Biology Chapter 4 Review

Explain how experiments can be used to test evolutionary hypotheses

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Discuss some applications of genomics

- Bioinformatics: computer programming, mathematics and modeling to analyze data. - can predict protein structure - synthetic biology: created biological organisms to solve problems - Diagnostics: - Medicine: identification of harmful genes - Forensics: ID bodily remains and weaponized pathogens - Ethical concerns - research on infectious diseases - gene patenting

Distinguish between the biological and phylogenetic species concepts

- Biological Species Concept: a group that breeds or could breed together, doesn't reproduce with anyone else, and if they did the offspring would be infertile - Phylogenetic Species Concept: a population that has been evolving independently from other groups- identified through phylogenetic analysis

Provide examples of model organisms used to study animal development.

- C. Elegant helps understand development because it was the first organism to provide a cell-lineage map. - Drosophila Melanogaster helps understand pattern formation in embryos- show development is made by changes in gene expression. - Xenopus Laevis: ideal for studying early embryonic development and morphogenesis

Correlate the diversification of life with the need for consistent nomenclature

- Consistent naming conventions are important for exploring the diversity of life - Newer discoveries about evolutionary relationships may lead to regrouping taxa (biological species concept vs phylogenetic species concept) but the method used to organize them remains the same. - Organisms are placed in a hierarchical system that typically includes domain, kingdom, phylum, class, order, family, genus, and species - Species are given binomial names (Genus species)

selection

- Darwin suggested natural selection as the mechanism of evolution.

Distinguish between a genetic map and a physical map, and provide examples of each

- Genetic maps have a recombination frequency and linkage analysis with relative locations - physical maps have precise location and nucleotide-level resolution.

Compare and contrast gradualism and punctuated equilibrium

- Gradualism: small changes occur very slowly and accumulate over thousands and millions of years leading to major changes - Punctuated Equilibrium: species experience periods of little to no change punctuated by bursts of evolutionary change occurring over geologically short periods of time.

Describe the mechanisms of reproductive isolation

- Pre-Zygotic - Post-Zygotic

Define reinforcement in the context of reproductive isolation

- When isolation between two different groups isn't complete and amplification occurs when previously isolated groups come in reproductive contact again.

genetic drift

- a change in allele frequencies due to sampling error - largest effect on populations - can substantially change allele frequencies

Explain the importance of genome annotation

- a complete DNA sequence is not important when the number, location, and kind of genes present is not known. - genome annotation assigns that information about the DNA sequences - Open Reading Frame Gene sequence: shows start to stop codon -GenBank -BLAST

Compare and contrast sympatric and allopatric species and speciation

- allopatric species: live in different places and are divided by geographical barriers. (EX: birds getting blown off course and settling on an island) - sympatric species: share the same space but use different parts (EX: birds eating different types of seeds. in the same forest.)

mutation

- any change in the base sequence of DNA - ultimate source of variation; gives rise to different alleles - mutations are rare and not the primary cause of changes in allele frequency within a population

Describe how the Earth is a dynamic (changing) system

- atmosphere constantly changing - continents move over time - plate tectonics - the plates under the earth shift a few inches each year, cause continents to move

Describe how cell division and differentiation contribute to animal development.

- cell division transforms single-celled zygote into a multicellular organism. - cell differentiation is the production of specialized (differentiated) cells that arise from the division of undifferentiated stem cells. Differentiation progressively restricts the number of fates of the cells within a lineage that can adopt multiple cell divisions.

Describe how cell migration, changes in cell shape, and apoptosis contribute to morphogenesis.

- cell migration: cells migrate through the ECM to provide them with support and protection- controlling the expression of adhesion proteins. - cell shape: changes are required for cells to work properly in embryo or adult stem cells. cell shape is associated with cell function. - apoptosis: induced by "cell death pathway" when cell fragments into a-optic bodies fragments recycled. - necrosis: caused by injury- cell membrane bursts and contents are released.

Distinguish between methods of phylogenetic reconstruction.

- cladistics - statistical approaches - the molecular clock

Explain the principle of parsimony and its use in systematics.

- cladistics relies on the principle of parsimony - the phylogeny that requites the fewest evolutionary events is considered to be the best hypothesis of the relationship between the taxa being studied

Relate mechanisms of evolution to the ever-changing life on Earth

- climate changes - changes in the atmospheres composition - continental drift

Sequence-tagged site maps

- combine high resolution and the ability to view large pieces of DNA at a glance - small stretch of unique DNA that is amplified with PCR - allows researchers to identify and organize DNA fragments - continuous sequencing

Differentiate between comparative genomics, functional genomics and proteomics

- comparative genomics uses information of one genome to learn about a related genome. bases on synteny(conserved arrangement of DNA in related genomes). can predict gene function. - functional genomics: uses biotechnology to highlight the connection between the genotype and phenotype- transcriptome, proteome. - proteomics: The study of proteome. more difficult to analyze than transcriptome.

