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BSC 2011 Exam 1 Study Guide

by: rcg16b Notetaker

BSC 2011 Exam 1 Study Guide 2011

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These notes cover all lesson objectives that Professor Dixon specified. Be sure to open the links and reference diagrams in the book. I hope this is of use to you! If you have any questions, feel f...
Biological Sciences II
Dr. Kevin Dixon
Study Guide
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This 9 page Study Guide was uploaded by rcg16b Notetaker on Friday September 23, 2016. The Study Guide belongs to 2011 at Florida State University taught by Dr. Kevin Dixon in Fall 2016. Since its upload, it has received 243 views. For similar materials see Biological Sciences II in BSC at Florida State University.


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Date Created: 09/23/16
Be sure to open the links to see diagrams! I hope this is helpful. Lecture 2 – Objectives Slide • Know that DNA is organized into structures called chromosomes and be able to describe the structure of a eukaryotic chromosome o -and-chromosome-and-DNA.jpg o DNA + Protein= Chromatin • Be able to explain the significance of the coiling of chromatin o After DNA replication, chromosomes condense as a part of cell division o Can now see chromosome with microscope in Prophase § Each duplicated chromosome has 2 sister chromatids (joined copies of original chromosome) § Each sister chromatid has a centromere (region of DNA where the chromatids are more closely attached) • Be able to describe the multiple functions of cell division o Reproduce unicellular organism o Growth and repair of tissues in multicellular organism o Formation of gametes for sexual reproduction • Know that cell division results in genetically identical daughter cells o Dividing cell replicates DNA and splits the two daughter cells o Exception: meiosis is eukaryotic division that produces sperm and eggs (gametes) • Be able to diagram the cell cycle indicating the timin g of all processes o See diagram: o Mitosis: 1 hour o G1: 5-6 hr o S: 10-12 hr o G2: 4-6 hr • Know that separation of sister chromatids occurs in Mitosis o -Anaphase.svg.png • Know the major stages of Mitosis and what happens in each o • Be able to explain one potential evolutionary pathway leading to mitosis o Might have evolved from prokaryote mechanisms of cell reproduction o Some proteins in bacteria binary fission are related to eukaryotic mitosis o During bacteria binary fission, origins of daughter chromosomes move to opposite ends of the cell • Be able to explain the experiment demonstrating that the spindle moves chrom atids through tubule shortening o Microtubules on kinetochore side shortened, those on spindle pole stayed the same o Conclusion: during anaphase, a chromosome is walked along a microtubule as the microtubule depolarizes at its kinetochore end o • Be able to explain the control of mitosis through CdK and cyclin o Cell cycle control molecules pace the events of the cell cycle § two main types • protein kinases- enzymes that activate/inactivate other proteins by phosphorylating them • cyclins § MPF is the cyclin -Cdk complex • cyclin-dependent kinases or Cdks - to be active, the kinase must be attached to a cyclin • The activity of a Cdk rises and fall with changes in the concentra tion of cyclin • The peaks of MPF activity correspond to the peaks of cyclin concentration • The cyclin level rises during the S and G2 phase and falls during the M phase • The MPF triggers the cell’s passage into the M phase § MPF complex phosphorylates a variety of proteins, initiating mitosis § During anaphase, MPF switches itself off by destructing its own cyclin § The noncyclin part of the MPF (the Cdk) stays in the cell, inactive and later becomes part of MPF again by associating with a new cyclin molecule which are made during the S and G2 phases of the next round of the cell cycle • Know that cancer is the result of a failure of control of the cell cycle o Cancer cells don’t stop dividing when growth cells are depleted o Change in genes that alters the function of th e protein products= faulty cell cycle control o Check points don’t function Terminology – histone, chromatin, nucleosome, sister chromatid, centromere, genome, somatic cell, gamete, mitosis, meiosis, G1, G2, and S phases, cytokinesis Reading: Chapter 16: 320-322 (review), Chapter 12 Concepts and Terms for Lecture 3 Reading: 18.2-18.3 (review chapter 11 and be able to perform the general objectives below only) Concepts: • Be able to explain what gene expression means (transcription and translation of genes) and be able to explain that the differences in phenotype (structure and function) of cells with identical genomes is due to differences in gene expression o Gene expression was originally studied in prokaryotes o Differential gene expression - the expression of different genes by cells with the same genome o Differences in phenotype (structure and function) of cells with identical genomes is due to differences in gene expression o Cell differentiation is largely a result of expression • Know that gene expression in eukaryotes can be controlled at multiple stages during transcription and translation o Between each these stages, there is a potential control point in which gene expression can be turned on or off (most common is transcription) § Signal > chromatin modification/DNA unpacking > Transcription > RNA