Starting Day 1 of Scott... Flashcards

Question

Problems with the Fossil Record – Dinosaur Extinction

Answer 1

Problems with the Fossil Record – Dinosaur Extinction Birds are dinosaurs There is only one area of the world that has good strata through the proposed extinction event There are only 2 non-avian dinosaurs in this strata Nothing killed the dinosaurs, they died out

Answer 2

Evidence For Evolution : Homology Related species can have features that are similar but function differently Homology – similarity resulting from common ancestry Homologous “The same organ in different animals under every variety of form and function" – Owen 1834 Traits of organisms that are evolutionarily related Either it’s homologous or it isn’t. There is not such thing as “highly homologous” or “% homology”

Answer 3

Divergent Evolution If enough differences accumulate between groups within a population, 2 new distinct populations may form When 2 groups of organisms are isolated reproductively or subjected to different selection pressures their traits diverge Gives rise to homologous features

Answer 4

Convergent Evolution The appearance of a similar trait or traits in unrelated organisms When groups organisms are subjected to the same selection pressure they tend to evolve similar designs Often gives rise to analogous features

Answer 5

Analagous Features A trait that appears similar in two unrelated organisms Not evolutionarily related

Answer 6

Evidence For Evolution : Homology Evolution can be viewed as a nested pattern of homologous characteristics Each group shares the deepest layer but adds it’s homologous features to form it’s own group This method lends itself to the creation of phylogenetic trees

Answer 7

Phylogenetic Trees AKA Evolutionary Trees Branching diagram depicting the evolutionary relationships among organisms based on their genetic and/or physical characteristics The organisms inhabiting the tree are implied to have descended from a common ancestor

Answer 8

Evidence For Evolution : Biogeography Biogeography – the geographic distribution of species This distribution is influenced by the movement of land masses Large areas of the surface of the Earth move slowly This has been going on for a long time

Answer 9

1. Variability: Individuals within a population must be different from each other. These differences may involve characteristics such as resistance to cold, susceptibility to disease, photosynthetic efficiency or the ability to attract a mate, to name just a few. 2. Heritability: Some of the variability between individuals must have a genetic basis. Thus offspring will tend to resemble their parents and have the same traits. 3. Differential Reproduction. Invidivuals with some traits will leave more descendants than others. This could be either because they survive longer (e.g. faster animals are better at escaping from predators) or because they have a higher reproductive rate (e.g. a bird with more colorful plumage may attract more mates.)

Answer 10

Population A population is a localized group of individuals capable of interbreeding and producing fertile offspring

Answer 11

Microevolution It is common to make the distinction between micro and macroevolution This is the same distinction between micro and macroscopic Microevolution A change in allele frequencies in a population over generations “Evolution on it’s smallest scale” according to your textbook Microevolution A change is DNA sequences in a population over time 3 mechanisms cause microevolution: Natural Selection Genetic Drift Gene Flow

Answer 12

Alleles Alleles are alternative forms of the same gene or same genetic locus They can be thought of as flavors in abstract ways such as Genetics In reality, alleles arise from differences in DNA sequence These differences in DNA sequence are not just single base pair changes, they can result from insertions, deletions, duplications, re-arrangements etc.

Answer 13

Genetic Loci The specific location of a gene or DNA sequence or position on a chromosome

Answer 14

Genetic Variation Within a population the individual organisms have various differences These differences are a result of different DNA sequences The genetic variation among individuals of a population is a result of the difference in nucleotide sequence

Answer 15

Gene Pool The set of all genes in any population, usually of a particular species

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Natural Selection and Variation If variation exists within a population, then evolution does not act equally on all the members of that population

Answer 17

It’s one character or the other with no in between Like flavors, or handedness and not continuous like height and weight Trait can be the result of a single gene or genetic locus Rare Lead to abstract mathematical modeling What Mendel focused on to prove his model

Answer 18

Variation Variation can be discrete or quantitative (continuous)

Answer 19

- the occurrence of different forms among the members of a population - two or more clearly different phenotypes exist in the same population This term is used differently for different types of biology EX: 1 Hawk - 2 Morphs

Answer 20

Quantitative Characters AKA continuous variation Like weight and height Trait can be the result of a multiple genes or genetic loci Common Lead to histograms and statistics Continuous Variation Can Appear Discrete

Answer 21

Measuring Genetic Variation Can measure the variation in genes – average heterozygosity Can measure the variation in nucleotide sequence – nucleotide variability AKA sequence identity

Answer 22

Average Heterozygosity The average percentage of loci that are heterozygous Compare all the loci on one chromosome vs. another Only works for diploids Nobody does this anymore

Answer 23

Nucleotide Variability Compare the DNA sequence between individuals in a population ~1% of the nucleotides are different between 2 fruit flies ~0.1% of the nucleotides are different between 2 humans

Answer 24

Geographic Variation Genetic Variation exists not just through time, but space as well Variations in population exist along spatial axes Geographic Variation Example Mice introduced to island in 1400s Mice populations isolated by mountains 2 different populations today Different populations have different numbers of chromosomes This is probably a result of genetic drift

Answer 25

Geographic Variation - Clines Geographic variation can occur as a cline A cline is a slope or a gradual and continuous change In biology, a cline is a graded gradient in a trait along a geographic axis

Answer 26

Sources of Genetic Variation Genetic Variation has to happen in the germ line cells of multicellular organisms for it to be passed on

Answer 27

Random Sources of Genetic Variation Genetic variation comes from random changes to the DNA sequence from base pair changes, insertions, deletions, duplications, re-arrangements, horizontal gene transfer etc.

Answer 28

Directed Sources of Genetic Variation Organisms have evolved to generate genetic variation through independent assortment, crossing over, random fertilization, etc. Organisms have evolved to generate genetic variation through base pair changes, insertions, deletions, duplications, re-arrangements, horizontal gene transfer etc.

Answer 29

Sources of Genetic Variation - Point Mutations A point mutation is the change in one base of a gene Often harmless due to the prevalence of non-coding regions and the redundancy of the genetic code Can be harmful as in sickle cell anemia

Answer 30

Sources of Genetic Variation - Changing Gene Number or Position Pieces of DNA in a chromosome can be duplicated, deleted, re-arranged, inverted, or moved to another location. Chromosomes can be fused or split Duplicated genes can evolve new functions by further mutation This is what Eukaryotes do

Answer 31

Genetic Variation Sources – Gene Duplication Duplicated genes can evolve new functions by further mutation Duplicated regions can increase genome size, increasing the material for evolution 1 ancestral odor-detecting gene has duplicated into over 1000 in humans

Answer 32

Genetic Variation Sources – Rapid Reproduction Some Prokaryotes can reproduce every 20 minutes Prokaryotes can also exist at high population densities This leads to high genetic variation

Answer 33

Genetic Variation Sources - Sexual Reproduction In prokaryotes, new DNA sequences are just one plasma membrane away, but multi-cellular eukaryotes have to incorporate changes into the germ line cells The random mutation rate is too slow for multi-cellular organisms who reproduce slowly and do not exist at high population densities Sexual reproduction evolved to overcome these problems ---- Sexual reproduction re-arranges alleles into new combinations Sexual organisms rely on recombination of alleles more than mutation to produce genetic variation

Answer 34

Genetic Variation Sources – Horizontal Gene Transfer AKA lateral gene transfer Horizontal gene transfer (HGT) is the transfer of genes from one organism to another in a manner other than reproduction There are many mechanisms to do this, and some organisms do it on their own Horizontal gene transfer drives the microbial world

Answer 35

The Gene Pool is Leaky Genes from one organism can become part of genome of another organism Nature has been making recombinant DNA too, a lot, and for a very, very long time Genetic material can be transmitted vertically and horizontally

Answer 36

Genetic Transmission The transfer of genetic material from parent to offspring during reproduction is called vertical The transfer of genetic material from one organism to another is called horizontal

Answer 37

Evidence for HGT 181 prokaryotic genomes were examined By their criteria, 80% of the genes had been horizontally transferred HGT and The Tree of Life HGT complicates phylogenetic trees, especially the tree of life

Answer 38

The Ring of Life If the early Earth harbored a pool of genes, perhaps this shared pool gave rise to the 3 distinct lineages we observe today

Answer 39

Revised “Tree” of Life

Answer 40

Hardy Weinberg Equation Can be used to test whether a population is evolving Early attempt develop mathematical methods to describe biology When aren't populations evolving? Over short time scales or when looking at single nucleotides Hardy Weinberg Principle: A population that is not evolving can be described by the HW principle A population is evolving if it does not meet the criteria of the HW principle The frequencies of alleles and genotypes in a population remain constant from generation to generation When gametes contribute to the next generation randomly, allele frequencies will not change in a given population This population is at Hardy – Weinberg Equilibrium

