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Bio 1362

by: Manaswini Mattegunta

Bio 1362 BIO 1362

Manaswini Mattegunta

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This is the mix of all the study guides from Dr. Cheek
Intro to biological sciences
Dr. Cheek
Study Guide
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This 18 page Study Guide was uploaded by Manaswini Mattegunta on Friday April 29, 2016. The Study Guide belongs to BIO 1362 at University of Houston Downtown taught by Dr. Cheek in Spring 2016. Since its upload, it has received 31 views.

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Date Created: 04/29/16
Exam 1 Preparation Guide Chapters 24 – 27, 19, and 11 Concepts Biodiversity – Chapters 24 - 27 ● List characteristics shared by Archaea & Bacteria, but not Eukarya o No nuclear envelope o No membrane bound organelles o One (1) circular chromosome ● List characteristics shared by Archaea & Eukarya, but not Bacteria o No peptidoglycan cell wall o More than 1 (>1) RNA polymerase o Initiator amino acid: methionine o No ribosome assembly sensitive to antibiotics ● List characteristics unique to each domain o Archaea ▪ Extremophiles: can live in harsh environments (salty, hot, freezing) ▪ Methanogens: producers, use CO to oxid2ze H 2 to CH 4 hydrothermal vents, cow and termite guts ▪ Growth at temperatures greater than 100°C o Bacteria ▪ Peptidoglycan cell wall ▪ One (1) RNA polymerase ▪ No introns or histones o Eukaryotes ▪ Nuclear envelope ▪ Membrane bound organelles ▪ No circular chromosomes ▪ Many introns, one histone Histones are proteins that coil with DNA Introns are noncoding DNA sequences   Bacteria Archaea Eukarya nuclear envelope 0 0 1 membrane­bound organelles 0 0 1 circular chromosome 1 1 0 peptidoglycan cell wall 1 0 0 RNA polymerase 1 >1 >1 initiator aa formyl Met Met Met Ribosome assembly sens to an1ibiotics 0 0 growth at > 100°C 0 1 0 membr lipids unbranched hc tail some branched hc taunbranched hc tail introns rare some many histones 0 0/1 1 ● Name the 5 kingdoms within Domain Bacteria and be able to draw a phylogenetic tree showing relationships among the 5 kingdoms o Proteobacteria ▪ Salmonella ▪ - Vibrio ▪ - Helicobacteria pylori ▪ - Rhizobium o Chlamydia o Spiro- parasitic ▪ Barrelia burgdorferi ▪ Treponema pallidum o Cyano=parasitic ▪ lichen o GramPositive ▪ - Streptomyces ▪ - Bacillus antrhacis ▪ - Clostridium botulinum ● Know the kingdom for each species of bacteria listed in lecture ● Know characteristic that differentiates gram-positive and gram-negative bacteria and which kingdoms belong to which category o Gram-positive ▪ No additional membrane covering cell wall ▪ thick layer of peptidoglycan ▪ dark stained ▪ Pathogenic vs. Nonpathogenic o Gram-negative ▪ Proteobacteria ▪ Cell wall, thin layer of peptidoglycan, with additional membrane ▪ Autotrophs (chemo and photo) vs. Heterotrophs can be pathogenic vs. nonpathogenic ▪ Pathogenic vs nonpathogenic ● Name the 4 supergroups within Domain Eukarya and be able to draw a phylogenetic tree showing relationships among the supergroups o Animalia o Fungi o Plant o Charophyte algae ● Know the supergroup to which each single-celled eukaryote listed in lecture belongs ● Explain what the branching pattern on a phylogenetic tree indicates about evolutionary relationships o The branch point represents a pattern of divergence o unknown shared traits ● Compare phylogenetic trees to see if they represent the same or different relationships between groups ● Use a phylogenetic tree to identify which groups descend from a more recent or more ancient common ancestor ● Define the ancestral characteristics that unite the Archaeplastida o Shared with green algae: chlorophyll a and b ● Define the shared derived traits that unite the plant kingdom o Alternation of generations-fertilization o Sporangia- multicellular organs that produce desiccation resistant spores o Gametangia- embryo o Apical meristem- cell division at the tip of the root ● Draw the cycle of alternation of generations – name each generation, indicate ploidy (1n or 2n) and type of cell division that produces the single cells that develop into the next generation ● Name the 7 phyla within Kingdom Plantae and be able to match the name of plants listed in lecture to the correct phylum o Liverworts o Hornworts o Mosses- o Lycophytes o Monilophytes o Gymnosperms o Angiosperms ● Draw a phylogenetic tree showing relationships among the 7 plant phyla ● Draw a phylogenetic tree showing relationships among these animal phyla: Porifera, Cnidaria, Chordata, Mollusca, Annelida, Nematoda, Arthropoda ● Be able to indicate on the phylogenetic tree which groups are part of the Bilateria, Deuterostomia, Lophotrochozoa, Ecdysozoa ● List ancestral characteristics common to all animals and choanoflagellates, distinguish animals from choanoflagellates by shared derived characteristic of animals o Genes encoding rRNA o Chaperone proteins o Tubulin ● List and map shared