicals = mutation causing environmental factors DNA polymerase acts as a proofreader Excision repair = defective base pair is cut out Cell Division Sister chromatids formed during S phase Centromere = holds sister chromatids together Aneuploid cells = daughter cells with abnormal numbers of chromosomes Interphase Prophase = chromatids become defined Mitotic spindles = attach to chromatids Kinetochore = protein complex Metaphase = chromosomes lines up along middle of cell Metaphase plate = line of chromosomes Anaphase = chromatids pull apart to opposite poles Telophase = nucleus reforms Cytokinesis = divides cell in two Differences in Mitosis Cytokinesis begins in anaphase in animal cells Cytokinesis in plants forms cell wall Controlling the cell cycle Cyclins = proteins that regulate progression through the cell cycle G1 cyclins – peak at S phase Mitotic cyclins – peak at metaphase Cyclins bind to kinases, which transfer phosphate from ATP, which activates other enzymes Cell cycle arrest = pausing of cell cycle while damage is fixed G1 arrest – damaged DNA S arrest – unreplicated DNA G2arrest – damaged DNA M arrest – defective spindle Mutations in genes can lead to inappropriate cell cycling = cancer Chapter 9 – Nucleic acid = DNA and RNA Consist of a long strand of repeating subunits, at like letters in a code Subunits arranged in pairs DNA specifies primary structures of proteins Indirectly dictates protein function Proteins carry out important cell activities Active genes make temporary RNA copy of DNA information mRNA = messenger RNA transcription is copying process translation – protein from pattern of amino acids written in mRNA protein synthesis occurs on the ribosomal RNA (rRNA) amino acids brought to ribosome by transfer RNA (tRNA) genetic code describes how a sequence of bases translates into DNA or RNA genetic code requires 20 different code words – one per amino acid 3 nucleotides are grouped at a time which allows for 64 different triplets codon = on mRNA anticodon = on tRNA importance of proteins keratin, collagen, and myosin make up cell structures and tissues enzymes and essential catalysts make chemical reactions of living systems happen fast hemoglobin binds to specific molecules insulin plays a key role in communication within an organism hormones are chemical signals given off by cells protein structure determines its function collagen is long fibers, bind cells together lysozyme is an enzyme with cavities or pockets that bind only specific substrates RNA synthesis Transcription enzyme RNA polymerase joins nucleotides according to base sequence in DNA Prokaryotes have one type of RNA polymerase Eukaryotes have three RNA polymerases, each make a different type of RNA (m,t,&r) Protein synthesis = outside nucleus RNA synthesis = inside nucleus rRNA strand combines with proteins to form ribosomes RNA has Uracil instead of Thymine Transcription has 3 stages” - initiation = RNA polymerase attaches to DNA - Elongation of RNA strand = RNA polymerase partially unwinds the DNA - Termination = RNA polymerase reaches terminator region, or end of DNA RNA Processing In prokaryotes new mRNA is translated and broken down by enzymes In eukaryotes mRNA can last for minutes to days Enzymes attach a cap of guanine to the starting end of the mRNA molecule Enzymes then replace part of the other end with a series of 100-200 adenine (poly-A) Final step is removal of introns (internal segment that does not code for protein) Exons remain – code for proteins Splicing = the process of removing introns and rejoining ends tRNA must undergo chemical modification of nucleotides so that a cloverleaf shape is formed rRNA is not involved in coding rRNA transcript is spliced and modified to produce mature rRNA Translation Happened in ribosome tRNA anticodon pairs with mRNA codon attachment of tRNA to the correct amino acid is called tRNA charging charging requires 1 ATP molecule the P site holds the tRNA carrying the growing polypeptide chain the A site holds the tRNA carrying the next amino acid to be added the E site is the exit site uncharged tRNA leave via the E site translation involves the same 3 stages as transcription: initiation, elongation, and termination energy for the first 2 steps provided by GTP (guanosine triphosphate) amino acids are joined together by peptide bonds the ribosome slides down repeatedly to move to new codons translation terminates at a stop codon a special protein called a release factor binds to the stop codon transcription produces all three types of RNA Transport and modification of proteins Many proteins must be folded into active structures to function Chaperone proteins often help stabilize the polypeptide as it folds The protein must then be transported A signal sequence is used and the protein is released into the inner ER Proteins to be released pass from the ER to the Golgi vesicles Once in the ER the signal sequence is cleaved off Errors sometimes occur Most are caught and corrected Frame shift = start of translation is shifted by one or two nucleotides Genetic Information and Viruses No cells Replicate and evolve Discovered in 1892 by Russian botanist Dmitri Ivanovsky Depend on gene expression machinery of host cells Nucleic acid with protein coat Some have DNA Others, like influenza, have RNA Bacteriophage (hexagonal protein coat, nuclein acid inside, elongated ‘landing gear’) HIV (RNA in middle, circular protein coat, lipid membrane, and reverse transcriptase) Viral replication can be lytic or lysogenic Lytic = host cell replicates viral DNA Lysogenic = viral DNA inserts into the cellular DNA, copied when cell replicates Impact of viruses Live at expense of host organism Antibiotics are not useful Air travel has made spread much easier and faster Ebola, influenza Many plant viruses __________________________________________________________________________________________________ __________________________________________________________________________________________________ Chapter 10 – New embryos start with fertilization Gametes = sperm or egg Animal sperm is flagellated Bigger eggs have yolk – energy rich nutrient full Gametes are haploid Zygotes are diploid Fertilization stimulates activation – turns on egg’s metabolism Causes rapid change in plasma membrane which blocks fertilization by other sperm Differentiation occurs Morphogenesis – organization of cells into tissues and organs of a complete animal All cells are different – muscle, nerve, blood, skin, etc Proteins are key to differentiation 1st stage is called cleavage – cells go from 1 – 2, 2 – 4, etc Morula – 16 – 64 cell stage, yolk can be evenly distributed or in one clump Blastula – multicell – all cells look about the same Gastrula – three layered structure Primary germ layers – form all body’s tissues Ectoderm – form skin Mesoderm – skeleton, muscles, heart, organs, blood Endoderm – tube, becomes digestive system The body plan (general shape) forms during gastrulation First mesoderm becomes the notochord – develops into backbone Above the notochord, dorsal ectoderm becomes neural tube, forms brain spinal cord and nerves Birds and mammals, develop into mini-adults Larva – a feeding individual that looks nothing like the adult Metamorphosis – a series of changes that transforms the larva into an adult Development of body plan differs greatly between animals, can help identify relatedness Similar genes are responsible for segmentation Called homeotic genes First discovered in fruit flies Each gene works on a different body part and contains the 180 base pair homeobox sequence Codes for a 60 amino acid protein called a homeodomain Mice have Hox genes Homeotic vs. Hox = same thing These genes have changed very little during evolution Most animals share the same basic body plan Mammalian development Ovipary Ovovivipary Vivipary Monotremes, marsupials, placental mammals After 5 days the embryo sinks into the uterine wall Amnion – immediately surrounds the embryo Chorion – encloses all other membranes and forms the blastocyst’s outer wall As gastrulation begins, the chorion extends villi into the uterine lining This forms the placenta Blood flows remain separate 40 weeks total After 8th week, called a fetus Organs form after 1st trimester Birth defects caused by gene abnormalities or