processing > mRNA transported to the cytoplasm > Translation > Protein Processing > transport of protein to destination • Be able to distinguish between cell signaling due to direct contact vs a long distance signal o Direct § Animals and plants have cell junctions that directly connect cytoplasm of adjacent cells § Signaling substances pass freely in cytoplasm § Animals can communicate between membrane bound surfaces • Important for embryonic development o Long Distance § Animals and plants use hormones that travel in the circulatory system § Ability of cell to respond if determined by whether they have a specific receptor molecule • Be able to explain cell signaling generally as consisting of reception of signal, transduction of the signal, and a cellular response o -L.jpg • Be able to explain the relation ship of apoptosis to cell signaling o Apoptosis- programmed cell death § Cellular agents chop up DNA and fragment the organelles and other cytoplasmic components § Cell shrinks and becomes lobed § Parts are ingested by scavenger cells § Skeleton forms inside soft tissue up until the end, at some point the cells in between must die § Duck feet are webbed, if combine chick and duck ectoderm, end up with chicken leg with webbed feet o Trigger § Outside- Signaling molecules released form other cells initiate a signal transdu ction pathway for cell death § Inside- if DNA is irretrievable damaged, protein-protein interactions pass along a signal that triggers cell death • Be able to explain two ways in which mo dification of histone structure can affect transcription (acetylation an d methylation) o Histone- protein around which DNA is wrapped, has a tail that is accessible to modifying enzymes that catalyze the addition or removal of modifying groups § Histone Acetylation - Promotes transcription by opening up chromatin structure § DNA Methylation- methylates bases in DNA (usually cytosine) and prevents expression. Removal of group can turn some genes on. • Know that enhancers and transcription factors can affect transcription o Transcription Factors § Needed by RNA polymerase to initiate transcription § Bind to the TATA box or proteins called control factors o Enhancers § Distal control elements, thousands of genes that move up and down a gene § Rate of gene expression can be increased or decreased by these • Know that enhancers and transcription factors can result in cell specific transcription and be able to explain that gene expression can either be induced or repressed and the situations in which that occurs o The rate of gene expression can be increased or de creased by the binding of specific transcription factors § Activators- protein mediated bending of the DNA brings activators into contact with the mediator proteins which interact with the proteins at the promoter. This helps assemble and position the initiation complex on the promoter. § Repressors- bind to control element and block the activator from binding. Some recruit proteins that remove acetyl groups from histones which decreases transcription. More commonly called silencing or chromatin modification. • Know that RNA modification can affect the product of tra nscription o Alternative RNA splicing - Different mRNA molecules are produced from the same primary transcript depending on which are treated as exons and introns o Regulatory proteins specific to the cell control which RNA segments are treated as exons or int rons • Be able to explain how non -coding RNA such as microRNA can affect mRNA o microRNA is crucial in regulating gene expression o microRNA are small single stranded molecules that can bind to complementary sequences in mRNA molecules § allows complex of RNA and protein to bind to any mRNA molecule with at least 7 or 8 nucleotides of complementary sequence § about half of the human genes may be regulated by microRNAs. § microRNAs degrade the target mRNA or blocks its translation. Terminology - Operon, operator, repr essor, binding site, promoter, acetylation, methylation, enhancer, transcription factor, microRNA Lecture 4: Gene Expression and Diversity of Cells (general model) Reading 18.4 Concepts • Be able to explain how the concentration of cytoplasmic determinants leads to differences in cell determination in early development. o Cytoplasmic determinant - important maternal substances in the egg that influence the course of early development o After fertilization, mitosis distributes the zygotes cytoplasm to separate cells, exposing the nuclei to different determinants o This determines the developmental fate of the cell o This makes the daughter cells a product of the mother’s genotype o -L.jpg • Be able to explain how bicoid works to d etermine the body axis in flies and know that t he earliest genes expressed determine axis polarity, followed by organization into body regions, segmentation, and specific characteristics (Drosophila). o Bicoid- gene that is two tailed o Mother’s bicoid gene is essential in setting up the anterior end ofly o Bicoid mRNA is concentrated at the anterior end of a mature egg o After the egg is fertilized, the mRNA is translated to protein o Protein diffuses from the anterior end to the posterior to form the head o Cytoplasmic determinants in egg initially establish the Drosophilia body which are encoded by the maternal effect gene (a gene from the mother that, when mutant in the mother, results in a mutant phenotype in the offspring) o Maternal effect genes are also