Answer 41

Harvey Weinberg Caveats The population at HW equilibrium must fulfill these 5 criteria: No mutations Random mating No natural selection Extremely large population size No gene flow

Answer 42

HW Equillibrium Populations can be evolving at some loci, while being in Hardy-Weinberg equilibrium at other loci

Answer 43

Changing Allele Frequencies Three major factors alter allele frequencies 1) Natural selection 2) Genetic drift 3) Gene flow

Answer 44

Natural Selection and Variation If variation exists within a population, then evolution does not act equally on all the members of that population Certain alleles are passed to the next generation in greater proportions due to differential success in reproduction

Answer 45

Changing Allele Frequencies - Genetic Drift Genetic drift is the change in the frequency of an allele in a population due to randomness The alleles in an offspring are a sample of those from their parents Whether a given individual survives and reproduces is random Genetic drift can cause alleles to disappear completely and reduce genetic variation

Answer 46

Effects of Genetic Drift Founder Effect: Occurs when a few individuals become isolated from a larger population Allele frequencies in the founder population can be different from those in the parent population Happens to island organisms or cults Bottleneck Effect: A large reduction in the size of a population due to random events Certain alleles can be over-represented in the survivors, while others can be absent

Answer 47

Genetic Drift in Action Humans kill almost all of a particular species Survivors suffer low genetic variability and are less fit This has happened many times

Answer 48

Genetic Drift Summary Genetic drift is significant in small populations Genetic drift causes allele frequencies to change at random Genetic drift can lead to a loss of genetic variation within populations Genetic drift can cause harmful alleles to become fixed

Answer 49

Changing Allele Frequencies - Gene Flow Gene Flow is the transfer of alleles from one population to another Alleles can be transferred by reproduction between members of the 2 populations Alleles can be transferred by the movement of gametes (pollen) Alleles can be transferred horizontally Gene flow can reduce (homogenize) genetic variation ---

Answer 50

Genetic Drift and Natural Selection Genetic drift may be random, but the outcome of natural selection consistently increases the frequencies of alleles that confer a fitness benefit Natural selection accomplishes this through ecological selection

Answer 51

Gene flow can increase fitness Antibiotic resistance genes can be transferred horizontally between microorganisms of different species ---- Gene flow can decrease fitness Island birds can breed with mainland birds Gene flow decreases the genetic diversity in the island birds Mainland birds are less adapted to island and are less fit Gene flow from mainland to island makes island birds less fit

Answer 52

Types of Natural Selection Ecological – natural selection minus sexual selection Sexual – maximize reproduction through sexual behavior

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Types of Ecological Selection Directional – One phenotype is favored causing the population to shift towards that phenotype Disruptive – extreme phenotypes of a trait are favored, dividing the population into 2 different groups Stabilizing - genetic diversity of a trait decreases as population stabilizes around one phenotype

Answer 54

Types of Ecological Selection

Answer 55

Sexual Selection Organism attracts mates Organism defeats rivals Done only by sexual creatures Used to explain any feature on an organism in the fossil record that doesn’t make ecological sense Sexual Selection Can result in, marked differences between the sexes called sexual dimorphism

Answer 56

Sexual Selection Intrasexual - selection within the same sex among individuals for mates of the opposite sex Intersexual - AKA mate choice, selection of sex partners Male showiness can increase a male’s chances of attracting a female and decrease his chances of survival

Answer 57

The Tree of Life I keep showing is based on nucleic acid sequences The tree is built by comparing the nucleic acid sequences for all the organisms depicted Which sequence(s)?

Answer 58

Preservation of Genetic Variation If natural selection is directional and stabilizing, why isn’t genetic variation wiped out? Neutral variation is variation that doesn’t confer advantages or disadvantages Other mechanisms exist --- Preservation of Genetic Variation - Ploidy Additional copies of the genome can have less favored alleles that can be hidden from selection When conditions change, these alleles could be useful

Answer 59

Preservation of Genetic Variation – Balancing Selection Balancing selection occurs when natural selection maintains stable frequencies of two or more forms in a population Balancing selection includes: Heterozygote advantage Frequency-dependent selection

Answer 60

Phylogenetics is the study of evolutionary relationships ## Footnote Phylogeny is the evolutionary history of an organism, organ, people, etc.

Answer 61

ALL organisms have ribosomes There are no other molecules that can substitute for rRNA so they are essential The rRNA sequences are usually the same within an organism

Answer 62

16S/18S rRNA Tree 16S/18S rRNA has a structural role in the ribosome 16S rRNA is part of the prokaryotic ribosome 18S rRNA is part of the eukaryotic ribosome 16S is used to build the prokaryotic part of the tree and 18S is used to build the eukaryotic part

Answer 63

16S/18S rRNA rRNA often has highly conserved sequences that flank its sequence or are within its sequence Conserved sequences are DNA, RNA, or protein sequences that are similar or identical between organisms These conserved sequences make it easy to use PCR to amplify rRNA genes from a variety of organisms In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within different molecules produced by the same organism (paralogous sequences). In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be. Since sequence information is normally transmitted from parents to progeny by genes, a conserved sequence implies that there is a conserved gene.

Answer 64

Using rRNA Sequences Get organism or part of organism Extract DNA Use PCR to amplify 16S/18S Use algorithm(s) to build the tree

Answer 65

Using Algorithms Algorithm - A process or set of rules to be followed in calculations or other problem-solving operations, especially by a computer Different algorithms can be used in phylogenetic analyses, often resulting in different phylogenetic trees

Answer 66

Problems with using rRNA in tree building Only works for extant organisms Eukaryotic trunk is really long and the deeply branching protist limbs are really long too Prokaryotes often have many copies of rRNA in their genomes and sometimes they are different

Answer 67

Balancing Selection - Heterozygote Advantage Heterozygote advantage occurs when heterozygotes have a higher fitness than homozygotes Two or more alleles will be maintained at that locus The sickle-cell allele causes mutations in hemoglobin but also confers malaria resistance

Answer 68

Balancing Selection – Frequency Dependent Selection In frequency-dependent selection, the fitness of a phenotype decreases if it becomes too common in the population Selection can favor whichever phenotype is less common in a population

Answer 69

Balancing Selection – Frequency Dependent Selection The surprise left hook may influence the prevalence of left- handed humans

Answer 70

Why Natural Selection Cannot Fashion Perfect Organisms Selection can act only on existing variations Evolution is limited by historical constraints Adaptations are often compromises Chance, natural selection, and the environment interact

Answer 71

Selection can only edit existing variations Natural selection favors the fittest, which may not be the ideal for long term New alleles do not arise on demand

Answer 72

Evolution is Limited by Historical Constraints Evolution can’t scrap everything and start over from the ground up Evolution co-opts existing structures and adapts them to new situations

Answer 73

Exaptation An exaptation is when a trait that evolved for one function becomes useful for another Feathers evolved for heat regulation later became useful for sexual displays and still later became useful for flight Deinococcus radiodurans evolved DNA repair for desiccation stress but it’s also useful for radiation stress

Answer 74

Adaptations are Often Compromises The flippers of a seal must allow it to walk on land AND swim efficiently The design of seal flippers is a compromise between these functions

Answer 75

Chance, natural selection, and the environment interact Studying biology is a lot like studying history because both are the result of so many random events

Answer 76

Chromosomal crossover (or crossing over) is the exchange of genetic material between homologous chromosomes that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs during prophase I of meiosis (pachytene) in a process called synapsis. Synapsis begins before the synaptonemal complex develops, and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

Answer 77

Mendel's Law of Independent Assortment This law states that allele pairs separate independently during the formation of gametes. Therefore, traits are transmitted to offspring independently of one another. Independent assortment Independent assortment of chromosomes generates haploid daughter cells with a combination of maternal and paternal chromosomes. In this example, the offspring can have any of four combinations: ry, RY, rY, or Ry, each leading to a specific phenotype. Independent assortment describes the combination of maternal and paternal chromosomes that make up the chromosome set in the haploid gamete.

Answer 78

Random fertilization According to random fertilization, any male gamete can combine with any female gamete. Given that there are 2^n different combinations of chromosomes for each gamete, each zygote can have (2^n) x (2^n) or 2^2n combinations of chromosomes. By affecting the combinations of alleles at different loci in a gamete, chromosomal behavior during meiosis contributes to genetic variation in three ways: an independent assortment of chromosomes, crossing over, and random fertilization of egg and sperm.