environmental factors Polydactyly – extra digits, abnormal genes Spina bifida – posterior end of neural tube fails to close Anencephaly – anterior part of neural tube fails to close, exposed brain degenerates, top of skull fails to form DNA-RNA Hybridization – adds marker to DNA to see if certain gene is active in cell Selective gene loss hypothesis – cells lose some unused genes when it differentiates Genetic equivalence hypothesis – all cells contain the same genes, some are just inactive Cells from a blastula when swapped in lead to complete formation of leopard frog tadpole Cells from adult skin lead to termination of development after gastrulation Determination is the process by which a cell commits to a particular course of development Sometimes determination happens as early as the first cleavage Snail cells split – 1 makes ectoderm, other makes endoderm and mesoderm Chapter 11 – Embryos and Seeds Sexual reproduction begins with fertilization New embryo called a zygote Plants also have asexual reproduction ~95% are flowering both kinds of plants mitotic cell division forms spherical mass developing embryo surrounded by endosperm tissue, transfers nutrients small bumps form called cotyledons (seed leafs) rapid division and differentiation of embryo cells shoot tip comes between cotyledons root tip at other end This area of undifferentiated cells is called the apical meristem and continues to be able to grow Maternal cells place a seed coat around the endosperm When the environment is suitable germination occurs Some seeds need to have weeks of cold followed by warm Some need to undergo fire Primary growth – growth from the meristem Node – meristem branching sections Root cap covers root meristem 3 tissue types Epidermis Vascular tissue Ground tissue – fill plant up give shape and volume Cells can grow, but this growth slows as the cell wall hardens Leaf cells only divide perpendicular to the existing meristem growth Uniform growth of ground tissue produces rounded leaves Rapid growth near veins produces lobed leaves Secondary growth increases diameter Vascular cambium – inner surface makes xylem, outer surface makes phloem Cork cambium is a meristem that produced bark Xylem in center stops carrying water and functions only in support Root branches arise from the pericycle Flowering depends often on day vs. light cycles Genes provide the control for when things grow, triggered by: Temperature, night length, nutrition, chemical signals, activities of neighboring cells Plant Growth Regulators (PGR’s) function like hormones in animals 5 major classes: Auxins – 1st identified, stimulate root elongation, promote fruit development Gibberelins – 1920’s stimulate stem elongation, produce flowers that produce seedless fruits, fruit growth Cytokinins – cell division and organ development, regulate total growth pattern of plant, produced in roots, chloroplast development Abscisic acid – synthesized in response to dry conditions, closes stomata, buds and seeds become dormant Ethylene – gas promotes aging of tissues, ripening of fruits, makes leaves flowers and fruit drop Ship fruit in carbon dioxide then treat with ethylene upon arrival Some plants droop when touched due to a loss of pressure Tropism – growth towards or away from a stimulus Phototropism – growth towards light often Gravitropism – stem negatively gravitropic, root positively gravitropic Photoperiodism – response to 24 hr light/dark period Long day plants – flower in the spring when days are long enough Short day plants – flower in the fall when days are short enough Day neutral – flower upon maturity Plants contain pigment called phytochrome Two slightly different chemical structures Pr – absorbs red light Pfr – absords far-red light Chapter 12 – Asexual reproduction Clone, 1 parent Binary fission – dividing in 2 Budding – hydra, animal, branches off Fragmentation – planaria, need part of neural cord Vegetative reproduction – plants, seedless varieties Each species has a characteristic number of chromosomes Prokaryotes – one circular strand Eukaryotes – varies Sexual reproduction, pairs of each chromosome, diploid, 2n Gametes – haploid, n Somatic cells – diploid 2n 2 chromosomes that make a pair are called homologous, similar in structure except sex chromosomes Meiosis makes gametes or spores (fungi) Grossing over can occur, gametes not identical 4 sperm produced, only 1 egg (2 polar bodies given off) Spores can grow into haploid organisms without fertilization Some plants and animals have lost the ability to reproduce sexually All females Sexual reproduction in microorganisms Conjugation Can have alternation of generations, haploid and diploid phases in cycle Many microbes switch between sexual and asexual based on environmental pressures Plants are usually sexual Alternation of generations Mosses and simple plants spend most of life as haploid Monoecious – both types on 1 plant Dioecious – either male or female Pollen, formed in the anther Flowering plants are the most successful, fused carpel, ovary at base, ovules are site of ovum development Pollination – pollen reaches stigma, two sperm emerge, one fertilizes ovum, other fuses with the 2 polar bodies. Diploid becomes embryo, triploid becomes endosperm Seed dispersal – wind, water, fruit (terrestrial mammals, reptiles, birds, bats) Animal sexual reproduction Gonads – gamete producing organs Basic animal produce both eggs and sperm – are still rarely self-fertilizing Some vertebrate produce both eggs and sperm, but never simultaneously External fertilization – spawning Internal fertilization – more efficient, greater parental care Insects can store sperm __________________________________________________________________________________________________ Egg production Ovaries, Fallopian tubes (oviducts), uterus Vagina used as exit or birth canal Menstrual cycle is ~28 days Endometrium builds up in preparation of the fertilized egg If no fertilization occurs then the lining and its rich blood supply disintegrate The nervous system, glands, and hormones regulate the menstrual cycle Leutenizing (more estrogen) and Follicle Stimulating (matures egg) hormones Estrogen – peaks right before ovulation and ~ day 24, thickens uterine lining Progesterone – prepares endometrium, peaks ~day 21 Ovulation – day 14, LH ruptures follicle, egg released, follicle become corpus luteum releases estrogen and progesterone Egg gets fertilized in the oviduct, begin mitosis on way to uterus Embryo implants, begins to form a placenta Placenta releases human chorionic gonadotropin (HCG) Gestation – time embryo is carried within uterus Oxytocin – released at time of birth, this hormone cause the muscles of the uterus to contract, expelling the baby Menstruation is a primate characteristic Other mammals have estrus, or heat cycles Humans have hidden ovulation In some mammals, copulation induces ovulation (rabbits) Sperm production Formed in the seminiferous tubules of the testes Stored in the epididymis, a coiled part of the vas deferens Prostate gland and seminal vesicles produce other seminal fluid which helps the sperm Sperm + seminal fluid = semen Expelled during ejaculation LH stimulate the release of androgens Testosterone is the major androgen secreted by the testes FSH stimulates sperm production Testes size to body ratio depends on breeding classification – sperm competition Secondary sex characteristics Controlled by estrogen and androgens Develop at puberty Females – estrogen controls breast, bone structure, fat deposits, Males – voice, body hair accumulation Infertility can be caused by one partner, or incompatibility In vitro fertilization Some contraceptive provide physical barriers – egg and sperm seperate (condoms) Some contraceptives provide chemical barrier – stops ovulation (pills) Iud causes lining irritation = no implantation, copper stops sperm’s ability to swim, can have progesterone (prevents ovulation) Vasectomy – cut vas deferens – sperm stored past that spot viable for ~ 1 week Tubal ligation – oviducts are cut and tied – fail when tube is missed or egg has already passed Essure – football shaped spring scars oviduct Condoms = 95% - 79% E + PG Pills = 99.7% [92%] when used correctly (no doses missed, same minute of every day) Progesterone only pills = [60%] MUST be EXACTLY