derived characteristics of Eumetazoa, Bilateria, Deuterostomia, and the Protostomes onto a phylogenetic tree ● List the 4 protostome phyla discussed in lecture o Ecdysozoa o Lophotrochozoa o Cnidaria o Deuterostomes ● List shared derived characteristics of Lophotrochozoa and list 2 phyla that belong to this group o Spiral cleavage pattern of embryonic cells o Hox genes o Annelida and Mollusca ● List shared derived characteristics of Ecdysozoa and 2 phyla that belong to this group o Shedding exoskeleton to grow larger o Invertebrates o Arthropoda and Nematoda ● List the 4 classes of arthropods and be able to match the name of arthropods listed in class (and in the Life video) to the correct class o Chelicerata o Myriapoda o Crustacea o Insecta Darwin and Natural Selection: Chapter 19 ● Describe Lyell’s ideas about geologic processes and inferences about Earth’s age o Lyell believed that geologic processes operate today at the same rate as in the past. ● Compare & contrast Lamarck’s ideas vs Darwin’s idea regarding mechanisms of change in living organisms o Lamarck ▪ Species can change into new species ▪ Use and disuse ▪ Inheritance of acquired characteristics o Darwin ▪ Adaptation ▪ Species are changing due to natural selection ▪ Survival of the fittest ▪ Descent with modification: all species descend from a common ancestor ▪ Artificial Selection ● Define descent with modification o All living spp descended from one ancestor ● List and recognize examples of descent with modification in living organisms, both within and between species, and fossil organisms ● Define 2 conditions necessary for natural selection and give examples that satisfy each condition o Variation in inherited traits o More offspring than environment can support ● Evaluate conditions under which natural selection could occur ● Understand that natural selection acts on individuals, but causes changes in populations ● Compare and contrast natural selection and artificial selection: conditions necessary, selection pressure, result o Both: variation in heritable trait o Artificial selection - trait desired by humans - desired trait increases o Natural selection - selection pressure - trait desired by environment - favorable trait increases Chapters 11: Heredity ● Define Mendel’s Law of segregation o Principles that governs heredity ● Define Mendel’s Law of independent assortment o When two or more characteristics are inherited, individual hereditary factors assort independently during gamete production, giving different traits an equal opportunity of occurring together. ● Monohybrid cross – use Punnett square to detail possible genotype of gametes and progeny and indicate progeny phenotypes o Two individuals- two or multiple alleles for a single locus. ● Dihybrid cross – use Punnett square to show possible genotypes of gametes and progeny and indicate progeny phenotype o Cross between two different lines (varieties, strains) that differ in two observed traits. ● Identify dominant or recessive modes of inheritance from the notation (example: A is the dominant allele, a is the recessive allele) ● Analyze a pedigree to determine whether a trait is dominant or recessive o instructions-PBA.pdf ▪ Dominance - whether the disease alleles are dominant or recessive; (2) ▪ Linkage- whether disease alleles are X-linked or autosomal ▪ Autosomal chromosomes - The 22 chromosome pairs other than the XX (female) or XY (male) sex chromosomes. ▪ Allele - A version of a gene. Humans have 2 alleles of all their autosomal genes; females have 2 alleles of X- linked genes; males have one allele of X-linked genes (and one allele of Y-linked genes). ▪ Recessive-if any affected individual has 2 unaffected parents. ▪ Dominant- if every affected child of non- founding parents has an affected parent. ● Use information in a pedigree to determine genotype and calculate the probability of a dominant or recessive trait being inherited by a son or daughter ● Use a Punnett square to figure out possible gamete genotype and progeny genotypes for autosomal traits ● Use genotype and phenotype of parents to figure out genotype and phenotype of offspring (and vice versa) ● Use correct notation for dominant, recessive, co-dominant, wild-type, mutant, sex-linked o co-dominant- relationship between two versions of a gene. o wild-type- characteristic that prevails among individuals in natural conditions, as distinct from an atypical mutant type. o mutant- organism or a new genetic character arising or resulting from an instance of mutation, which is a base-pair sequence change within DNA or chromosome o sex-linked- trait associated with gene that is carried only by male or female parent. ● Define gene, locus, and allele. Know how many alleles an individual diploid organism can have for each locus. o Gene: the biological code of all traits o Locus: location on a chromosome where a gene sits o Allele: version of gene that codes for specific version of a character o An individual can