Explain how systematics is used in biology.

- constructing phylogenies to reconstruct and understand evolutionary relationships - present hypotheses

Define "development" and identify the primary mechanism responsible for development.

- development is the process by which a single-celled fertilized egg (zygote) becomes a fully-formed adult. Changes in gene expression over time - The primary mechanism responsible for development is gene expression (DOUBLE CHECK)

Explain how Earth's early environment shaped living systems.

- early environment likely had high levels of CO2 - 2 million year cooling period CO2 was taken out of the atmosphere through the weathering of rocks - then precipitation of calcium - several periods of glaciation have decimated life

Conceptualize the geological timescale.

- four eons - divided into eras - divided into periods

Explain the role of genetic variation in evolution

- genetic variation is the presence of different alleles of genes in a population. - changes in allele frequencies in population over time - evolution is the result of any process that changes the genetic composition of a population over time

Identify the major components of genomics

- genomics is the early efforts focused on isolating and sequencing genes. -mapping genomes - sequencing genomes -genome annotation - genome analysis

Next generation sequencing

- group of automated techniques used for rapid DNA sequencing - faster, cheaper, and has the ability to sequence larger fragments of DNA - utilizes DNA attached to solid surface - multiple copies of fragments ensure accuracy - uses "reversible" chain terminating nucleotides

Describe factors which complicate phylogenetic reconstruction.

- homoplasy complicated classic analysis - it refers to shared character traits that have not been inherited from a common ancestor - can result from convergent evolution or evolutionary reversal.

Genome Analysis

- identifying the role/purpose of DNA elements in the genome - comparative, functional, or proteomics

ENCODE

- importance of non-coding DNA has remained unclear - ENCODE project created to identify functional elements in the human genome and it claims the 80% of DNA is functional due to biological activity. - some disagree that biological activity does not mean functional and that sites of enzymatic activity are not functional

mapping genomes

- maps helping to navigate through a genome. - have differing levels of resolutions:low and high - Genetic maps and physical maps

Discuss possible roles of non-coding DNA

- may include as much as 99% of DNA in the human genome - multiple categories - possible roles are transcribing into noncoding RNA, turning into transcriptional or translational protein sequences, or origins of DNA replication.

Describe the four processes that can cause evolutionary change

- mutation - gene flow - genetic drift - selection - nonrandom mating

Determine the difference between evolution and natural selection

- natural selection: the process that occurs when environmental conditions affect which individuals produce the most offspring - evolution:a change In populations of organisms over time, more specifically the change in allele frequency over time.

Compare and contrast the two main methods of nuclear reprogramming.

- nuclear reprogramming reverses by resetting a differentiated cell to an undifferentiated stem cell. Requires reversal of epigenetic changes present in differentiated cells - Somatic Cell Nuclear Transfer: nucleus of a differentiated cell is removed and put into a zygote to create a embryonic stem cell. Made the first cloned embryo - direct reprograming: introduce the expression of stem cells associated with transcription factors then turning into a pluripotent stem cells.

Describe how pattern formation and morphogenesis contribute to animal development.

- pattern formation creates the body plan of an organism- and depends on differential gene expression based on location within the embryo. - HOX genes are expressed in different body segments that determine the body's segment. (highly conserved) - morphogenesis: generation of an organisms body form. depends on cell growth, division, migration, changes in cell shape, and programmed cell death.

Interpret a phylogeny using common systematics vocabulary.

- phylogeny are made up of outgroups, clades, synapomorphy, and nodes

Explain how living systems have changed the Earth

- plants contributed to glaciation by removing the CO2 - first major glaciation after colonization by plants - second after vascular plant diversification - living organisms alter the environment around them through carbon fixation -incorporate C12 into their cells before other isotopes and thus can alter the ratios of these isotopes in the atmosphere -uses calvin and krebs cycle

Distinguish between the different types of stem cells.

- potency: - totipotent: form all tissues of an organism, plus the extraembryonic tissues (EX: zygote: individual blastomeres from first few cleavages of the zygote) - pluripotent: forms all tissues of the organism. can not form extra-embryonic tissues. (EX: Embryonic stem cells from blastocysts inner cell mass) - multipotent: can only form certain cell types (EX: adult stem cells) - unipotent: can only form one cell type (EX: spermatogonia (Germ ) stem cells

Differentiate between reproductive and therapeutic cloning and their uses.

- reproductive cloning: creates a genetically identical copy of a given organism with somatic cell nuclear transfer and implants the cell into a surogent. - therapeutic cloning: The cloning of human cells by nuclear transplantation for therapeutic purposes, such as the generation of embryonic stem cells to treat disease.