on the minute every day Injection depo-provera = 99.7% i.u.d. = 99.9% Sterilization = 99.8% Only 100% reliable = abstinence Chapter 13 – Inheritance Nature vs. nurture Twin studies 1860’s Gregor Mendel – peas Easy to grow, self fertilizing Focused on traits that didn’t fit the blending theory 7 characteristics: seed shape, seed color, flower and see coat color, pod shape, pod color, flower position, stem length Round + wrinkled peas = 100% round Self fertilized this one = 25% wrinkled + 75% round Mendel called these traits factors – now we call them genes Alleles – different forms or varieties of a gene Some traits are multigene – hair color, handedness, skin color, nose shape 90% of prokaryote DNA is coded, also have plasmids with extra genes Homologous chromosomes carry same genes, but may have different alleles of these genes Chromosome banding helps identify (7 and X have similar length and shape, different bands) Easiest to make a karyotype during metaphase Probability can predict the results of matings Fractions, percents, or ratios Larger sample size will show less deviation from average Monohybrid cross, P (parent) generation First filial or F1 generation Second filial or F2 Dominant vs. recessive Genotype vs. phenotype Homozygous vs. heterozygous Punnett square Dihybrid crosses – two characteristics at once Principle of independent assortment – one gene doesn’t affect the other gene Principle of segregation – one allele from each parent is passed on Sex chromosomes Humans, most other mammals, fruit fly = Xy Lemmings = X, W, y Insects = XX female and X male Fish = ZZ males and ZW females Incomplete dominance = white + red = pink Codominance = white + red = spotted (blood types) Multiple alleles = blood types, IA, IB, i Antibodies Linked traits Genes on the same chromosome are often inherited together Frequency of crossing over can be used to map the chromosome Studies of fruit flies by Thomas Hunt Morgan in the 1910’s Eye color is a sex linked gene X-linked trait – gene only carried on the X chromosome Red-green colorblindness and hemophilia Barr bodies = inactive X’s in female cells Calico cat coloration caused by one X randomly being expressed and the other being shut off Nondisjunction – the failure of homologous chromosomes to separate in meiosis XXX, trisomy 21 Multifactorial – traits affected by several genes Can also be affected by environmental factors (height and intelligence) Chapter 14 – Mutations cause different expression of different genes Not all genes are automatically used Before genes can be transcribed RNA polymerase must bind to the promoter site An entire gene and its control system is called an operon In bacteria several genes can be transcribed from the same promoter: P O G1 G2 G3 Steroids can influence gene transcription Acts as transcription factor Binds to regulatory DNA sequence called a response element Cytoplasmic inheritance – females pass it on, males don’t, mitochondria (mtDNA) Seven daughters of Eve Genomic imprinting – which parent gave the allele is important Epistasis – one gene cannot exert is phenotypic effect unless a second gene is also expressed Genetic anticipation – genes are expressed earlier than they were in previous generations Huntington’s Disease Trinucleotide repeat expansion – the repetetions of the error increase with subsequent copying Myotonic dystrophy – muscle disorder Friedreich’s ataxia – neurologic disorder Huntington’s has CAG as repeated random filler in chromosome 4 Transposable elements = move from one chromosome to another Transposons – segments in genetic code that can be inserted into existing code Often put on plasmids Retrotransposons = DNA copy from RNA transposon, made via reverse transcriptase HIV may have evolved from one of these __________________________________________________________________________________________________ Chapter 15 – Genome = all of an organisms genes Human Genome Organization – regulate genome work worldwide HGP – determined the sequence of ~3 billion base pairs that make up the human genome One of the first mapped was E. coli Brewer’s yeast was first eukaryote Caenorhabditis. elegans was first multicellular organism (nematode) Now we are studying rice, corn, cotton, pigs, cows, More directed changes to genetics – not random artificial selection Using lots of computer modeling now Use recombinant DNA, insert into host cells Makes multiple copies, PCR, polymerase chain reaction Restriction fragment length polymorphism – used to compare lengths Used to identify individuals, dye added, bands appear Mutations are changes in the DNA sequence due to chemicals or radiation Usually caused by the failure of the DNA copying and repair mechanisms Point mutation = one base pair changes into a different one Missense mutations = point mutations that changes an amino acid that is important to protein structure and function Nonsense mutations = change the codon into a stop codon, makes a short protein Frameshift mutation = one or two base pairs are inserted or deleted from the DNA Changes every amino acid past that mutation point Different mutations can sometimes cause the same phenotype A mutation that reduces the activity of the enzyme phenylalanine hydroxylase results in the disorder phenylketonuria (PKU) – screen babies Sickle cell anemia and achrondroplasia (dwarfism) caused by 1 point mutation This makes detection easier because you can test that one gene Deletion = part of chromosome is deleted Translocation = part of chromosome A moved to chromosome B Inversion = part of chromosome flips Many somatic mutations are not important and lead to the death of a single cell, or cancer Gene amplification = normal production of more copies of a specific gene Gene therapy = attempt to treat the genetic defect rather than its results Germ line therapy = DNA of individuals gametes are changed so they are not passed on This requires the new genes being brought into the cells Place genes in a lipid vesicle that will allow it to move through the plasma membrane Insert the gene into a lysogenic virus Some tissues are easier than others We have had some success inserting normal CFTR gene into nose – cystic fibrosis Ethical, legal, social issues Is it good to know if you have a defective allele? Chapter 16 – Genetic variation in populations Evolution = change in populations over time Microevolution = change within a species, short time period, over dozens or hundreds of generations Macroevolution = longer periods of time, new species, extinction Population genetics = field of biology that studies microevolution Gene pool = all the genes of a local population Differences in humans are due to genetic differences Polymorphic population = a population with two or more alleles present Most sexually reproducing species have variation in their gene pool In humans the gene pools of any two people are 99.9% the same The ultimate source of variation is mutation Crossing over also helps stir alleles during meiosis Population geneticists use the Hardy-Weinburg Model which is an idealized mathematical model of gene pools The HW Model makes several simplifying assumptions: Organisms are diploid Generations are nonoverlapping Populations size is large Mutation is negligible Reproduction is sexual Gametes unite randomly Migration is negligible Natural selection does not operate Purple and white alleles The allele for purple flowers has a frequency of p The allele for white flowers has a frequency of q p+q=1 the frequency of plants that are homozygous for the allele for purple flowers for the next generation will be p 2. The frequency of homozygous white flowers will be q2. And the frequency of heterozygous plants will be 2pq. Allele frequencies tend to be stable over time Natural selection is the most important factors that changes gene pools In 1850 peppered moth had 95% light colored alleles and 5% dark alleles By 1900 these percentages had reversed Sickle cell polymorphism Up to 20% in regions of Africa Protects against malaria Migration can change frequencies and introduce new alleles to certain populations Gene flow = the effects of migration between gene pools Mutation also causes changes in populations, especially when the mutation is advantageous Genetic drift = affects small populations more than big