Bio Exam 2 PDF

Lecture 5: DNA Replication FIGURE 14.11 These figures illustrate the compaction of the eukaryotic...

Lecture 5: DNA Replication FIGURE 14.11 These figures illustrate the compaction of the eukaryotic chromosome. DNA inside of cells is highly condensed through coiling. What is a gene? This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. The process of DNA replication : 1. DNA unwinds at the origin of replication. 2. Helicase opens up the DNA-forming replication forks; these are extended bidirectionally. 3. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. 4. Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling. 5. Primase synthesizes RNA primers complementary to the DNA strand. 6. DNA polymerase III starts adding nucleotides to the 3'-OH end of the primer. 7. Elongation of both the lagging and the leading strand continues. 8. RNA primers are removed by exonuclease activity. 9. Gaps are filled by DNA pol I by adding dNTPs. 10. The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds. FIGURE 14.14 First Components of DNA Replication. HHMI Short Video (credit: Rao, A., Ryan, K. Fletcher, S. and Tag, A. Department of Biology, Texas A&M University) This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources.  Continuous synthesis of DNA on leading strand. Okazaki Fragments on the lagging strand. FIGURE 14.19 Nucleotide excision repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced. (credit: Rao, A., Fletcher, S. and Tag, A. Department of Biology, Texas A&M University) This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. FIGURE 14.21 Mutations can lead to changes in the protein sequence encoded by the DNA. This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. FIGURE 10.5 The cell cycle consists of interphase and the mitotic phase. During interphase, the cell grows and the nuclear DNA is duplicated. Interphase is attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. followed by This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be MITOSIS AND MEIOSIS BIOLOGY for AP® COURSES Chapter # Chapter Title PowerPoint Image Slideshow FIGURE 11.2 Overview of Meiosis (credit: Rao, A., Tag, A, Fletcher, S., and Ryan, K. Department of Biology, Texas A&M University) This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. FIGURE 11.5 (credit: Rao, A. and Fletcher, S. Department of Biology, Texas A&M University) This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. FIGURE 11.8 This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources.  BIOLOGY for AP® 2e BIOLOGY COURSES Chapter # Chapter Title Chapter 12 MENDEL ’S EXPERIMENTS PowerPoint Image Slideshow AND HEREDITY PowerPoint Image Slide Show FIGURE 12.3 Mendel worked with traits that were inherited in distinct classes (specifically, violet versus white flowers); this is referred to as discontinuous variation. In one of his experiments on inheritance patterns, Mendel crossed plants that were true-breeding for violet flower color with plants true- breeding for white flower color (the P generation). The resulting hybrids in the F1 generation all had violet flowers. In the F2 generation, approximately three quarters of the plants had violet flowers, and one quarter had white flowers. F = Filial (offspring) Some important concepts: Genotype Phenotype Diploid vs. Haploid Homozygous Heterozygous Dominant vs. Recessive Codominance Incomplete Dominance Epistatis X-Linked vs. Autosomal Trait FIGURE 12.4 In the P generation, pea plants that are true-breeding for the dominant yellow phenotype are crossed with plants with the recessive green phenotype. This cross produces F1 heterozygotes with a yellow phenotype. Punnett square analysis can be used to predict the genotypes of the F2 generation. A Punnett Square is a diagram that predicts the possible outcomes of a genetic cross between two individuals. FIGURE 12.5 A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a heterozygote. Two big laws of Mendelian Inheritance Law of Segregation. Paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. Law of Independent Assortment Genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. (UNLESS THERE IS LINKAGE!)  