have 2 alleles, one from each parent, in each locus. ● Explain why the number of alleles per gene in an individual can be different from the number of alleles per gene in a population o An individual has one allele per gene in each chromosome, meaning the individual exhibits only one trait. Vocabulary ● Phylogenetic tree- branching diagram representing the evolutionary history, group of organisms ● Archaea- unicellular prokaryotes distinguished by cell walls made of certain polysaccharides not found in bacterial or eukaryotic cell walls ○ plasma membranes composed of unique isoprene- containing phospholipids, ○ ribosomes and RNA polymerase similar to those of eukaryotes ● Bacteria- consisting of unicellular prokaryotes distinguished by cell walls ○ composed largely of peptidoglycan, ○ plasma membranes similar to those of eukaryotic cells, ○ ribosomes and RNA polymerase that differ from those in archaeans or eukaryotes. ● Eukarya- unicellular to multicellular organisms that have a membrane-bound nucleus containing several chromosomes. Sexual reproduction is common. ● Cyanobacteria- unicellular organisms ○ photosynthetic ○ oldest fossil autotroph ○ ancestor of chloroplast ○ form soil crust ○ forms a symbiotic relationship with fungi resulting in lichen ○ early cyanobacteria began releasing oxygen into the Earth’s atmosphere. With this rising concentration of atmospheric O2, several prokaryotic groups went extinct ● Excavata- Feeding groove along one side of cell ○ mitochondria that do not use O2 ○ many are heterotrophs and many are parasites ○ Giardia Intestinalis - intestinal parasite in mammals, transmitted by infected feces ○ Trypanosoma - parasite that causes sleeping sickness in mammals; transmitted by tsetse fly bites. ● Stramenopile­ unicellular diatoms ○ 2­part silicon dioxide wall ○ Photosynthetic ● Alveolate- Dinoflagellates ○ Photosynthetic ○ Some are symbiotic with corals (ex. Cnidaria) ○ Red tide ○ Some are bioluminescent ● Plastid- organelle surrounded by multiple organelles ● Diatom- unicellular, major group of algae ● Dinoflagellate- Photosynthetic ○ Some are symbiotic with corals (ex. Cnidaria) ○ Red tide ○ Some are bioluminescent ● Giardia- intestinal parasite in mammals, transmitted by feces ● Trypanosoma- parasite that causes sleeping sickness in mammals, transmitted by tsetse fly bites ● Plasmodium- causes malaria ● Autotroph- able to make its own food and energy ● Heterotroph- Consumes other organisms for energy ● Saprotroph- acquiring energy by absorbing nutrients from the environment ● Archaeplastida- land plants ● Ancestral characteristic- shared by the ancestral and current descendants ● Shared- derived trait shared by descendants ● Apical meristem- cell division at roots ● Sporangia- multicellular organs that produce desiccation-resistant spores ● Gametangia- either makes eggs OR sperm ● Sporophyte- is dominant generation, spores develops into a microscopic gametophyte within the parent sporophyte ● Gametophyte- produces sperm or egg ● Sporopollenin- resistant polymer that prevents spore from drying out or being crushed ● Unikonta- Fungi/Animalia ● Metazoa- Animalia ● Eumetazoa- eukaryotic clad in Kingdom Animalia that contains most major groups ● Bilateria- two-sided symmetry ● Lophotrochozoa- Spiral cleavage pattern of embryonic cells ○ Hox genes ○ Annelida and Mollusca ● Ecdysozoa- shedding of the exoskeleton to grow larger ● Gastrulation- tissue formation ● Mycorrhizae- symbiotic relationship between fungus and plant roots ● Adaptation-inherited trait that enhances survival and reproduction in the envi ● Natural selection- Darwin ○ mechanism of descent with modification ○ Individuals that inherit certain traits will survive better and produce more offspring in current local environment ● Artificial selection- intentional reproduction of individuals to have certain traits ● Evolution- theory that individuals descend from a common ancestor into better and more diverse forms ● Homology- existence of shared characteristics between structures or genes in different species. ● Analogy- similarity of function and resemblance of structures that have different origins ● Biogeography- study of species in different environments ● Hutton- Earth’s physical features are changing ● Lyell- Geological process operate today at the same rate as the past ● Lamarck-Species can change into new species ● Cuvier- Species go extinct due to a catastrophe ● Extant- opposite of extinct ● Allele-alternative version of the gene ● Blending hypothesis-mixing of the two parents ● Particulate hypothesis-mixing of the particles ● Character-varies between individuals ● Trait- variant of character ● P generation- parent ● F1 generation- 1st offspring ● F2 generation- 2nd offspring ● Law of segregation- Alleles separate from each other in the formation of gametes ● Law of independent assortment- Individual hereditary factors assort independently, so it gives an equal chance of occurring together ● Genotype-Genetic