Differentiate between clone-contig and shotgun sequencing approaches

- shotgun method: cut DNA of entire chromosome into small fragments and clone and then sequence each segment and arrange based on overlapping nucleotide sequences - clone-contig: Break genome into large "clone" fragments Arrange clones using STS

dideoxy(automated) sequencing

- start with a strand of unknown sequence - amplify using PCR - incorporate dideoxynucleotides - labeled with fluorescent A,T,C, G - fragments are separated by electrophoresis - utilize laser and photodetector to identify base

Distinguish between systematics and classification.

- systematics: the reconstruction and study of evolutionary relationships - classification: the practice of placing species and groups of species into the taxonomic hierarchy

Principles of DNA sequencing

- the highest-resolution physical map is the base-pair sequence - methods of sequencing rely on PCR, electrophoresis, chain-terminating nucleotides (dideoxynucleotides)

gene flow

- the movement of an allele from one population to another - can occur when an organism moves to a new location

Types of physical maps

- use landmarks within the DNA sequence - show the exact location on a DNA marker - restriction sites - small segments of DNA - RESTRICTION MAPS: map cut-sites - CHROMOsOME MAPS: utilize staining techniques which are viewed through a microscope at low resolution

Genetic Drift: Bottleneck Effect

A rapid decrease in population size due to a disturbance or natural disaster reduces the abundance of a species and removes individuals with some alleles from the population, altering gene frequencies through drift.

Describe adaptive radiation

An evolutionary pattern in which many species evolve from a single ancestral species

Human Genome Project

An international collaborative effort to map and sequence the DNA of the entire human genome.

explain how evolutionary forces interact with each other

Evolutionary forces can work together or in opposition. -Mutations and genetic drift can counter selection -Gene flow can either promote or prevent evolutionary change.

Demonstrate how the operation of evolutionary processes can be detected

Finding that a population is not in Hardy-Weinberg equilibrium indicates that one or more evolutionary agents are operating.

Explain how genetic drift and natural selection can lead to speciation

Genetic Drift and natural selection can lead to speciation because there is a smaller genetic pool to begin with and the more generations progress the less variation there is.

Explain the role of homeobox-containing genes in animal development.

Homeobox genes play a crucial roles in specifying cell identity and positioning during embryonic development, and mutations in these genes can cause dramatic developmental defects

Recognize that the Earth is still changing

Human activities have an influence on our planet Biodiversity Climate Radioactive materials Significant changes in biodiversity and climate have been used to name sections of the geological timescale Many feel that we are now living in a new epoch: the Anthropocene Debate continues over the proper criteria for defining what future generations will likely consider to be a key stretch of our planet's history

Describe the characteristics of a population that is in Hardy-Weinberg equilibrium

The population size is large: A large population reduces the chance of fluctuations in allele frequencies.*No gene flow: No movement of individuals into or out of the population*No Mutations*Random mating: No preferential selection of mates.*No Natural Selection

Define evolution

evolution is defined as a change In populations of organisms over time, more specifically the change in allele frequency over time. - evolution happens at a population level and individuals do not evolve.

Apply the geological timescale to the early Earth and origins of life.

first evidence of life found in the precambrian -hadean, archaen, proterozoic eons

Describe how geographic isolation impacts a population

geographic isolation impacts a population because it is a prerequisite for the evolution of differences in populations.

Genetic Drift: Founder Effect

occurs when a few individuals become isolated from a larger population; can affect allele frequencies in a population

Describe how phylogenies are used as hypotheses in biology.

phylogenetics is the basis of comparative biology, much can be learned about why evolution proceeded the way it did by examining traits among species in the context of their evolutionary relationships - phylogenies can illustrate convergent evolution - phylogenies reveal sequence of evolutionary change - phylogenies help explain species diversification - phylogenies can illustrate patterns of dispersal - phylogenetics are used to study how disease can jump between species

trasncriptome

study of RNA molecules produced by the genome - are studied by DNA microarrays which see which genes are being expressed in a particular location or time - must create microarray chip in the known genes -RNA-sequencing use next-generation technology to capture all the mRNA created.

Proteome

study of all the proteins produced by the genome - viewed through mass spectrometry, which uses charge-to-mass ratio to identify protein and amino acids. - also viewed through protein microarrays that rely on protein-specific antibodies to identify protein translated.

Define evolutionary fitness

success in passing genes to the next generation - the combination of survival, mating success, and number of offspring per mating

Summarize evidence for the order of evolution of early life.

there are many hypotheses to explain the emergence of metabolic pathways

Explain the outcome of gene flow between partially isolated populations

when partially isolated populations come together, gene flow will occur to some degree if an of the resulting hybrids is fertile.