ones, random chance Founder effect Causes gradual loss of heterozygotes Inbreeding = gradual increase of homozygosity California condor = 20 left in wild in 1980’s Population bottleneck = dramatic loss in size over a few generations Inbreeding depression = survival and reproduction rates drop as a result of inbreeding Cheetahs Inbreeding good for experiments and laboratories Many traits are multifactorial – influenced by more than one gene Artificial selection = breeders pick with quantitative traits they want to augment Pigeons Humans Identical vs. fraternal twins Environmental factors Controversies surround human intelligence and genetic aspects __________________________________________________________________________________________________ Chapter 17 – The big bang Measurement from deep space shows that the universe is expanding Doppler effect, red shift 1920’s Edwin Hubble studied light Backtrack to approximately 15 billion years ago Gravity pulled clumps together, caused orbits Earth formed ~4.6 billion years ago Moon formed from Earth being hit by meteor (?) The decay of radioactive elements such as uranium and thorium as well as some isotopes of potassium – 40 is the primary source of heat energy within the Earth Atmosphere probably formed from cooling gases Early atmosphere likely consisted of volcanic gases like N2, CO2, H2O, and H2, with some CO All early evidence indicates the O2 was probably not present Oxygen began to accumulate after the first photosynthetic organisms started to produce it about 2.1 – 2.4 billion years ago Modern oxygen levels were most likely reached around 360 mya (land plants abundant) Organic compounds do not form easily in N2 and CO2 rich atmosphere UV radiation bathed surface Extreme temperature variations Scarce supply of oxygen gas Ozone layer in stratosphere – 17 to 50 km Popular explanations for the origins of life on Earth: Life originated on another planet and traveled through space Life originated by unknown means on Earth Life evolved from nonliving substances through interaction with the environment Many people believe that a supernatural force created life That explanation is not within the scope of science, therefore these are not parts of scientific debates In the 1920’s Alexander Oparin and J. B. S. Haldane separately described the process of life evolving from nonliving substances Heterotrophy Hypothesis Requires 3 major steps: Had to be supply of organic molecules, produced by nonbiological processes These had to be assembled into nucleic acids and proteins Had to organize into something that could replicate itself In the 1950’s Harold Urey and Stanley Miller worked on how organic compounds could form in inorganic environments They were able to create organic compounds in airtight apparatus under conditions that may have been present 4.6 bya Recent experiments have made 13 of the 20 amino acids Also have formed all nitrogenous bases and ribose Evidence of step 1: Organic compounds have also been found on meteorites and in Haley’s Comet tail Also at mid-ocean vents Evidence of step 2: For complex molecules to form smaller molecules must have been extremely concentrated In 1985 A. G. Cairns-Smith suggested that clay particles may have helped form the first polymers by catalyzing the bonding together Evidence of step 3: Research has led to the belief that life began in an RNA world RNA served as information molecule and catalyst DNA later became information molecule Protein enzymes later became biological catalyst So far, we have not found any RNA that can replicate itself completely RNA molecules can undergo simulated Darwinian evolution in labs Boundary between chemical and biological evolution is the formation of self-replicating polymers Biological evolution consists of three processes: Self reproduction Mutation that can be inherited Natural selection Cell theory holds that all life is made of cells and all cells come from preexisting cells Origin of cells and membranes are still not understood In the 1980’s Carl Woese suggested that life may have begun with water droplets functioning as primitive cells Amino acids could have formed proteins randomly in the oceans There is no known way for proteins to replicate themselves RNA can direct the synthesis of DNA as in the AIDS virus Some scientist maintain that the early life forms could only have survived if they contained both proteins and nucleic acids Viruses probably evolved after their host cells, their role in evolution is unclear All of these ideas have supporters and opponents within the scientific community Some scientists have tried to investigate early life forms by searching for fossils What may be the oldest know microfossils were found in northwestern Australia in 1993 They are simple single celled cyanobacteria-like organisms are 3.5 billion years old This led to the understanding that life appeared on Earth much earlier than previously thought These fossils had stromatolites = dome like structure secreted by cyanobacteria Woese thought that the first organisms may have been methanogens Today these type of bacteria are found near hydrothermal vents First eukaryote fossils are around 2.1 billion years old Became common by 750 million years ago Margulis proposed that eukaryotes originated from a symbiosis Eventually the partners or endosymbionts lost the ability to live independently Endosymbiont hypothesis Some single celled organisms currently surviving may be descendants of weird evolution Giardia – two haploid nuclei and no mitochondria Paramecium – one large nucleus and ~20 smaller nuclei Chapter 18 – Taxonomy = effort to classify organisms in ways that show relationships and distinguish them Basic grouping used is a species = group of individuals capable of breeding and producing fertile offspring Individuals may look very different from each other These differences are known as variations Inherited variation is the raw material of evolution Natural selection works on variation Variations of populations include: Polymorphism Geographic variation Individual variation *dog breeds Differences between males and females is an example of polymorphism Geographic variation – human populations Some rare interbreeding does not necessarily make a new species – coyote and dogs Species remain separate in three basic ways: Potential mates do not meet Potential mates meet but don’t breed Potential mates meet and breed but do not produce fertile/viable offspring Limitations: Does not work well for asexual reproducing species Some sexual species may be only partially separated Does not accommodate slow evolutionary changes Classification is important to: Identify wild relatives for breeders Identifying parasites and disease vectors Identify indicator species Use: structure, behavior, biochemistry, and genes to group organisms by relatedness Homologies = structural resemblances that indicate a relatedness Analogies = structures that are similar in appearance and function but are not the result of a shared ancestry Arm bones Two factors make anatomical characteristics important: Easy to observe in fossils and organisms Fossils are the only record of past extinct species DNA sequencing also helps Carolus Linnaeus Swedish botanist developed modern binomial nomenclature (genus, species) scientific name – always in Latin to make it universal K P C O F G S – plants use divisions instead of phyla Domains 2 systemic approaches to classification were developed in the 1950’s Phonetics = equal importance to all characteristics Cladistics = groups organisms according to ancestry and homologous traits Eukarya Archaebacteria Eubacteria 5 kingdoms first outlined in 1959by Robert Whittaker Protista – most diverse, hodgepodge Protozoa Algae Absorptive Plantae – photoautotropic, multicellular, eukaryotic, develop from embryos Animalia – heterotropic, multicellular, eukaryotic, develop from embryos Arthropods – most abundant multicellular group Vertebrates – backbones Mostly sexual, motile, have senses and nervous system Fungi – heterotropic, eukaryotic Mostly multicellular, cell walls of chitin, reproduce from spore formation, decomposers Classification systems change Linnaeus had two – plants and animals Monera was added after microscopes confirmed differences between prokaryotes and eukaryotes