makeup ● Phenotype- What they look like ● Dominant allele- is heterozygous for that trait, or possesses one of each allele, then the dominant trait is expressed. ● Recessive allele- is only expressed if an organism is homozygous for that trait, or possesses two recessive alleles. ● Heterozygous- having 2 different versions of hereditary particles for a character ● Homozygous- having the same version of hereditary particles for a character ● Punnett square- method to predict possible combinations of gametes and offspring ● Monohybrid cross- one mixture of traits ● Dihybrid cross- mating between parents heterozygous for 2 characters 1­bio­ch­12­flash­cards/ Ch. 9 Mitosis Mitosis, the division of the genetic material in the nucleus, is Diagram ? Section / Topics  usually followed immediately by cytokinesis, the division of the cytoplasm Chromatin Colored stuff Chromosome Colored body, 1 double­stranded molecule of DNA wound  around the nucleosomes. Genetic information is stored in it  Cell Cycle ● Life cycle of a cell. ● The life of a cell from the time it is first formed  from a dividing parent cell until its own division into  two daughter cells. Interphase G1: growth (first gap) S: synthesis of DNA, chromosome duplication (synthesis) G2: more growth (second gap) During all three subphases, a cell that will eventually divide  grows by producing proteins and cytoplasmic organelles such as mitochondria and endoplasmic reticulum Mitosis Division of chromosomes Mitosis, the division of the genetic material in the nucleus, is  usually followed immediately by cytokinesis, the division of the cytoplasm Prophase Nucleoli disappear, sister chromatids form, centromere forms Chromatin are tightly coiled. Chromosomes duplicated and are  joined at centromere. Mitotic spindle begin to form.  Centrosomes move away from each other. These are sometimes  called the as the polar microtubules. ProMetaphase Nuclear envelope disappears. Chromosomes are now even more condensed. Chromatids of each chromosome have kinetochore Metaphase Centrosomes are now at opposite poles of the cell.  Chromosomes align on an imaginary central line. Metaphase plate Which is an imaginary rather than an actual cellular structure. Anaphase Shortest phase in the entire cycle, lasting only upto few minutes The two chromatids separate from each other and move towards the poles. The cell elongates as the non kinetochore lengthen. Telophase Two daughter nuclei from in the cell. Nucleoli reappear.  Chromosomes become less condensed. Mitotic division is now  2 complete. Cytokinesis In animals, cytokinesis involves in the formation of cleavage  furrow, which pinches the cell into two.  In plant cells cell wall materials are deposited in between the  cell allowing it to form to complete the cell wall. Sister chromatid Copies of a single chromosome Centromere Part of the chromosome where the sister chromatid are closely  attached Spindle Array of microtubules Kinetochore Protein structure that attached to the centromere, connects  centromere to spindle fibers Cleavage furrow Forms inside animal cell membranes, actin and myosin  filaments contract, pinches membrane inward making 2  complete cell membranes Fun Facts! The term binary fission, meaning “division in half,” refers to  this process and to the asexual reproduction of single­celled  eukaryotes, such as the amoeba in Figure 9.2a. However, the  process in eukaryotes involves mitosis; the process in  prokaryotes does not.  bacterial chromosome begins to replicate at a specific place on  the chromosome called the origin of replication, producing two  origins Cell Cycle Control  a cyclically operating set of molecules in the cell that both  System triggers and coordinates key events in the cell cycle. Check point A control point where stop and go­ahead signals can regulate  the cycle.Three check points are present: G1 Checkpoint, G2  Checkpoint, M Checkpoint. G1 Checkpoint  When a cell receives a go­ahead signal at the G1 it completes  the rest of the cycle. If it does not receive the signal at that  point, it will exit the cycle, switching into a nondividing state  called the G0 phase. Most cells of the human body are actually  in the G0 phase.cells can be called back from the G0 Phase to  complete the cycle. cyclins The cell cycle is regulated at the molecular level by a set of  regulatory proteins and protein complexes, including kinases  and proteins  Growth Factor Is a protein that is released by certain cells that stimulates other  3 cells to divide Density­dependent  A phenomenon in which crowded cells stops dividing inhibition Anchorage   density, anchorage is signaled to the cell cycle control system  dependence via pathways involving plasma membrane proteins and elements of the cytoskeleton linked to them.  