called egg polarity genes because they control theientation of the egg, and the orientation of the fly § One group of these sets up the anterior -posterior axis of the embryo § One sets up the dorsal -ventral axis • Hox gene- genes that code for transcription factor proteins which in turn, control sets of genes important for animal development Terms – Hox, Homeotic, Differentiation, Determination, Induction, Maternal Effect, Cytoplasmic Determinant, Lecture 5 Reading: 21.6 (whole thing*), 25.5 – Change from syllabus • Be able to explain the different insights to be gained from comparison of closely related vs distantly related organisms o Distantly- clarifies evolutionary relationships amount species that diverged long ago o Closely- can use one genome to help map the other, particular genetic differences can be mo re easily correlated with phenotype differences • Know that developmental genes are highly conserved across animals (be able to explain what ‘highly conserved’ means) o Highly conserved - genes that remain similar § Homeotic genes § Encoding components of signaling pathways • Be able to explain how evolutionary change can occur through changes in genes coding for enzymes or structural proteins or through changes in regulatory genes and be able to describe the different results that wou ld occur if an evolutionary change was due to a regulatory gene vs a ‘coding’ gene. o Regulatory gene § Can limit change to one cell type § Fewer side effects § Researchers suggest that changes in the form of organisms are causes by changes in regulation of genes o Coding gene § Affects function wherever expressed • Be able to explain how changes in growth and development can result in new phenotypes with an example. o FOX P2 gene- development of speech and language in vertebrates o Produced mice with copies of FOX P2, som e with disrupted genes and some without disrupted gene o Led to brain abnormalities (phenotypic) • Paedomorphosis- reproductive organ development exceeds other body organs so sexually mature species retain juvenile structures in ancient species Terms: paedomorphosis, hox (homeobox) gene Lecture 6 Reading 47.1 (through page 1027), 32.3 (section on protostome and Deuterostome development only pages 660 -661) Concepts • Know that development consists of fertilization, cleavage, gastrulation, and organogenesis be able to distinguish the basic processes occurring in each. o Fertilization- formation of a diploid zygote from a haploid egg and sperm § Sperm dissolves and penetrates protective layer on egg § Molecules on sperm surface bind to receptors on egg § Surface of the egg changes to prevent polyspermy § Sperm contacts jelly coat of egg causing acromosomal reaction in sperm (discharge of enzyme from acrosome, tip of sperm, to penetrate jelly coat § Sperm and egg fuse plasma membrane § Sodium ions in the egg cause depolarizatio n= decrease in the membrane potential • This acts as a fast block to polyspermy § Slow block to polyspermy - caused by vesicles that lie just beneath the egg plasma membrane in the cortex • Vesicles fuse with the egg plasma membrane • Cortical reaction triggered w hich makes a protective fertilization envelope by a spreading wave of Ca++ ions § Embryonic development triggered § Fertilization is slower in mam mals o Cleavage- rapid mitotic division that forms blastula § Successive rapid cell division (S and M phases) § G1 and G2 are skipped so no increase in cell mass § Small cells called blastomeres form blastula which surrounds a fluid filled cavity called the blastocoel § Patterns • Sea urchins- division is uniform • Frogs- division is asymmetric § The pattern of cleavage planes is species specific and important to development because cleavage partitions maternal cytoplasmic determinants o Gastrulation- folding of the blastula onto itself to make the gastrula § A set of cells near the surface of the blastula move inward (like a punch ed volley ball) § This establishes cell layers • Endoderm- mucous membrane, digestive and respiratory tracts, digestive glands • Ectoderm- epidermis and nervous system • Mesoderm- skeletal muscle, bone, blood, gelatinous tissue § Forms a primitive digestive tube o Organogenesis- continued cell movement and cell differentiation § Neuralation • Early steps to form brain and spinal chord in vertebrates • Notochord- rod that extends along the dorsal side of the chordate embryo to form neural plate (example of induction) • Neural plate rolls into neural tube • Neural tube becomes the brain and spinal chord, the notochord disappears § Morphogenesis • Movement of cells • Microtubules and microfilaments essential and make up cytoskeleton • Cytoskeleton directs convergent extension causing a sheet of cells to converge and become longer • Induces mesoderm to form somites (migratory cells formed when groups of cells located in strips of mesoderm separate into blocks and create muscles • Cell can recognize its position in the embryo through the c oncentration gradient of a morphogen o Bicoid is not a morphogen b/c not in organogenesis • By able to explain the 2 mechanisms blocking polyspermy in sea urchins o Sodium ions in the egg cause depolarization= decrease in the membrane potential § This acts as a fast block to polyspermy o Slow block to polyspermy - caused by vesicles that lie just beneath the egg plasma membrane in the cortex § Vesicles fuse with the egg plasma membrane § Cortical reaction triggered which makes a