FIGURE 12.6 Alkaptonuria is a recessive genetic disorder in which two amino acids, phenylalanine and tyrosine, are not properly metabolized. Affected individuals may have darkened skin and brown urine and may suffer joint damage and other complications. In this pedigree, individuals with the disorder are indicated in blue and have the genotype aa. Unaffected individuals are indicated in yellow and have the genotype ofAAtheir or Aa.offspring. Note thatFor it example, if neither parent has the is often possible disorder but theirtochild determine a must be heterozygous. Two individuals does, they person’s on genotype the pedigree havefrom anthe unaffected phenotype but unknown genotype. Because they do not have the disorder, they must have at least one FIGURE 12.16 This dihybrid cross of pea plants involves the genes for seed color and texture. This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. FIGURE 12.20 Dihybride Cross with Epistasis (antagonistic interaction between genes such that one gene masks or interferes with the expression of another) In mice, the mottled agouti coat color (A) is dominant to a solid coloration, such as black or gray. A gene at a separate locus (C) is responsible for pigment production. The recessive c allele does not produce pigment, and a mouse with the homozygous recessive cc genotype is albino regardless of the allele present at the A locus. Thus, the C gene is epistatic to the A gene. Figure 14.22 Figure 14.23 Evolution, Hardy-Weinberg and the Diversity of Life Living things may be single-celled or complex, multicellular organisms. They may be plants, animals, fungi, bacteria, or archaea. This diversity Parental allele frequencies Gene pool Offspring genotype frequencies p  p  p2 p  q  pq q  p  pq q  q  q2 2 2 A1A1 genotype 0.21  0.21  0.42 A1A2 genotype A2A2 genotype 𝑝 +2 𝑝𝑞 +𝑞 =1 frequency is frequency is frequency is All will contribute Alleles contributed to the All will contribute next gene pool will be Offspring allele A1 alleles to the new A2 alleles to the next frequencies gene pool. half A1, half A2. gene pool. Gene pool Allele A1 p  0.7 Allele A2 q  0.3 If population is NOT in Hardy-Weinberg Equilibrium, then it is evolving by one or more Evolutionary Process. Phylogenies, Adaptative Radiations and the History of Life Summary Table 28.1 Summary Table 28.2  Adaptive Radiation new branches on the tree of life. Figure 28.11 Cambrian Explosion (a big adaptive radiation) (a) A time line of early animal evolution (b) Early animals from two major macroscopic fossil assemblages Phanerozoic Eon Cambrian fossils Proterozoic Eon 1 cm 1 cm Cambrian Cambrian fossils are diverse, large, and have hard parts. Ediacaran fossils Archaean Eon Doushantuo 1 cm 1 cm microfossils (tiny sponges and corals) Ediacaran fossils are soft-bodied. Figure 28.13 Hox Genes and Animal Diversification Protist outgroup Hox-like genes, but no Hox genes Sponges Comb jellies Boxes represent genes within the Hox cluster Origin of Sea anemones animals Acoels Rotifers Flatworms Mollusks Annelid worms Arthropods Roundworms Echinoderms Early chordates Vertebrates Radiation of animals during the 1 2 3 4 5 6 7 8 9 10 11 12 13 Duplication of the Cambrian explosion Hox cluster occurred in vertebrates. Mice and humans have four clusters  Prokaryotic Domains – Bacteria and Archaea Bacteria Archaea Common ancestor of all species living today Eukarya  Fig. 25-9-4 Cytoplasm Plasma membrane Ancestral DNA prokaryote Nuclear Membrane and ER Endoplasmic reticulum Nucleus Nuclear envelope Aerobic Endosymbiosis heterotrophic Photosynthetic and Plastids in prokaryote prokaryote Plants and Mitochondrion related Protists Ancestral Mitochondrion heterotrophic eukaryote Plastid Endosymbiosis and Mitochondria in all Ancestral photosynthetic Eukaryotes eukaryote  Choanoflagellates ANIMALIA Porifera Fungi Choanoflagellates Cnidaria ANIMALIA Ctenophora Multicellularity Acoelomorpha Hox Bilateral symmetry? LOPHOTROCHOZOA Rotifera Genes Loss of coelom Platyhelminthes and Bilateral symmetry Segmentation Annelida PROTOSTOMES Animal Protostome development Molluska BILATERIA Diversity ECDYSOZOA Nematoda Coelom, cephalization, CNS Arthropoda Segmentation DEUTEROSTOMES DEUTEROSTOMES Radial symmetry Echinodermata (in adults) Chordata Segmentation  (a) Fly Hox genes Fly embryo Head Thorax Abdomen (b) Mouse Hox genes Mouse embryo Fig. 25-21 Hypothetical vertebrate ancestor (invertebrate) with a single Hox cluster First Hox duplication Hypothetical early vertebrates (jawless) with two Hox clusters Second Hox duplication Vertebrates (with jaws) with four Hox clusters