Answer 79

Genes Definition: Genes are segments of DNA located on chromosomes. Genes exist in alternative forms called alleles. Alleles determine distinct traits that can be passed on from parents to offspring. The process by which genes are transmitted was discovered by Gregor Mendel and formulated in what is known as Mendel's law of segregation. Genes contain the codes for the production of specific proteins. The information contained within DNA is not directly converted to proteins, but must first be transcribed in a process called DNA transcription. This process takes place within the nucleus of our cells. Actual protein production takes place in the cytoplasm of our cells through a process called translation.

Answer 80

Conserved Sequence In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within different molecules produced by the same organism (paralogous sequences). In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be. Since sequence information is normally transmitted from parents to progeny by genes, a conserved sequence implies that there is a conserved gene.

Answer 81

Anagenesis – the evolution of an entire population that transforms into a new species (gradual evolution) ## Footnote Cladogenesis – the splitting of a gene pool into 2 or more groups or clades giving rise to at least one new species Your book doesn’t talk about either one Your book assumes Cladogenesis

Answer 82

Speciation Speciation is the process by which one species splits into two or more species It explains the differences and similarities between species Forms a conceptual bridge between macroevolution and microevolution

Answer 83

Micro vs Macroevolution Microevolution consists of changes in allele frequencies within a population Macroevolution refers to evolutionary change at or above the species level

Answer 84

What makes a group a species? Traditionally, morphology was used to describe species More recently, biochemistry and physiology were used Now, nucleotide sequences are the norm in extant organisms

Answer 85

The Species Concept “But Scott, I thought you said species were and abstractions and not really real.” It depends on which organisms you are looking at and how you define “species” So yes, they aren’t real, but neither are chemical bonds as we understand them --- The Species Concept It has utility It allows us to describe some things accurately Like Newtonian Physics, it works fine for large, slow moving things

Answer 86

Approaches to the Species Concept Biological – reproductive isolation Morphological – anatomical differences Ecological – roles in the environment Phylogenetic – smallest group on organisms sharing a common ancestor as determined by morphology or molecular sequences

Answer 87

The Biological Species Concept A species is a group of populations whose members have the potential to interbreed and produce viable, fertile, offspring A species cannot reproduce with members of other species, which is known as reproductive isolation

Answer 88

Two “Different” Species Eastern vs. Western Meadowlarks One lives in the East US and the other the West Your book says their songs and other behaviors are different enough to prevent interbreeding in the wild Ornithologists say their territories overlap in the central US and they hybridize

Answer 89

Reproductive Isolation Gene flow occurs between populations of a species and this keeps the species together Reproductive isolation stops this gene flow and causes speciation Reproductive isolation prevents the creation of hybrids that result from mating between species

Answer 90

Barriers to Reproduction Prezygotic barriers prevent mating or fertilization Postzygotic barriers prevent the zygote from developing into a viable and fertile adult

Answer 91

Prezygotic Barriers Habitat Isolation Temporal Isolation Behavioral Isolation Mechanical Isolation Gametic Isolation

Answer 92

Prezygotic Barriers - Habitat Isolation 2 species can share the same geographic location but live in different habitats and thus never meet to mate

Answer 93

Prezygotic Barriers - Temporal Isolation Species that are active at certain times of day can’t mate with members of species active at other times of the day Species that breed at a specific time of day, season, or year cannot mix

Answer 94

Prezygotic Barriers - Behavioral Isolation Behaviors such as courtship rituals that are unique to a species prevent interspecies mating (and intraspecies mating too)

Answer 95

Prezygotic Barriers - Mechanical Isolation “Mating is attempted but morphological differences prevent it’s successful completion.”

Answer 96

Prezygotic Barriers – Gametic Isolation The sperm and eggs can mix but the sperm can’t fertilize the egg

Answer 97

Postzygotic Reproductive Barriers Reduced Hybrid Viability Reduced Hybrid Fertility Hybrid Breakdown

Answer 98

Postzygotic Barriers - Reduced Hybrid Viability Genetic incompatibility can abort development of the hybrid or produce a hybrid that is frail

Answer 99

Postzygotic Barriers - Reduced Hybrid Fertility Even if the hybrid matures normally, chromosomal differences between the parents can impair meiosis in the hybrid resulting in the hybrid producing abnormal gametes

Answer 100

Postzygotic Barriers - Hybrid Breakdown Even if the hybrid matures normally and is fertile, if it breeds with either parent species, or with each other, the resultant offspring are feeble and/or sterile

Answer 101

What are these domains? The rRNA tree is broken into 3 domains: Archaea, Bacteria, and Eukarya These domains supersede Kingdom level designations They supersede Linnaean taxonomy

Answer 102

Traditional Taxonomic Organization Before molecular methods, the old Linnaean taxonomic ranking did not include domains The traditional hierarchy goes: Kingdom, Phyla, Class, Order, Family, Genus, Species Mnemonic: King Phillip Came Over For Good Sex

Answer 103

The 3 Domain System Carl Woese ALL life on Earth is divided into 3 domains Introduced by Carl Woese in 1977 Arguably the most important evolutionary scientist since Darwin Established molecular methods for determining phylogenetic relationsips Proposed horizontal gene transfer Proposed the RNA World hypothesis Did not get a Nobel Prize

Answer 104

Prokaryotes vs. Eukaryotes

Answer 105

Prokaryotes: By definition, prokaryotes do not have membrane bound nuclei Archaea and Bacteria are prokaryotes Maybe the first living cells. Maybe Unicellular and multicellular Reproduce by binary fission Transfer DNA between cells

Answer 106

Eukarya By definition they have nuclei, but also contain other internal membranes/organelles Have mitochondria, or had at some point Have a lack of diversity in cellular metabolism Unicellular and multicellular Don’t often transfer DNA between cells Reproduce cells through mitosis Have specialized cellular reproduction called meiosis

Answer 107

Differences in Gene Expression Prokaryotes have many, many genes organized into operons while this is not as common in Eukaryotes Eukaryotes genes have many introns while prokaryotes have a few

Answer 108

Operon Its a cluster of adjacent genes They are co-regulated and transcribed together The genes often perform related functions The resulting mRNA is referred to as polycistronic (vs. monocistronic)

Answer 109

Intron It is sequence within a gene that is removed before translation Introns are more common in eukaryotes

Answer 110

In molecular biology and genetics, translation is the process in which cellular ribosomes create proteins. It is part of the process of gene expression. In translation, messenger RNA (mRNA) produced by transcription is decoded by a ribosome complex to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. In bacteria, translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome are located, and bind to the mRNA. In eukaryotes, translation occurs across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. The ribosome facilitates decoding by inducing the binding of tRNAs with complementary anticodon sequences to that of the mRNA. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome in a fashion reminiscent to that of a stock ticker and ticker tape.

Answer 111

DNA Transcription DNA transcription is a process that involves transcribing genetic information from DNA to RNA. The transcribed DNA message, or RNA transcript, is used to produce proteins. DNA is housed within the nucleus of our cells. It controls cellular activity by coding for the production of proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA. This ensures that the information contained within the DNA does not become tainted.

Answer 112

Prokaryotic and Eukaryotic Gene Organization

Answer 113

Bacteria Live in every environment on Earth The dominant life form on Earth, in terms of mass and total numbers Have diverse metabolisms Drive every nutrient cycle Prokaryotic pathogens are bacteria

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Archaea Originally isolated from extreme environments but found everywhere on Earth Despite the fact that archeans can live in the human body, no known pathogens exist, yet

Answer 115

Extreme Environments Some environments are physically or geochemically detrimental to most life Extremes can be temperature, pH, pressure, or salinity Organisms that thrive in these environments are called extremeophiles

Answer 116

Archaea More closely related to Eukarya than Bacteria Share a gene pool with Bacteria Have features in common with both domains, and features unique to themselves

Answer 117

They both change frequencies of alleles within a population Gene Flow is the transfer of alleles from one population to another It’s the movement of alleles into and out of a gene pool ---- Gene Flow vs. Speciation In speciation, one population becomes reproductively isolated and alleles no longer flow between them and another population In gene flow, the opposite happens and alleles flow between 2 different populations

Answer 118

Genetic Drift Genetic drift is the change in the frequency of an allele in a population due to randomness Genetic drift can cause alleles to disappear completely and reduce genetic variation Examples: The founder and bottleneck effects Drifting is a stunt in motor sports It’s a controlled skid around sharp turns It still subject to randomness when they crash The genetic diversity can crash due to genetic drift

Answer 119

The allelic frequency of allele A in a population is the fraction of all the alleles in the population's gene pool that are A. For example, if all the organisms in the population have the genotype Aa, then the frequency of allele A is 0.5 (because half the alleles are A). Note that the allelic frequency is not the fraction of the organisms that have an A allele, or the fraction that have a particular genotype or phenotype.