Whittaker realized fungi were different from plants Chapter 19 – The idea of biological evolution did not start or end with Darwin’s The Origin of Species 1859 – stands out because it introduced evolution as a testable scientific theory Scientists have expanded and refined this idea One of the most important areas of biology Area of active research Scientists are currently exploring how species are related and change Fossil record very important Paleontology is the branch of biological sciences that studies fossils Hard parts most likely to be preserved Soft tissues can leave impression in mud that is then saved Whole bodies preserved in amber ~250,000 fossil species have been found and identified Estimates are that only 1 out of 10,000 actually get fossilized Fossils help offer record of organisms no longer on Earth Comparisons from different time periods help determine relationships Extinction Extinction rate has increased in recent days Coevolution = the continuous adaptation of different species to each other Red bellied newt and garter snake Cheetah and gazelle Human and tiger Controlled experiments can show how natural selection works Homologous genes responsible for similar body plans in related species The study of genetics has provided most of the support for molecular evolution Scientists can compare the amino acid sequence of homologous proteins in different species Provide a lot of information for the scientists and doctors currently studying disease Widespread antibiotic use over the last 50 years has led to resistance Genetic variation, what causes resistance? Speciation = the appearance of a new species Often slow, but artificial selection has sped up this process so it can be observed Genetic variation, stable populations are in dynamic equilibrium Often isolation leads to new species Inability to mate often results, gamete incompatibility or physical barriers Behavioral incompatibilities Seasonal and location barriers Prezygotic vs. postzygotic mechanisms Polyploidy in plants Adaptive radiation = rapid increase in number of species Common ancestor, new environment No to little change – horseshoe crabs crocodiles Gradualism = slowly accumulated changes lead to new species Punctuated equilibrium = rapid change at key times Chapter 20 – Human evolution Mammalian, primates, monkeys and apes ~55 mya human ancestors of monkey ape and human diverged from other primates Arboreal, opposable thumbs, nail not claws, manipulate objects with hands, sensitive fingers, wide range in shoulder and hip joint, erect form, binocular vision, optic chiasma allows brain to process 3D depth perception, color vision, Color vision most developed in old world primates, red, green, blue Large well developed brains, social groups, mostly omnivorous, usually 1 baby per birth, provide parental care, Humans, chimps, and gorillas share a brain structure. Human’s larger per body size Humans are bipedal Speech developed by many social species Skeleton’s pelvis and femur tell a lot about its movement, Hominids identified from fossils, few complete skeletons found, Ape vs. hominid Semi erect – upright Arms longer than legs – legs longer Low arch, grasping toe – nonopposable, toes in line for walking Gaps between canine teeth – no gaps Skull angled forward – on top of spinal column Heavy jaw, wide nasal opening – distinct chin, narrow nose, prominent nasal arch Brain 280 – 705 cc’s – 400 – 2,000 cc’s (average human 1400cc) Puberty at 10 to 13 – puberty at 13 Estrus at regular intervals – continuous Teeth and skulls very information about diet and brain size Only 1 type of hominid – all existing human one species, can interbreed Human and chip ~7mya Human and gorilla ~10mya Molecular data not usually available in fossils, compare structure and physical appearance Radiometric dating of surrounding layers Stratigraphy = analysis of layers of rock C-14 works for up to 50,000 years K-40 and U-235 or U-238 used for older things Hominids walked upright by 4mya Lived in Africa, grew taller and got bigger brains over time Lived in open land and used tools, spread Current questions: When and where did early humans leave Africa? What was the last common ancestor between us and apes? How many hominid species ever lived? Which ones died out, and which ones turned into humans? Ramapithecus lived 8 – 12 mya Have to incorporate sexual dimorphism Two major genera: homo and Australopithecus A. Anamensis ~4mya A. Afarensis ~3.2mya nicknamed Lucy found in Ethiopia in 1974 Lucy: 1 m tall, chimp sized brain, protruding face, relatively longer arms A. Africanus ~2.5 mya – 2 mya : then australopithecines underwent adaptive radiation Stone tools began to appear, at least 2 hominid species present A. Boisei and H. Habilis also A. robustus H. habilis 1st homo, disappeared from Africa ~1.5mya H. ergaster ~1.6mya first modern skeleton Turkana Boy, brain only half human size H. erectus present in Asia and Africa 1mya to 300,000ya, large stone axes and fire H. heidelbergensis 780,000ya in Spain, probably Neanderthal ancestor More robust than modern humans, buried their dead, wore jewelry 150,000 to 28,000 H. sapiens 130,000ya probably in Africa, lived alongside Neanderthals for thousands of years Interbreeding? Competition? Out-of-Africa = humans evolved in Africa and dispersed Multiregional = evolved at similar times from H. erectus and maybe Neanderthal Some evidence to support each Early H. sapiens were cave dwellers, used bone and stone tools, had art, maybe language Developed agriculture by 11,000 years ago Isolation of small groups caused differentiation, blood type B very high in Asia Genetic disorders found in specific populations Eye, hair, skin color, facial features __________________________________________________________________________________________________ Chapter 21 – The nervous system, along with the endocrine system, helps control and integrate all body activities. In humans, the nervous system serves 3 basic fxns. (All relate to homeostasis) 1. Sensing changes, both inside & outside the body (Sensory fxn.) 2. Interpreting these changes (Integrative fxn.) 3. Reacting to these changes by causing muscle contractions or glandular secretions (Motor fxn.) Branch of medical science that deals with nervous system = neurology CNS = Integrative fxn. = Interpret sensory info. & generate a response PNS = Sensory & Motor fxns. Sensory component = Afferent (incoming) = many different Rc’s which sense changes Motor component = Efferent (outgoing) = conduct impulses from CNS to muscles & glands PNS is also subdivided: Somatic (voluntary; conscious control) nervous system (SNS) Rc’s to the Neurons which conduct impulses from cutaneous & special sensory CNS (sensory or afferent) Motor neurons which send impulses from CNS to skel. Muscles (Efferent) Autonomic (INvoluntary) nervous system (ANS), somatic = voluntary, skeletal muscles Sensory (afferent) neurons from visceral organs to CNS Motor (efferent) neurons from CNS to smooth muscle, cardiac muscle, and glands ANS is made up of 2 opposing functional branches: 1. Sympathetic division 2. Parasympathetic division Found in CNS: Astrocytes = star-shaped cells with many processes Oligodendrocytes = look like small astrocytes Microglia = phagocytic cells derived from monocytes; protective Ependymal cells = simple cuboidal/columnar epithelial cells; may be ciliated; line brain ventricles & central canal of spinal cord; produce CSF Found in PNS: Neurolemmocytes = Schwann cells Flat cells wrapped around axons in PNS Produce part of the myelin sheath around one axon Satellite cells Flat cells around the cell bodies of PNS neurons support PNS ganglia (clusters of neuron cell bodies) 2 types of neuroglia produce myelin: a. Oligodendrocytes & Schwann cells (CNS axons) (PNS axons) Myelin sheath = lipid + protein; electrically insulates the axon & rate of nerve impulses Gaps in the myelin sheath = neurofibral nodes = nodes of Ranvier increases conduction Multiple Sclerosis (MS) = progressive destruction of myelin sheaths in CNS (oligodendrocytes); nerve impulses “short-circuit” Tay-Sachs disease = accumulation of excess lipids in CNS; MR & death Neurons = nerve cells Cell body = soma (cytoplasm, nucleus, organelles) Many dendrites a. short, tapering, & highly branched processes from cell