Metastasis The spread of cancer cell to location distant from their original  site. ● In cancer cells , the growth factors are absent. Chp 10 Scientific study of heredity and hereditary variation. Meiosis Genetics Genes coded information in the form of hereditary units Gametes/Somatic  Are the vehicles that transmit genes from one generation to the  cells next./ All cells in the body except the gametes and their  precursors. Locus  A gene’s specific location along the length of a chromosome  Life Cycle Stages in an organism’s life from fertilization to make offspring Meiosis Cell division that reduces a 2n number of chromosomes to a 1n  set Synaptonemal  proteins complex Crossing Over Chunks of DNA are swapped between non­sister chromatids  (happens between homologous chromosomes) Chiasma Point at which crossover occurs Meiosis II Separation of sister chromatids during the formation of gametes Locus  A gene’s specific location along the length of a chromosome is  called the gene’s locus Fertilization The union of gametes, culminating in fusion of their nuclei Zygote The resulting fertilized egg, or zygote, is diploid because it  contains two haploid sets of chromosomes bearing genes  4 representing the maternal and paternal family lines Alternation of  This type includes both diploid and haploid stages that are  generations (Fig  multicellular. 10.6 b)  sporophyte The multicellular diploid stage Meiosis in the sporophyte produces haploid cells called spores.  Unlike a gamete, a haploid spore doesn’t fuse with another cell  but divides mitotically, generating a multicellular haploid stage  called the gametophyte Chiasmata (occurs  Each Homologous pair has one or more X­shaped regions called in the Prophase I) chiasmata. It exists where a crossover has occurred. Prophase I Paired homologs become physically connected this is called  synapsis. Crossing Over occurred. At the end microtubules attach to the two kinetochores. Metaphase I Microtubule attached to kinetochore, centromere with  Kinetochore Anaphase I Homologous chromosomes separate and sister chromatids  remain attached Telophase I and  Two haploid cells form and each chromosome still consists of  Cytokinesis two sister chromatids Prophase II A spindle apparatus form Metaphase II Positioned at metaphase plate.  Anaphase II Breakdown of proteins holding the sister chromatids. Crossing  over occurs again. Telophase II and  Haploid daughter cells forming. 4 daughter cells are formed a  Cytokinesis single Cohesins Sister chromatids are attached along their lengths by protein  complexes. Meiosis I is called the reductional division as it halves the #of  chromosomes. The second meiotic division is called the equational division as  sister chromatids separate producing haploid daughter cells. 5 Genetic Variations Independent assortment Crossing Over can produce recombinant chromosomes­­ individual chromosomes that carry genes derived from different  parents. Random Fertilization Different types of sexual life cycles. 6 Chp 12.1 & 13 Pauling proposed three stranded  DNA Structure &  Watson Crick proposed double stranded model after looking the  Replication X­Crystallization produce by Rosalind Franklin Chargaff proposed that number of A=T and G=C Conservative model The two parental strands reassociate after acting as templates for  new strands thus restoring the parental double helix. Semi­conservative model The two strands of the parental molecules separate and function as 7 a template for synthesis of a new complementary strand Dispersive model Each strand of both daughter molecules contains a mixture of old  and newly synthesized DNA Origin of replication The replication of a DNA  molecule begins at particular sites   Replication Fork Replication bubble appears, at each end of a bubble is a fork a Y­ shaped region where the parental strands of DNA are being  unwound. Helicases Are enzymes that untwist the double helix at the replication fork,  Transformation  Defined as the change in the genotype and phenotype due to  assimilation of external DNA by a cell. Leading from the starting point (3' to 5') Lagging Strand  from remaining parts to starting point (3' to 5') also called  Okazaki fragments DNA Ligase Enzyme that catalyzes bond formation between 3’ end of one  DNA fragment and 5’ end of another DNA polymerase Enzyme that adds deoxyribose nucleotide to the 3’ carbon (­OH)  of one preceding deoxyribose nucleotide Catalyzes the synthesis of new DNA by adding nucleotides to a  preexisting chain Single strand binding Bind to the unpaired DNA strands keeping them from repairing  proteins Topoisomerase Helps relieve the strain by breaking swiveling and rejoining DNA  strands. (ahead of the Replication fork) DNA ligase Joins the end of the fragments primase lays down an RNA "primer" (5' to 3') that is complementary to the DNA template Nucleotide excision  DNA repair system repair Main components are the DNA polymerase and DNA ligase heterochromatin,  chromatin, visible as irregular clumps with a light microscope, euchromatin    less compacted, more dispersed euchromatin (“true chromatin”)


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