Answer 120

Frequency of A = 1X.1 + .5X.6 + 0X.3 = .4 Frequence of a = 1-.4=.6

Answer 121

Genotypic frequency is the fraction of the population that is a particular genotype. For example, if a population is 20 percent AA, 20 percent Aa, and 60 percent aa, the gentypic frequencies are .2AA, .2Aa, and .6aa. If we cannot assume HW equilibrium, there is no necessary relationship between allelic frequencies.

Answer 122

An allele frequency is the fraction of all alleles in the population's gene pool that are of that allele. For example, if all the organisms in the population have the genotype Aa, then the frequency of allele A is .5.

Answer 123

If you have a complete list of genotypic frequencies for apopulation, you can calculate allelic frequencies if the populations are in Hardy-Weinberg equilibrium. However, if those populations are not at HW equilibrium, it is not possible to determine allelic frequencies.

Answer 124

A simple Mendelian trait has two alleles, D and d. If a population is in HW equilibrium and is 49 percent homozygous dominant, what percentage is heterozygous? What are the allelic frequencies in the population? DD = 49% 49% = dd Dd = 2% Allelic frequency of D is .5 Allelic frequency of d is .5

Answer 125

If you know allelic frequencies, you can calculate gentypic frequencies if the population is at HW equilibrium, where the frequency of A = p, and the frequencey of a = q, we will always see the following genotypic frequencies: AA = p^2 Aa = 2pq aa = q^2 If we cannot assume HW equilibrium, there is no necessary relationship between allelic frequency and gentypic frequencies, and so we cannot determine genotypic frequencies.

Answer 126

The field devoted to the classification of organisms

Answer 127

What ecological conditions might result in the rapid diversification of some lineages? Rapid diversification occurs oftentimes after an extinction event, and the survivors have access to additional resourcees. Diversification can also occur when a species occupies a new niche, and adapts to the new environment in this niche.

Answer 128

In the real world, what factors might increase or decrease the probability of a species going extinct? A species is more likely to go extinct if it is small and specialized. Generalized species tend to avoid extinction more easily. Also, extinction may be more likely during habitat destruction due to catastrophic weather events. Elevated predation can increase extinction rates as well. For example, predation of the elephants by humans for their ivory nearly drove them to extinction.

Answer 129

vestigial structures have lost most if not all of their originial function through evolution. EX: The appendix in humans previously had digestive functions. Also, the ear muscles in humans are vestigial structures that are remnants of the muslces that human's ancestors utilized to better hear potential predators.

Answer 130

cladistics An approach to systematics in which common ancestry is the primary criterion used to classify organisms

Answer 131

parsimony The most parsimonious tree (which is the most likely) requires the least evolutionary events (molecular changes) to have occurred

Answer 132

synapomorphy a synapomorphy is a trait that is shared by two or more taxa and inferred to have been present in their most recent common ancestor, whose own ancestor is inferred to not possess the trait

Answer 133

apomorphy any character that the outgroup lacks. An apomorphy is a "derived," specialized," or "advanced" character. The cladist assumes that the common ancestor of the ingroup and outgroup possessed only ancestral characters, and that they still are prevalent in the outgroup. Thus, any character that the outgroup displays must be a plesiomorphy, and any character that the outgroup lacks must be an apomorphy

Answer 134

ingroup In cladistics, the monophyletic group that includes all taxa of interest to the current study

Answer 135

outgroup a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (the ingroup)

Answer 136

systematics a discipline focused on classifying organisms and determining their evolutionary relationships. Systematists use data from fossils to molecules and genes to infer evolutionary relationships.

Answer 137

character state Characters (heritable traits) are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.

Answer 138

plesiomorphy A plesiomorphy is an ancestral, less specialized, or primitive character. Any character that the outgroup displays must be a plesiomorphy, and any character that the outgroup lacks must be an apomorphy.

Answer 139

monophyletic group A monophyletic group (clade) is one ancestor and all of its descendants. It is defined by at least one Synapomorphy (all gropu members have the synapomorphy or synapomorphies).

Answer 140

A paraphyletic group consists of an ancestor and some of its descendants. A paraphyletic group is an incomplete clade, or a grade. It is defined by the absence of at least one character (all group members lack some particular character(s).

Answer 141

A polyphyletic group includes two or more taxa (populations of organisms), but not the common ancestor of those taxa. A polyphyletic group is defined by at least one similar character that evolved independently (by convergent or parallel evolution) in each group member. Taxa are placed in a polyphyletic group because they share some superficial similarity, not because they are closely related to one another.

Answer 142

Everything alive today has evolved a lot All living organisms have spent the same time under the hammer of natural selection They just have evolved to do different things than you

Answer 143

Taxonomy Taxonomy = Naming Things One of the oldest human endeavors Being able to agree on a word for something is essential to communication It is part of the “triumph of man.” ----- Taxonomy as the basis of language Animals consume a huge variety of plants Stone age people used a even larger variety of plants People needed to be able to remember and talk about the plants and animals they were using There are a lot of plants!

Answer 144

Taxonomy Needs to be Anal Common names are too varied and things need to be exact! Specific names are needed for specific things. Everyone who cares agrees on these names. Every field does this. Argot = the special vocabulary and idiom of a particular profession or social group

Answer 145

History of Biological Taxonomy 1500 BC Medicinal plants in ancient Egyptian paintings 350BC Aristotle divides invertebrate animals from vertebrate animals “Insects, jelly fish, and crabs are different from fish, frogs, and humans.” This system says things are different because of their features or morphology

Answer 146

Morphology Study of the form and structure of organisms and their structural features Anatomy is the study of the form and structure of the internal features of an organism Nobody studies the form and structure of just the external features of an organism anymore

Answer 147

History of Biological Taxonomy Started by the Greeks and continued by the Romans Later done by educated rich men in different places Latin was still their common language Therefore we use Latin names today --- 15th century long Latin names Tomato: Solanum caule inermi herbaceo, foliis pinnatis incisis Or, “solanum with the smooth stem which is herbaceous and has incised pinnate leaves.”

Answer 148

Father of Biological Taxonomy Carl von Linne (AKA Carolus Linnæus) 1735 Systema Naturæ “No man has ever transformed science in the way that I have.” “Jehovah created, Linnæus organized.”

Answer 149

Systema Naturæ All matter is in one of 3 kingdoms: animal, vegetable, or mineral Linnaean Taxonomy: Binomial Nomenclature Classification System

Answer 150

Binomial Nomenclature A system of naming organisms by giving them a name composed of two parts, both in Latin “Latin Name” The first name is the genus and the second name is the species

Answer 151

Classification System Categorize organisms into groups called taxa There is a hierarchy to these groups 5 Initial levels: Kingdom Class, Order, Genus, Species --- 7-8 Level Classification System Phylum and Family added Minerals kicked out Domain slapped on top

Answer 152

5 Kingdom System

Answer 153

Problems with Linnaean Taxonomy It’s based on opinion “This is a taxonomic group because I say so” Even when rationalized by morphological analyses, it’s still essentially qualitative. “It lives in the water so it’s a fish.” It has nothing to do with evolution.