body b. usually NOT myelinated c. Dendrites conduct impulses from Rc’s to the cell body (receive info.) Axon = long, thin, cylindrical projection from cell body a. Conducts impulses from one neuron to the dendrites or cell body of another neuron OR to an effector organ (muscle or gland) b. Axons may be < 1 mm long (CNS) or several meters long (PNS) c. Axon terminals and synaptic end bulbs Nerve fiber = general term; usually means an axon + its sheath; may also mean dendrite Nerve = bundle of nerve fibers (sheathed axons); found in PNS a. b. Usually contain BOTH sensory & motor nerve fibers Btwn. the nerve fibers/bundles is CT Ganglia = clusters of nerve cell bodies in PNS If you cut into brain or spinal cord, some areas are white; others gray White matter a. aggregations of myelinated processes from many neurons (axons) b. located around the periphery of spinal cord c. In brain, white matter forms the inner mass of brain tissue Gray matter a. cell bodies, dendrites, & axon terminals, unmyelinated axons & neuroglia (NO myelin) b. located in center of spinal cord; shaped like butterfly or letter H c. In brain, gray matter forms a thin shell over brain surfaces Mb of a nonconducting neuron is (+) outside & (-) inside (due to electrochemical gradients across the mb; Na/K pump) Typical RMP = -70 mV (mb is polarized) a. ECF contains mostly Na+ and Clb. ICF contains mostly K+, PO43-, and Proteinsc. Mb is also more permeable to K+ than to Na+ (K+ leaks out very quickly; Na+ leaks in very slowly) Refractory Period = time when another impulse cannot be generated All - or - None Principle = if a stim. is strong enough to generate an AP, the impulse travels at a constant, maximum rate & strength Saltatory conduction = impulse “jumps” from neurofibral node to node insulator; blocks mb-depolarization Nodes of Ranvier = contain many voltage-gated Na-channels Mb depolarizes very quickly at nodes Stops at myelin sheath Ions “carry” the electrical signal thru ECF & cytosol, to next node Nerve impulse “leaps” from node to node; travels very FAST Propagation Speed NOT related to strength of stimulus Larger the diameter of nerve fiver, faster the impulse travels Myelinated fibers conduct impulses faster than unmyelinated fibers Warm nerve fibers conduct impulses faster than cooled fibers Myelin sheath = electrical An excitatory NT = can depolarize the postsynaptic neuron membrane (less negative; closer to threshold potential) An inhibitory NT = hyperpolarizes the mb of the postsynaptic neuron (more negative; more difficult to start a nerve impulse) The same NT may be excitatory in some locations, and inhibitory in other locations! Each neuron may release several different NT’s simultaneously Ach: Excitatory at neuromuscular jxn., Inhibitory at other synapses (binds to different Rc’s), such as parasympathetic fibers to the heart; slows heart rate Glutamate & Aspartate = excitatory (Amino Acid NT’s) GABA & Glycine = inhibitory (Amino Acid NT’s) Biogenic amines / Catecholamines (synth. from the amino acid tyrosine) a. b. c. Norepinephrine Epinephrine Dopamine excitatory at some synapses; inhibitory at other synapses Strychnine binds to/blocks Glycine Rc’s in spinal cord Glycine = inhibitory; can no longer inhibit skeletal muscle contractions Meninges = 3 coverings that surround the spinal cord & brain Meningitis = inflammation of the meninges Spinal tap = lumbar puncture removal of CSF from subarachnoid space used to diagnose meningitis, etc. & to introduce Abics, anesthetics, chemo Reflex = a fast, predictable, automatic response to changes in the environment that helps to maintain homeostasis Reflexes help to maintain homeostasis by allowing the body to make RAPID adjustments to homeostatic imbalances Types of reflexes: Spinal reflexes = occur in the gray matter of the spinal cord (ex: patellar, Achilles, crossed extensor, flexor/withdrawal reflexes) Cranial reflexes = occur in the gray matter of the brainstem (ex: gag reflex, corneal (blink) reflex) Somatic reflexes = involve contraction of skeletal muscles (voluntary) (Some somatic reflexes are spinal and some are cranial reflexes) Autonomic (visceral) reflexes = involve smooth muscle, cardiac muscle, or gland responses (Involuntary) (ex: pupillary responses, salivation, etc.) Reflex Arc = simplest type of neuronal circuit / pathway; at least 1 synapse 5 functional components of a reflex arc: Receptor = responds to some stimulus; causes impulse Sensory neuron = carries impulse from Rc to integrating center Integrating center = inside CNS Motor neuron = carries impulse from integrating center to effector Effector = muscle or gland; responds to motor nerve impulse Brain Stem = (major function is to regulate visceral activities: breathing, heart rate, blood pressure, temp., etc.) Medulla = medulla oblongata (white matter) Pons = superior to the medulla, “bridges”/connects sp.cord with brain, & brain regions to each other Midbrain = connects the pons to the diencephalon; autonomic functions, regulates auditory & visual reflexes (moves head: buzzing bee; etc.) Cerebellum (major function is to coordinate muscle mvmnts.; subconscious) Control subconscious skeletal muscle mvmts. (muscle tone, posture, & balance) Diencephalon = Pineal gland = secretes melatonin, which is involved in diurnal cycles, Also helps regulate body rhythms, emotions; secretes hormones, Diencephalon acts as a relay station, Melatonin is secreted mostly at night; causes sleepiness, In some animals, melatonin is related to seasonal breeding patterns Cerebrum = Largest part of the brain, Surface layer = cerebral cortex = gray matter (cell bodies & dendrites), contains billions of neurons (only 2-4 mm thick!), Gyri = folds / convolutions Fissures = deep grooves Limbic System = Involved in emotions, memory, pleasure, & pain Frontal-responsible for skeletal muscle movements, motor speech movements, predicts consequences Parietal-receives sensory info, taste, interpretation of speech, and general interpretation of sensory info (language, math calculations) Temporal-receives info about special senses such as hearing and smell Occipital-receives visual info Brain is NOT symmetrical, either anatomically or functionally Left hemisphere is more important for: a. right-handed control b. spoken & written language c. numerical & scientific skills Right hemisphere is more important for: a. left-handed control b. musical & artistic awareness c. space & pattern perception d. insight e. imagination f. generating mental images of sight, sound, touch, taste, & smell Electroencephalogram (EEG) Brain waves = graded potentials & AP’s generated by the cerebral neurons simultaneously) Characteristic brain wave forms for certain mental states: a. Alpha waves = calm, awake with eyes closed b. Beta waves = seen during sensory input & mental activity c. Theta waves = normally seen in children; adults with stress or brain disorders d. Delta waves = normally seen in awake infants & sleeping adults; also seen with brain damage cortex (millions of Many drugs act at specific synaptic clefts Different classes of neurotransmitters Alzheimer’s Disease patients produce less acetylcholine Parkinson’s is cause by not enough dopamine ADHD is caused by imbalance Drug = something without nutrient value that is entered into the body to create a biological effect Depressants, stimulants, hallucinogens Psychoactive drugs = alter the psychological process Addictive, develop tolerance Alcohol and barbiturates = depressants, reduce nerve impulse transmission in part of the brain Cocaine, nicotine, caffeine, amphetamines = stimulants, increase alertness for a time, then cause period of depression Hallucinogens like lysergic acid diethylamide and mescaline interfere with serotonin and dopamine, thereby altering sensory perception Nerve cells are very similar, but nervous systems are broadly different. Many animals have ganglia arranged around the body so each part can act independently Hydra – nerve net, no ganglia, neurons evenly distributed Planaria – small anterior brain, 2 dorsal nerve cords Vertebrates – developed CNS 3 parts: hindbrain, midbrain, forebrain Stem, optic lobes, cerebrum Size is not as important as folds, and size compared to body Modifications: puffer neurotoxin does not affect its cells, electric rays navigate