Answer 154

Modern Taxonomy 1960: Cladistics AKA: Phylogenetic Systematics ------- Cladistics Categorize organisms into groups called clades A clade is an ancestor organism and all their descendents Still based on morphology but now it’s systemized Grouping organisms is no longer a matter of opinion, there are rules Now taxonomy includes evolution

Answer 155

Cladogram A cladogram is a phylogenetic tree formed by using cladistics

Answer 156

Rotating Branches

Answer 157

Reading a Cladogram

Answer 158

Synapomorphy A derived character (or trait) shared by 2 or more taxa that was present in their most common recent ancestor Plesiomorphy A primitive character (or trait) shared by 2 or more taxa

Answer 159

Reading a Cladogram

Answer 160

Monophyletic Group An ancestor organism and all its descendants It is defined by at least one synapomorphy Polyphyletic Group Two or more taxa, but not the common ancestor Can be the result of convergent evolution Paraphyletic Group An ancestor organism and some of its descendants Reptiles is a paraphyletic group if it does not include birds Mono vs. Poly vs. Paraphyly

Answer 161

Molecular Phylogenetics Instead of looking at the features or morphology look at the DNA sequence Conceived in the 1960s Begun in earnest in the 1970s -- Get the DNA sequence and compare between organisms This is how it’s done now. As long as you can get DNA… --- Get DNA sequence Compare the sequence of gene(s) Make tree based not on physical characteristics, but nucleotide sequence -- Molecular Phylogenetic tree

Answer 162

Phylogenetic Tree vs. Cladogram The terms phylogeny, evolutionary tree, phylogenetic tree, and cladogram are often used interchangeably Technically this is incorrect -- A phylogenetic tree can contain information about evolutionary distance. This information is included in the length of the branches In a cladogram the branch lengths are arbitrary and have no meaning

Answer 163

Phylogenetic Tree Branch Length The length of a branch in a phylogenetic tree can indicate evolutionary distance This can be described by time or number of changes Number of changes can be described by morphological changes or changes in nucleotide sequence

Answer 164

Multifurcation vs. Bifurcation Bifurcation - the division of something into two branches or parts Multifurcation – the division of something into more than two branches or parts Cladistics uses bifurcation only Molecular methods include multifurcation -- Multifurcation is Acceptable

Answer 165

Rooted vs. Unrooted Trees Phylogenetic Trees can be either rooted or unrooted A rooted tree assumes a common ancestor An unrooted tree does not

Answer 166

Rooting Trees

Answer 167

Rooted Tree One unique node on the tree is the common ancestor of everything else on the tree Often trees are rooted by choosing an outgroup

Answer 168

Unrooted Tree Unrooted trees depict the relationships between the members on the tree without assuming a common ancestor Computational methods often generate unrooted trees, and people pick outgroups to root them

Answer 169

How many trees are possible? If I have 4 groups, 3 unrooted trees are possible 5 species, 15 possible trees 6 species, 105 possible trees ...60 species, 10^70 trees possible!

Answer 170

You had 105 trees to chose from in lab

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How many trees are possible? Researchers routinely make trees with many groups They can’t possibly screen all the possible trees for the best tree They use tricks to reduce the number of possible trees For example, the most likely tree has the fewest evolutionary events (i.e. parsimony)

Answer 172

Parsimony Parsimony is the adoption of the simplest assumption in the in the interpretation of data Occham's razor – principle stating that the hypothesis that has the fewest assumptions is the best

Answer 173

Computational Phylogenetics Traditional phylogenetics uses morphological features to make trees Molecular phylogenetics uses nucleotide sequence to make trees Computational phylogenetics uses algorithms to make trees

Answer 174

An algorithm is a process or set of rules to be followed in calculations or other problem-solving operations, especially by a computer

Answer 175

Computational Phylogenetics You can use computational phylogentics on morphological and molecular data When using morphological data, you have to pick and define characters to use to make the tree When using molecular data, the characters are already defined

Answer 176

Using Computational Phylogenetics There are many different techniques They can generate many, many different trees --- What features should be used to construct a tree? Morphological features are used when molecular data is unavailable Use features the are homolgous

Answer 177

Homologous Features of organisms that are evolutionarily related These features can be organs or nucleotide sequences Either it’s homologous or it isn’t. There is not such thing as “highly homologous” or “% homology” Homologous Organs

Answer 178

Homologous Genes Two or more genes that are derived from the same ancestral gene PAX6 is a gene in humans that regulates eye development Similar genes exist in many, many animals that encode for proteins that also regulate eye development The most parsimonious explanation is that these genes are homologous

Answer 179

Multiple Sequence Alignment These are proteins that are made up of amino acids! DNA = Brain or "blue print" RNA = thoughts proteins = doing

Answer 180

Multiple Sequence Alignment 2 3 or more DNA, RNA, or protein sequences that are aligned usually to indicate evolutionary relationships It’s a character matrix of sequences You did character matrices in the cladistics labs

Answer 181

Data Matrix in Lab

Answer 182

Molecular Data Matrices

Answer 183

One Letter Code for Amino Acids

Answer 184

Using Computational Phylogenetics Use homolgous genes and align them Use alignment to build tree There are many methods to do this A popular method is maximum parsimony

Answer 185

Building a tree with Maximum Parsimony Create all possible trees Choose the tree that has the minimum number changes

Answer 186

Feeding All living things do it Called –trophy Both energy and reduced carbon are needed

Answer 187

Energy vs. Reduced Carbon Energy is used to do work Reduced carbon is used in the synthesis of biological molecules One food source can be both energy and reduced carbon

Answer 188

Naming Organisms Based on Lifestyle ALL organisms can be grouped by the methods they use to solve their feeding needs Some organisms can switch methods -- Needs All living things need: Energy - needed for work Electrons – needed for redox reactions Reduced Carbon- needed for biosynthesis The source of electrons is often omitted when naming groups

Answer 189

Named by Nutritional Needs Example Chemoorganoheterotroph

Answer 190

Energy Needs Energy is needed for movement, growth, development, and for chemical reactions The energy is stored as potential energy in the chemical bonds in nucleotides, carbohydrates, proteins and fats (sort of)

Answer 191

Energy source + -troph Phototrophs get their energy from sunlight Chemotrophs get their energy from the oxidation of electron donors

Answer 192

Reduced Carbon Needs Reduced carbon is used in the synthesis of biological molecules Reduced carbon is needed to make all 4 classes of biological molecules

Answer 193

Carbon source + -troph Autotrophs get their energy from CO2 Heterotrophs get their carbon from organic compounds

Answer 194

Combining Names

Answer 195

Reduced Carbon CO2 + 4e- + 4H+ → CH2O + H2O The carbon in CO2 is not biologically available By reducing it, it becomes available for biosynthetic reactions

Answer 196

Fixing Carbon Organisms take CO2 from the environment and make it into reduced carbon This process is called fixing carbon This takes energy The reduced carbon is used to make biological molecules

Answer 197

Redox Reactions Redox stands for reduction - oxidation Redox reactions involve the transfer of electrons between atoms --- Reduction is the gain of electrons Oxidation is the loss of electrons OIL RIG or LEO says GER

Answer 198

Electron Needs Electrons are needed in redox reactions that involve the transfer of energy The electrons can come from organic or inorganic sources This distinction is only common amongst the Chemotrophs

Answer 199

Electron source + -troph Organotrophs get their electrons from organic compounds Lithotrophs get their electrons from inorganic compounds

Answer 200

Heterotroph Examples Chemoorganoheterotrophs – use organic reduced carbon sources for energy, electrons, and biosynthesis Chemolithoheterotrophs – use reduced inorganic substrate for energy and electrons and eat molecules for biosynthesis Photoheterotrophs- use light for energy but consume reduced carbon from the environment

Answer 201

Chemoorganoheterotrophs Decomposers You

Answer 202

Chemolithotrophs They can oxidize minerals such as Sulfur, Iron, Uranium, or even Hydrogen

Answer 203

Photoheterotrophs They use light for energy They eat fatty acids, sugars, and alcohols Aphids may have symbiotic photoheterotrophs

Answer 204

Autotrophy “Self feeding” Primary producers – base of the food web Harness light or chemical energy in the environment to make cellular energy and make complex organic compounds

Answer 205

Types of Autotrophs Chemoautotrophs – get energy from oxidation of electron donors in their environments Lithoautotrophs - get energy from reduced compounds of mineral origin Photoautotrophs – get energy from light

Answer 206

Photoautotrophy = Photosynthesis Use sunlight to get energy Use CO2 to fix carbon

Answer 207

Homologous Genes The claim than genes are homologous is not verifiable without a time machine However, the higher the similarity in two sequences the lower the probability that the two sequences originated independently due to chance This probability can be calculated ---- Homologous Genes Example Compare a: 100 nucleotide sequence from organism A and a 100 nucleotide sequence from organism B If the sequences are 80% the same the probability that they evolved independently in the last 4 billion years is very, very low

Answer 208

Nutritional Modes (Wikipedia)

Answer 209

Carbon source + -troph Autotrophs get their carbon from CO2 Heterotrophs get their carbon from organic compounds

Answer 210

2 Names Are Not Enough For Chemotrophs Chemoheterotrophs and Chemoautotrophs can be further subdivided into 2 more groups depending upon where they get their electrons for electron transport

Answer 211

Lithotrophy Lithos means rock So they are rock eaters Rock eaters! ---- Why are chemolithoautotrophs important? They don’t rely on sunlight for energy or need to eat photoautotrophs or heterotrophs They make life on other planets much more likely

Answer 212

Chemolithoautotrophs II Most are bacteria Most, but not all are extremophiles Participate in biogeochemical cycling Found 2 miles below the surface of the earth Help make soil from rock

Answer 213

“Kingdom” Protista ---- Protists, Protozoans and Protista The traditional view: Protists are single celled eukaryotes including protozoans and algae Protista is a kingdom level taxanomic unit that is composed of protists Protozoans are unicellular eukaryotic heterotrophs, usually motile ---- Wastebasket Taxa Wastebasket taxa are used to classify organisms that do not belong anywhere else Many eukaryotes are not plants, animals, or fungi, so they were all lumped together in one taxon, protista Invertebrates is another wastebasket taxon

Answer 214

Protists are a paraphyletic group!

Answer 215

So what do we call them? This is still a hotly debated issue Molecular phylogenetics destroyed many earlier assumptions Wait a few years for a better view of the organization of this group --- Protist/Protozoan is still commonly used Single celled eukaryotes is also common but technically incorrect as there are many colonial organisms in this group Eukaryotic microbes or Eukaryotic microorganisms is also used, but incorrect due to microscopic eukaryotic animals --- Eukaryotes that aren’t plants, animals, or, fungi is too long Tissueless Eukaryotes is probably the best term, but not popular because I just made it up My made up term also depends on the definition of tissues

Answer 216

Tissue A tissue is a group of specialized cells from the same origin performing the same function

Answer 217

Tissue in the Multicellular Hierarchy Tissues are made up of cells Organs are made up of tissues Biological systems are made up of organs An organism is made up of biological systems

Answer 218

Tissue in the Multicellular Hierarchy II

Answer 219

Protists Don’t Have Tissues While this group contains colonial organisms, their cells are not differentiated into tissues Or are they? ---- Chlamydomonas Unicellular flagellated “algae” Swims Has a chloroplast Has an eyespot

Answer 220

Volvox Volvox is basically a bunch of Chlamydomonas stuck together It’s a colonial “alga” with up to 50,000 cells Their flagella beat together to propel the colony like a tissue They have specialized reproductive cells

Answer 221

Volvox is basically a bunch of Chlamydomonas stuck together It’s a colonial “alga” with up to 50,000 cells Their flagella beat together to propel the colony like a tissue They have specialized reproductive cells --- Can reproduce by making daughter colonies or sexually Has specialized reproductive cells that make sperm and eggs Some species are diecious ---- Monoecious (Greek for one household) species are hermaphroditic and contain all sexes Dioecious species are divided into genders Even though Di means two, there are many species that have more than one gender

Answer 222

Protist Examples - Amoeba Genus level taxon No definite shape – moves by pseudopods 10X the genome of humans Originally thought to be asexual but this view is changing

Answer 223

Protist Examples - Euglena Genus level taxon Unicellular and flagellated Can do chemoorganoheterotrophy or photoatutotrophy Originally thought to be asexual but this view is changing

Answer 224

Protist Examples - Paramecia Genus level taxon Unicellular and cilliated Have multiple nuclei Have sex

Answer 225

Deinococcus radiodurans Most radiation resistant organism known 500-1000 rads will kill a person Deinococcus can survive 1,500,000 rads Can survive toxic environments Can survive desiccation Doesn’t make spores ---- Instead of hiding in a spore it can repair its DNA from fragments Has multiple copies of its genome to serve as templates DNA repair helps it survive desiccation

Answer 226

exaptation An exaptation is when a trait that evolved for one function becomes useful for another Feathers evolved for heat regulation later became useful for sexual displays and still later became useful for flight Deinococcus evolved its DNA repair for desiccation stress but it’s also useful for radiation stress This means Deinococcus didn’t evolve for space travel, but perhaps could survive it now

Answer 227

spores Made by bacteria, fungi, plants, algae, and protozoans for dispersal Like a seed but smaller and tougher Can remain dormant for millions of years Resistant to radiation

Answer 228

bacterial endospores DNA and protein surrounded by a protein coat Not a true spore as it’s not produced by reproduction It’s a place for the bacteria to hide when times are tough When times are good the spore germinates ---- Don’t need food Can survive high temperatures, extreme freezing, ultraviolet radiation, desiccation, and chemical disinfectants Contains internal proteins that protect DNA from UV damage Have been isolated from inside rock Have been germinated after 25-40 million years

Answer 229

Endospore Formation

Answer 230

Interplanetary Panspermia is Happening Now The methods exist The organisms exist Very hardy forms of life are leaving the Earth and traveling into space --- If Panspermia can be interstellar, then life is more prevalent in the Universe It makes evolution on many worlds easier However life still had to evolve at least once somewhere

Answer 231

Abiogenesis The study of how life could evolve from inorganic matter Describes how life could have arose on Earth

Answer 232

Elements in Biology Sulfur Phosphorus Oxygen Nitrogen Carbon Hydrogen SPONCH The key elements that compose living things.

Answer 233

Early Earth Atmosphere was probably different There was little oxygen, so the atmosphere was not oxidizing The early atmosphere was reducing and contained sulfur, oxygen, nitrogen, carbon, and hydrogen All we need is phosphorus and the atmosphere is SPONCH

Answer 234

Urey-Miller Experiment Recreate the hypothetical early Earth atmosphere Subject it to artificial lightning Make amino acids, nucleotide bases, and energy rich hydrocarbons Make molecules similar to the ones found on Titan It’s very easy to make adenine

Answer 235

ATP: Adenine to Adenosine

Answer 236

ATP: Adenosine Triphosphate

Answer 237

Adenosine vs. Deoxyadenosine

Answer 238

NAD+ Nicotinamide adenine dinucleotide Found in all living cells Involved in electron transfer Used to shuttle electrons from Glycolysis and the citric acid cycle to the electron transport chain

Answer 239

Redox and NAD(P)H

Answer 240

FAD+ Nicotinamide adenine dinucleotide Found in all living cells Involved in electron transfer Used to shuttle electrons from the citric acid cycle to the electron transport chain

Answer 241

Acetyl-CoA

Answer 242

Kreb's Cycle, etc.

Answer 243

T/F: Plant cells contain mitochondria True!

Answer 244

T/F: Polymorphisms are a result of discrete variations of traits within a population True!

Answer 245

Photosynthetic organisms are photoautotrophs T/F? True!

Answer 246

Metabolically, eukaryotes are not a very diverse group of organisms: T/F True!

Answer 247

Urey Miller Experiment (Picture) Recreate the hypothetical early Earth atmosphere Subject it to artificial lightning Make amino acids, nucleotide bases, and energy rich hydrocarbons Make molecules similar to the ones found on Titan It’s very easy to make adenine

Answer 248

RNA World Hypothesis RNA can store information and catalyze reactions What if the reaction you are catalyzing makes more of you? RNA can regulate transcription RNA can bind substrate and direct transcription

Answer 249

Organic Soup Model The early earth’s reducing atmosphere was exposed to energy through sunlight and lightning This produced simple organic compounds or monomers These compounds accumulated and concentrated at various locations and localized sources of energy By further transformation, more complex organic polymers developed

Answer 250

From Molecules to Cells Phospholipids Can form structures called coacervates in water, abiotically Make up the cell membrane Coacervates A microscopic sphere of lipid molecules held together by hydrophobic forces from a surrounding liquid Can form spontaneously Are selectively permeable Plasma membrane Surrounds the cell Made of a phospholipid bilayer Selectively permeable Coacervates (picture)

Answer 251

First life on Earth Only known from fossilized stromatolites 3.5 billion years old Life probably began earlier Stromatolites Microorganism collects sediment and deposits it around itself After a long time this sediment builds up and forms rock Can also be produced abiotically

Answer 252

Ecological Questions Who is where? Study the distribution of organisms or biodiversity What are they doing? Study nutrient and energy cycling Ecology Ecology is the study of the interaction between organisms and their environment It’s also study of relationships between organisms The fact that humans are organisms causes some confusion --- Ecology includes abiotic factors like weather, climate, seasonality, and geography Its complexity lends itself to statistics heavy analyses Ecological studies often favor holistic approaches rather than traditional reductionism

Answer 253

Reductionism is the idea that a complex system is the sum of its parts ## Footnote Naive reductionism is the belief that reductionism leads to a complete understanding of a phenomenon

Answer 254

Holism Holism is the idea that a complex system should be seen as a whole and not a sum of its parts Naive holism is the belief that a qualitative and subjective assessment leads to a complete understanding of a phenomenon Holism is popular now --- Holism Example and Reductionist Rebuttal The Yankee$ have the best players, but don’t always have the best team A baseball team is more than the sum of it’s players Reductionists would say you didn’t study enough parts and try to measure things like morale and esprit décor

Answer 255

Systems Theory Systems theory is the interdisciplinary study of systems in general with a focus on the interrelatedness of all phenomena The goal of systems theory is to elucidate principles that can be applied to all types of systems at all nesting levels in all fields of research Something that can not be reduced to it’s component parts is called a system

Answer 256

Systems Biology Systems Biology is the study of interactions within biological systems using a more holistic approach Systems Ecology is interdisciplinary ecology with a holistic approach Hasn’t ecology always been that way?