etc. Chapter 22 – Stimulus and response Organisms react to changes in their environment through changes in behavior Stimulus = anything that triggers a behavior Response = organisms actions Behaviors can be either innate or learned Instinct = innate behaviors Fixed action patterns = patterns of behavior that are characteristic of a given species Learned behaviors develop as a result of experience Imprinting = learned, can only occur during a certain time period in the organisms life Konrad Lorenz’s geese Habituation = an animal is exposed to a stimulus over and over may slowly lose its response, or habituate, to that experience Learning not to respond Conditioning = a stimulus is associated with another unrelated stimulus Ivan Pavlov, bell ringing means dog food, triggers salivation Habits and fears are often the result of conditioning Children are not afraid of mice or bugs Trial-and-error = food options, locations in nature The brain and nervous system control much behavior Genes affect the structure and development of the brain at every level There is a genetic basis for a variety of behaviors in many organisms Insects and fish = behavior dominated by genes Mammals = behavior dominated by environment The endocrine system also regulates behavior via hormones Courting and reproductive behavior depend on hormone levels Scientists observe behavior, and ask humans about their behavior Twin studies help determine what is nature and what is nurture Correlation = how closely two measurements are to each other Some animals live in large colonial societies Predator and prey relationships Leaders, followers, specialists Dominance hierarchies Caste systems – each individual does its job Societies provide predator defense Young born at certain time of year, safety in numbers Solitary benefits – large territory, weakest link Communication by sight, sound, etc. Pheromone secretions – chemicals that alter behavior of own species Be careful of anthropomorphism Humans live in highly structured social groups Hand holding, hugging, language is the most important Include things from the present, past, and future Chapter 23 – Immunity = free of disease; resistant to infection Susceptible = lack of resistance (immunity) Immune system is a functional system, rather than an organ system Structures & cells (lymphoid organs/lymphatic tissues) are scattered throughout entire body Immunity involves 2 components that work hand-in-hand: Innate (nonspecific) immunity; Innate = inborn Responds to invaders within minutes 2 lines of defense (external & internal) Adaptive (specific) immunity Not innate; must develop this type of immunity Adapts to a person’s environment; different for each individual Specifically attacks foreign pathogens Cellular and Humoral responses Innate Defenses Surface barriers (First Line of Defense) Skin provides a physical barrier against invaders, & sloughs dead cells Skin secretions are acidic Sebum contains certain FA’s to inhibit bacteria & fungi Mucus membranes line all body cavities & tracts open to external environment Sticky mucus traps invaders Nasal hairs filter some pathogenic invaders, dust, pollens, etc. Cilia in the bronchi "sweep" invaders upward to the throat Vaginal & stomach secretions are acidic (kills many pathogens) Tears & saliva contain lysozyme (kills bacteria) We also remove invaders by rinsing action of tears, saliva, urination, defacation, vomiting, etc. Internal defenses (2nd Line of Defense) = Involves cells & chemicals Phagocytes Monocytes routinely leave the bloodstream & develop into macrophages Which macrophages recognize & phagocytize pathogens, they release cytokines Some cytokines are involved in chemotaxis Chemically attract neutrophils & other monocytes/macrophages to infection site Other cytokines stimulate (activate) other types of leukocytes Mechanism of phagocytosis: Adherence = receptors on macrophage surface recognize & bind to antigens on the pathogen (invader) Endocytosis / formation of phagosome Formation of phagolysosome Killing, digestion & formation of residual body Exocytosis of residual material Neutrophils not only perform phagocytosis Also release defensins (puncture membrane of pathogens) May release toxic chemicals into ECF; neutrophil also dies (pus) Natural Killer (NK) cells Subpopulation of lymphocytes; these cells are NOT phagocytic Directly kills many different types of cancer cells & virus-infected body cells Very quick, before the adaptive immune system gets activated NK cells are stimulated by cytokines from macrophages & by interferons Receptors on surface of NK cells recognize & bind to antigen on surface of infected or malignant cells NK cells then release perforins (chemicals which create pores in membrane of infected or malignant cell) NK cells also release inflammatory chemicals Inflammation = response to infection, physical trauma, intense heat, irritants Inflammation functions to prevent spread of injury, clear away debris, allow for repair Damaged cells release many chemicals (histamine, prostaglandins, kinins, cytokines) These chemicals cause the 4 cardinal symptoms = Redness, heat, swelling, pain Redness: chemically-induced local vasodilation Increased permeability of blood vessels delivers needed cells & chemicals (Ab’s, phagocytes, coag. factors, Complement proteins, etc.) Increased blood flow helps remove dead cells and toxic substances Heat: due to chemically induced vasodilation; increases metabolic rate of cells Swelling: due to increased permeability Nutrients & oxygen leave blood; available for immune cells Harmful substances get diluted Clotting proteins (fibrin) forms a mesh barrier around injured site Pain: caused by bacterial toxins, inflammatory chemicals, and/or swelling Inflammatory chemicals also induce Phagocyte Mobilization (4 stages): Leukocytosis (rapid release of phagocytes from bone marrow into blood) Margination (inflamed endothelium sends out signaling chemicals) These chemicals bind to phagocytes as they pass by Phagocytes slow down, then cling to capillary walls Diapedesis (phagocytes squeeze out of capillaries Chemotaxis (inflammatory chemicals attract phagocytes to site of injury) Macrophages later attract other types of leukocytes to area Fever Inflammation is a localized response; fever is a systemic response Our own leukocytes secrete pyrogens (chemicals which trigger a fever) Fever creates a less favorable environment for many pathogens Fever intensifies the effects of interferons Fever also speeds up cellular repair Adaptive Defenses (3rd line of defense) Antigen-specific; system must be primed by prior exposure to a certain antigen Each lymphocyte and each antibody molecule is directed against only 1 specific antigen Adaptive defense is systemic; not limited to just the infection site Adaptive defense has memory (stronger response with subsequent exposures to same antigen) Antigens = ANTIbody-GENerating substances; usually proteins Complete antigen is capable of stimulating antibody production & binding with Ab Cells of adaptive immunity T and B Lymphocytes T-cells develop in the thymus (primary lymphoid organ) B-cells develop in the bone marrow Each type of Lymphocyte has it’s own function, and it’s own Ag-receptors Lymphocytes leave the primary lymphoid organs (bone marrow & thymus) Some migrate to secondary lymphoid organs (lymph nodes, spleen, etc.) Some migrate to peripheral lymphoid tissues Some lymphocytes circulate in blood & lymph All these lymphs constantly watch for foreign antigens Humoral immunity: Is the basis of vaccines Fights bacterial & viral infections Is responsible for transfusion reactions Antibody = a plasma protein which protects the body's cells from foreign invaders Primary immune response This occurs within 3-6 days after the first encounter with a foreign Ag Example: first Rh+ pregnancy in Rh-neg mother Latent or Lag phase - several hours or days; no detectable Ab's Then plasma cells produce Ab's Plasma cells live 4-5 days; Ab levels peak about 10 days after exposure Secondary immune response (Anamnestic response) This occurs with subsequent / repeated exposure to the same Ag Within hours after re-exposure, B memory cells produce Ab’s Within 2-3 days → very high Ab titer Titer stays high for a long time, & tapers off slowly Plasma cells live much longer