Answer 257

It must be a real field because it has a journal

Answer 258

Nested Levels From smallest to largest: atoms, molecules, macromolecules, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biomes, biosphere

Answer 259

Nested LEvels 2 From smallest to largest: atoms, molecules, macromolecules, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biomes, biosphere

Answer 260

Nested Levels 3 From smallest to largest: atoms, molecules, macromolecules, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biomes, biosphere

Answer 261

Population A population is a localized group of individuals capable of interbreeding and producing fertile offspring Community A community is all of the organisms that inhabit a particular area It’s an assemblage of populations of different species that can interact

Answer 262

Biome A biome is one of the worlds major ecosystem types Terrestrial biomes are classified by predominant vegetation and weather Aquatic biomes are classified by physical environment

Answer 263

Biosphere The biosphere is the entire portion of earth that is inhabited by life It is the sum of all biomes -- How big is the biosphere? Microbes have been isolated at an elevation of 41 km (25 mi) Microbes have been isolated from 11km (6.8 mi) deep in the ocean and 5km (3 miles) deep on land

Answer 264

Population Ecology It’s the study of populations in relation to their environment It’s concerned with the density, distribution, size, and age structure of a population

Answer 265

Population Density It’s the number of individuals per unit of area or volume Dispersion is the pattern of spacing among individuals within the boundaries of the population

Answer 266

Population Dynamics Population dynamics studies changes in the size and age composition of populations, and the biotic and abiotic processes influencing those changes It deals with birth and death rates, immigration and emigration, and studies topics such as aging populations or population decline

Answer 267

Emigration is leaving a population ## Footnote Immigration is entering a population

Answer 268

Metapopulation A metapopulation is a number of linked local populations It’s of a group of spatially separated populations of the same species which interact at some level It’s a population of populations

Answer 269

Population Dynamics

Answer 270

Population Ecology Methods Counting organisms Estimating the amount of organisms by counting evidence of organisms Estimate life expectancy of individuals Estimate reproductive rates Study demographics of a population

Answer 271

Demographics Demographics are the quantifiable statistics of a population Demography is the study of the statistics of a population and how they change over time What statistics are studied depends on who is doing the studying Demographics are used extensively by marketers, advertisers, politicians, and other parasites

Answer 272

community ecology It’s the study of the interactions between species in communities. It includes the study of the distribution, structure, abundance, demography, and interactions between coexisting populations What constitutes a community and the size of it’s territory is open to debate

Answer 273

Interactions Between Species Different species within a community can interact with each other These interactions are classified by ecologists into competition, predation, symbioses, and facilitation Interactions Between Species Competition Predation Symbioses \>Parasitism \>Mutualism \>Commensalism Facilitation

Answer 274

Competition Interspecific competition is when different species compete with each other over finite resources The species can compete for food, habitat, sunlight, etc. If 2 species occupy the same niche, one of them is going to die

Answer 275

Ecological Niche An ecological niche is the sum of a species’ use of the biotic and abiotic factors in its environment It’s a species way of life It’s analogous to a species’ job Can be pronounced neesh, nitch or nish

Answer 276

Organisms Occupying the Same Niche Can Evolve the Same Traits Convergent Evolution

Answer 277

Ecological Niche Modeling Its hard to determine where a species is and where it likes to live Instead, combine the observations of a species with abiotic data (temperature, altitude, rainfall, etc.) Use an algorithm to build a model of the tolerances of the species and find it’s niche

Answer 278

Ecological Niche Modeling II

Answer 279

Predation Predation is when one species eats another species The predator doesn’t always kill the prey nor always consume the entire living organsim This includes herbivory, the eating of plants and algae Predation overlaps with parasitism in the case of parasitoids Predation and predator defense drive evolution in many organisms

Answer 280

Predator Adaptations Teeth, claws, speed, patience, venom, smell, vision, echolocation, camouflage, social behavior, etc. Anti-predation Adaptations Mimicry, camouflage, poison, detachable tails, speed, smell, vision, social behavior, thorns etc.

Answer 281

Evolutionary Arms Races An evolutionary arms race is a fight between competing sets of co-evolving organisms or genes that develop adaptations and counter-adaptations against each other The war can be fought between predator and prey or parasite and host

Answer 282

Co-evolution Co-evolution is the joint evolution of two interacting species, each in response to selection imposed by the other It can occur at the species level or the molecular level It can occur in predator/prey, host/parasite, and mutualistic relationships Darwin wrote about it

Answer 283

Warning Coloration Anti-predator adaptation Advertising that the potential prey tastes bad or is poisonous The coloration can be mimicked by other organisms

Answer 284

Mimicry Mimicry - The similarity of one species to another conferring an evolutionary advantage to one or both species Camouflage – When a species resembles its surroundings Can be visual, aural, or olfactory EX Below (and butterflies!)

Answer 285

Interactions Between Species Competition Predation Symbioses \>Parasitism \>Mutualism \>Commensalism Facilitation Symbiosis A symbiosis is an ecological relationship between two different species that live together in direct contact Symbioses can be bad for one of the species Types of symbioses are parasitism, mutualism, and commensalism

Answer 286

Parasitism Parasitism is a symbiotic relationship where one organism benefits at the expense of the other The parasite lives either on (ectoparasite) or inside (endoparasite) of the host and feeds on cell components, tissues, or body fluids Parasites don’t usually kill the host as this would deprive them of a host EX: Worms infect 3.8 billion people in the world

Answer 287

Parasitoids A parasitoid lives attached to or within a single host organism in a parasitic relationship, but eventually sterilizes or kills, and sometimes consumes the host Insects are most famously parasitoids, but other arthropods, prokaryotes, vertebrates, and even plants can be parasitoids

Answer 288

Parasitoid Wasp

Answer 289

Plants Use Parasitoids for Defense

Answer 290

Mutualism is a symbiotic relationship where both organisms benefit EX Below, and Nemo & Sea anenome

Answer 291

A mycorrhiza is a mutualistic association between a fungus and the roots of a vascular plant 95% of plants have mycorriza Sometimes these associations are pathogenic

Answer 292

Commensalism Commensalism is a symbiotic relationship where one organism benefits and the other is neither harmed nor helped Some relationships appear commensal but are not when viewed more carefully or are not commensal for all members of the population Commensalism? Remora fish hitchhike on larger organisms Sometimes the remoras clean the larger organism’s teeth (mutualism) sometimes the remoras eat their poop Sharks have been observed eating remoras attempting to attach onto them

Answer 293

Demodex Demodex is a mite that lives in human hair follicles Not everybody has them, but most do They eat your skin cells and oil They mate, lay eggs, defecate, and die in hair follicles They crawl out at night --- Considered to be a commensal skin organism Can cause skin problems in some people May cause acne in some people

Answer 294

Lichens Lichens are a symbiosis between fungi and algae or bacteria Their associations can be mutualistic, commensal, or parasitic depending on species

Answer 295

Endosymbiotic Theory Endo = within, sym = together, biosis = living Several eukaryotic organelles were originally free living microorganisms They now live with Eukaryotes in a symbiotic relationship Secondary endosymbioses have occurred

Answer 296

Facilitation Facilitation is an interaction where one species has a positive effect on the survival of another species without the intimate association of a symbiosis Some plants may make it easier for other plants to grow in the area

Answer 297

Ecosystem All of the organisms in a given area and the abiotic factors they interact with One or more communities and physical environment around them The biotic and abiotic factors of an ecosystem interact through nutrient cycles and energy flows

Answer 298

Ecosystem Ecology Ecosystem Ecology is the study of energy flow and the cycling of chemicals among the various biotic and abiotic components in an ecosystem The cycling of nutrients and energy are regulated by physical laws

Answer 299

Energy Energy is the ability to do work Energy is defined by the laws of thermodynamics

Answer 300

First Law of Thermodynamics Energy can be changed from one form to another, but cannot be created or destroyed. The total energy of a system remains constant. You can’t win You can’t get something for nothing ----- Example: The energy in sunlight is stored in chemical bonds by plants and then released again when we eat them

Answer 301

First Law of Thermodynamics in Biology

Answer 302

Second Law of Thermodynamics In all energy conversions, the potential energy of the final state will always be less than the potential energy of the initial state You can’t break even There is always an increase in entropy (disorder) when energy is transferred ---- Example: When a cow eats a plant, only 10% of the energy stored in the plant gets used by the cow When a human eats a steak, only 10% of the energy stored in the steak gets used by the human Every time you go up a trophic level, most of the energy is lost as heat

Answer 303

Trophic Structure The trophic structure is the different feeding relationships within an ecosystem which determine the route of energy flow and the pattern of chemical cycling A trophic level of an organism is it’s position in a food web

Answer 304

How Organisms Get Food Producers – reduce carbon. They are autotrophs Consumers – eat reduced carbon in the form of living organisms. They are heterotrophs Decomposers – eat reduced carbon in the form of dead organisms. They are heterotrophs

Answer 305

Food Web A food web demonstrates feeding relationships in an ecosystem It includes a feeding hierarchy with trophic levels Energy is lost each time you go up a level due to the 2nd law of thermodynamics --- Primary producers consist of 1000 kg of plant material. This is 2-3 bales of hay Herbivores consist of 100 kg of biomass, about the size of a large male deer Predators consist of 10 kg of biomass What a 10kg predator looks like → (puppy!)

Answer 306

Food Web II

Answer 307

Food Web III

Answer 308

Biomagnification In the food web, predators consume many prey animals Predators of predators consume many predators Top predators then represent an accumulation of material from many lower animals If there are molecules in the environment that are not readily broken down or metabolized, they can reach high concentrations in top predators through biomagnification

Answer 309

Rainforest Layers

Answer 310

Biomagnification in Your Meal Also, "Eat this, not this (for SF Bay)

Answer 311

Nutrient Cycles AKA Biogeochemical cycles Pathway by which an element moves through biology and the environment

Answer 312

Water Cycle

Answer 313

Carbon Cycle

Answer 314

Nitrogen Cycle

Answer 315

Sulfur Cycle

Answer 316

Lumpers vs. Splitters Any field that has defined categories can have lumping and splitting tendencies Lumpers have a holistic view and define groups broadly Splitters are precise and create new categories to further subdivide groups -- Lumpers use fewer groups than splitters The more you care about a field, the more likely you are to be a splitter within that field

Answer 317

Terrestrial Biomes (List) Deserts and xeric shrublands Tropical and subtropical moist broadleaf forests Tropical and subtropical dry broadleaf forests Tropical and subtropical coniferous forests Temperate broadleaf and mixed forests Temperate coniferous forests Boreal forests/taiga Tropical and subtropical grasslands, savannas, and shrublands Temperate grasslands, savannas, and shrublands Flooded grasslands and savannas Montane grasslands and shrublands Tundra Mediterranean forests, woodlands, and scrub or sclerophyll forests Mangroves

Answer 318

Deserts and Xeric Shrublands Xeric means of, characterized by, or adapted to an extremely dry habitat This group varies by amount of rainfall but dry conditions and evaporation rule This group varies by temperature -- Located around the world Created by man in some regions through the process of desertification Have uniquely adapted flora and diverse reptile fauna

Answer 319

Tropical and subtropical moist broadleaf forests This group includes: Tropical rainforests Moist deciduous forests Montane rain forests Flooded forests This group is characterized by low temperature variability and high rainfall -- Dominated by semi-evergreen and evergreen deciduous tree species High species diversity – half the world’s terrestrial species live here An estimated 17,000 species disappear from this biome annually due to deforestation

Answer 320

Tropical and subtropical dry broadleaf forests Characterized by moderate temperatures but long dry seasons Dominated by deciduous trees, many that lose their leaves during the dry season Loss of leaves in the canopy allows the under canopy and shrub layers to receive more light Have less diversity than rainforests Have higher mammalian biomass than rainforests

Answer 321

Tropical and subtropical coniferous forests Characterized by low rainfall and moderate variability in temperature Populated by diverse groups of conifers whose needles are adapted to low rainfall and variable temperatures Thick canopy often leaves only ferns and fungi capable of living on the ground

Answer 322

Temperate broadleaf and mixed forests Characterized by variable temperatures and variable rainfall Includes conifers in the canopy layer

Answer 323

Temperate Coniferous Forest Characterized by warm summers and cool winters and enough rainfall to sustain a forest Dominated by evergreen conifers Have the highest levels of biomass of any terrestrial biome Include temperate rainforests

Answer 324

Boreal forests / Taiga Characterized by low rainfall and cold temperatures Located in Northern latitudes Dominated by conifers World’s largest land biome (29% of the world’s forest cover) Still has relatively undisturbed large animal migrations Under threat due to climate change

Answer 325

Tropical and subtropical grasslands, savannas and shrublands Characterized by low rainfall (not enough to sustain a forest) and moderate to warm temperatures Dominated by grasses with some trees Home to large mammals Soon to only exist in natural parks - Characterized by low rainfall (not enough to sustain a forest) and moderate temperatures Dominated by grasses with few trees Home to large mammals AKA prairie, which doesn’t exist anymore in the US

Answer 326

Flooded grasslands and savannas AKA swamps Located tropically or sub-tropically and flooded seasonally or year round High avian diversity with both resident and migratory birds

Answer 327

Montane grasslands and shrublands Located at high altitude (alpine or subalpine) and above or below the treeline Plants adapted to cool temperatures and high light

Answer 328

Tundra Treeless cold climate This group includes: Artic – polar desert Antarctic – polar desert Alpine – above the treeline Dwarf vegetation and lichens

Answer 329

Mediterranean forests, woodlands, and scrub AKA Chaparral, maquis etc. Characterized by dry summers and rainy winters Most plants are fire adapted Highly distinctive fauna with many endemic plants --- Only 5 places in the world are a part of this biome 10% of all plant species in the world are here 40% of the plant speices in US and Canada are here, in an area the size of Maine

Answer 330

Mangroves Waterlogged salty coastal soils in the tropics and subtropics are home to a forest of various mangrove trees Plants uniquely adapted to temporally flooded, brackish, low oxygen conditions Protect against storms and tsunamis 50% of this biome is gone compared to 100 years ago

Answer 331

Aquatic Biomes Lakes Wetlands Streams and Rivers Littoral Zone Pelagic Zone Coral Reef Benthic Zone

Answer 332

Lakes Standing body of water that can be large or small Surrounded by land and localized in a basin Weak tidal forces More temporary than an ocean in geologic time scales The Caspian Sea is a lake Sensitive to pollution

Answer 333

Wetlands AKA marshes, swamps, bogs, and fens A wetland is a habitat that is inundated with water at least some of the time and that supports plants adapted to water-saturated soil Includes mangroves and flooded grasslands and savannas By 1993, half the worlds wetlands were drained

Answer 334

Streams and Rivers Characterized by flowing water Upland headwaters tend to be faster, cooler, clearer, and more turbulent while lowland downstream water tend to be slower, warmer, turbid, and less turbulent

Answer 335

Littoral Zones Contains both the intertidal zone and estuary zones

Answer 336

Intertidal Zone Flooded with water twice a day Has sub-zones depending on amount of flooding. These sub-zones are compressed into narrow bands Biologically productive despite harsh conditions

Answer 337

Estuaries An estuary is where a freshwater stream or river merges with the ocean It’s a transition zone with temporal variation in salinity and temperature Very productive, but very impacted 60% of the world’s population lives here

Answer 338

Coral Reef A coral reef is a warm water tropical ecosystem dominated by the hard skeletal structure secreted by corals. Some also exist in cold and/or deep waters Disappearing faster than rainforests and could be gone in 100 years

Answer 339

Pelagic Zone AKA The water column The pelagic zone is the open water component of aquatic biomes It’s not near the shore or the bottom Primary producers are phytoplankton

Answer 340

Benthic Zone The benthic zone is the bottom surface of any aquatic environment Begins at the shoreline and extends down the continental shelf The deeper regions are dark and nutrients come from detritus raining down from above or thermal vents from below

Answer 341

The 6th Great Extinction There have been great extinctions many times in the history of the world There is a man made one occurring right now It’s your fault Stop it