than 4-5 days; titer can remain high for several months Back to Rh-disease example: 2nd baby is the one affected Natural = not artificially acquired (NOT from a syringe) Ab’s were produced because of exposure to an actual infection Artificial = acquired by injection (vaccines) Ab’s were produced because of exposure to a vaccine (NOT an infection) Vaccines may contain dead or attenuated pathogens, cells parts, inactivated toxins, or may be genetically engineered Vaccines provide foreign antigens, without serious symptoms Cellular Immunity (Cell-mediated; T-cells attack foreign cells) Responsible for tissue rejection, delayed hypersensitivity, intracellular parasites (ex: TB) Helper T cells (T4 cells) These lymphs have surface protein CD4 These cells get activated when “presented” with a foreign Ag (by the APCs) Helper T-cells secrete cytokines (lymphokines) Some cytokines stimulate macrophages Some cytokines activate Cytotoxic T-cells Other cytokines activate B-cells and NK cells [HIV destroys CD4 / Helper T cells] Cytotoxic T-cells (T8 cells)(Killer T-cells) These lymphs have surface protein CD8 APCs present foreign Ag to activate Cytotoxic T-cells Cytotoxic T-cells destroy foreign cells with perforins (punch holes in cell membranes) Perforins directly kill virus-infected or bacterial-infected body cells Perforins also kill cancer cells and transplanted tissue cells Suppressor T-cells Release cytokines that inhibit T-cell and B-cell activity when the Ag has been inactivated Keeps our immune response under control Memory T-cells Formed during a primary cellular response (first week after initial exposure) Similar to Memory B-cells Live for years; “remember” that same Ag and respond quickly upon re-exposure Organ Transplants / Prevention of Rejection 4 types of transplants: Autograft = donor is yourself (skin, bone, cartilage, vessels) Isograft = donor is identical twin (genetically identical) Allograft = donor is same species; not genetically identical; most common type of transplant Xenograft = donor is another species (pig, baboon) If the transplant is genetically identical tissue (Autograft, Isograft), transplant always successful For Allografts, must perform matching tests Immunosuppressive therapy is required, to prevent rejection of transplanted tissue Side effects of immunosuppression: high risk of infection; most frequent cause of death Homeostatic Imbalances of Immunity Immunodeficiencies SCID = Severe Combined Immunodeficiency Genetic deficiency of both B and T cells Requires life in a bubble, until bone marrow transplant can be performed AIDS = Acquired Immunodeficiency Syndrome HIV is transmitted via blood & body secretions through torn membranes HIV infects & destroys Helper T-cells HIV is a Retrovirus (RNA chromosome; reverse transcriptase; can make DNA from RNA) Viral genome mutates regularly (back & forth between DNA/RNA; many errors) HIV may remain dormant for many years Death often from secondary infection (pneumocystic pneumonia, tuberculosis) or cancer (Kaposi’s sarcoma) __________________________________________________________________________________________________ Chapter 24 – Biosphere – all of Earth’s ecosystems Consist of abiotic and biotic factors Climate and availability of water affects what organisms can survive Special adaptations prevent water loss, plants land animals ocean fish Sunlight also important – not limiting on land, photosynthesis in ocean occurs near surface Structure, pH and mineral composition of soil Wind shapes organisms and leads to water loss Fire, flood, avalanche can clear organisms for a while Transpiration from forests causes humidity Plant roots and lichen break down rock Some organisms tolerate extreme environments, usually only adapted to one or two Organisms require energy Producers – comsumers, photosynthetic amount determines biomass of an ecosystem Trophic structure – each step down has 10 times more energy Energy pyramid Food chain Food web Producers – plants algae Consumers – Apex predators – Decomposers – Herbivores, omnivores, carnivores Biomass – amount of living matter in an area Productivity – rate at which new biomass forms Predator/prey Competition Niche Competitive exclusion principle – no two species can occupy exactly the same niche Adaptive radiation helps reduce competition Mutualism – two species benefit each other Parasitism – one benefits at the expense of the other Commensalism – one benefits, other not affected Chloroplasts and mitochondria may have arisen from mutualistic relationships Circle of life, everything is recycled CO2, O2, N2 cycled through the air Soil is reservoir for P and S Carbon cycle Nitrogen fixation only done by some prokaryotes Turns N2 into NH3 (ammonia) Other bacteria turn ammonia into nitrite or nitrate which plants can use in a process called nitrification Limiting factors When limiting factors are not at play populations show exponential growth Population density – number of individuals per unit land Scarcity of resources, accumulation of waste Growth slows to a linear pattern, and eventually levels off Called logistic growth pattern, s shaped curve Top leveling off is carrying capacity Often wavers back and forth With fast reproduction in a species, times can occur when population explodes above carrying capacity Boom-and-bust cycle – over limit causes population to crash Predator and prey lines mimic each other only offset Chapter 25 – 25% of Earth’s surface is above water, terrestrial biomes Temperature, altitude, precipitation, soil components, topography, local disturbances Tropical rainforest – more than 250 cm rain per year Most complex, deforestation is huge problem Savanna – tropical or subtropical grasslands, seasonal precipitation 30 cm or less, center of continents Cool dry, hot dry, warm wet, largest herbivores Desert – hot, dry less than 25 cm per year, can be very cold in winter, no perennial vegetation, many succulents Chaparral – mild rainy winters, hot dry summers, midlatitude coastal, dense spiny shrubs, deer, fires Temperart grasslands – like savanna but with trees near streams, 25 – 75 cm, deep rich soil, periodic fires Three types in North America: tall grass prairie east/north, short grass prairie west, mixed grass prairie great plains Temperate deciduous forests – 75cm or more Taiga – northern coniferous forests, snow is major precipitation, not available to plants until spring thaw Tundra – very cold , north, or high, short plants, permafrost, alpine tundra found in Rocky Mountains Animals migrate, hibernate, only a few stay active year round Most of biosphere is aquatic Freshwater and marine Rivers and streams: salt content increases, temp increases, dissolved oxygen decreases, Lakes and ponds Zooplankton, phytoplankton Marine ecosystems: photic and aphotic zomes (sun penetrates or not) Intertidal, neritic (continental shelf), oceanic zones Open water = pelagic zone Benthic zone = sea floor, abyssal = sea floor with no light Organisms can move away from their current site or normal range Competition leads to dispersion Seed dispersion mechanisms Colonize – organism enters and unoccupied habitat and moves in Exotic species – new species Kudzu, zebra mussels Nutria Fireants New species cause ecosystem changes This process is called succession Primary comes from bare rock, glacial deposits, in lake beds Secondary comes where soil is already present, after fire, disturbance Annuals to perennials to climax community Ecosystems provide resources Wood, fuel, paper, grain, grazing land, 20% human protein consumption from oceans Ecosystems: modify climate, prevent erosion and build soil, break down wastes, store carbon maintain C cycle Control pests, maintain biodiversity, sources of drugs, recreation Called ecosystem goods and services Commons – common pool resources, air, water, little to no regulation, exploitation and pollution 1 year $33 trillion in ecosystem services Current population ~7 billion Human activity affects every ecosystem 11% of land surface for agricultural crops 7% pasture 4% cities, towns, roads = 22% land surface devoted to human use Loss of biodiversity Air pollution Acid rain CFC’s ozone depletion Greenhouse gases Need some greenhouse effect, too much? In 100 years 2C higher Rise in sea level of 50cm Current use is unsustainable