protective fertilization envelope by a spreading wave of Ca++ ions • Be able to explain why blocking multiple fertilizations is important. o Multiple sperm in an egg (polyspermy) is lethal because the embryo can inherit multiple paternal of centrioles and disrupts the cleavage furrow • Know that cleavage is cell division without growth o Successive rapid cell division (S and M phases) o G1 and G2 are skipped so no increase in cell mass • Be able to distinguish different patterns of cleavage in different organisms and explain the reasons for these differences o Sea urchin § Microlecithal - little yolk § Holoblastic- cell completely divides through cleavage o Frog § Mesoolecithal- medium yolk § holoblastic § has animal (less yolk) and vegetal pole (denser yolk) § blastocoel is reduced and offset because of uneven yolk § high yolk= cells divide slower o Chick § Macrolecithal - lots of yolk § Meroblastic- cleavage does not proceed all the way through § Blastoderm in chick= blastula in frog and sea urchin Terms: sperm, egg, polyspermy, acrosome, vitelline layer, fertilization envelope, protostome, deuterostome, types of cleavage (radial, spiral determinate, indeterminate), morula, blastula, blastocoel, microlethical, holoblastic Lecture 7 Reading: 47.1, 47.2 Concepts • Be able to distinguish cleavage pattern based on the type of egg o Protostomes § Spiral (8 cell stage) § Determinant fate § Can’t remove cell at this stage o Deuterostomes § Radiant (8 cell stage) § indeterminant fate § Can remove cell or split embryo in half and it will be fine • Be able to explain the process of gastrulation in the sea urchin o Migration/ingression of inner cells of blastula into the blastocoel at vegetal pol o Invagnation- outer blastula cells move inward at vegetal pole and forms blastopore which becomes the anus for the sea urchin § For deuterostomes it forms the inner digestive tube (archenteron) o Continued elongation of archenteron and digestive tube is pulled by inside cells o Gastrulation is the folding of the blastula on itself. There are three main egg types. Microletcithal eggs, such as sea urchins, have a small yolk that causes holoblastic cleavage. This means that the cleavage furrow passes entirely through the egg. Invagination starts at the vegetal end of the egg. This kind of gastrulation forms a radial organism. • Be able to distinguish the differences in gastrulations among the sea urchin, frog, and chick (location of infolding, formation of the gut) o Frog § Invagination- outer cells push inward (not at vegetal pole), blastopore and dorsal lip established § Involution- cells roll inward, filling the blastocoel and making the archenteron and inner germ layers (endoderm and mesoderm) § Animal pole cells spread over surface § From practice exam “Mesolecithal eggs such as frogs, have a moderate yolk that causes holoblastic cleavage like the sea urchin. The blastocoel in these eggs is smaller and offset because of the uneven yolk. Invagination does not happen at the vegetal pole because there is so much yolk there in the frog egg. The cells with a higher yolk content divide slower causing big yolk filled cells and small animal cells. This causes there to be larger cells at the vegetal pole. So, invagination happens at the boundary between the vegetal and animal poles. The blastocoel is displaced. In the sea urchin it is just moved through. The animal cells migrate down the outside so that they cover most of the embryo and form the ectoderm. This is called involution and does not happen in sea urchins. The gastrulation sets up bilateral symmetry rather than radial as in the sea urchin.” o chick § blastoderm= blastula § epiblast cells on the surface of the blastoderm invaginate inward toward the middle of the blastoderm forming a primitive streat (aka blastopore) § Macrolecithal eggs, such as chicks, have a large yolk which cause meroblastic cleavage. Meroblastic cleavage is the incomplete cleavage of a yolk rich egg. This happens because it is very energetically expensive and time consuming to divide through the yolk. The epiblast cells migrate to the middle and go down to form a primitive streak. The cells that stay on top form the ectoderm, and the cells that go to the bottom form the endoderm. A blastoderm forms which sits on top of the yolk. In the middle of the blastoderm, there is a primitive streak which eventually helps form the endoderm, ectoderm and mesoderm. This is very different from the sea urchin and the frog which both have a complete cleavage. The chicken has bilateral symmetry like the frog. • Understand that the archenteron is the embyronic gut - forms as a result of gastrulation • Know the difference between deuterostomes and protostomes. o Protostomes § Mouth developes form first opening § Arthropods, mollusks, annelids o Deuterostomes § Mouth develops form sec ond opening § Vertebrates o Terminology - gastrula, blastopore, filipodia, archenteron, mesoderm, endoderm, ectoderm, mesolethical, macrolethical, meroblastic, holoblastic Lecture 8 Reading - 47.2, 47.3 Concepts • Be able to explain how the position of regions of the embryo relative to one another provides information that determines the formation of organs. • Be able to describe and explain the example given (notochord stimulates the formation of the neural plate, neural tube stimulates neural crest cells) o Explained above • Know the adult structures formed from endoderm, mesoderm, and ectod erm o Ectoderm § Skin, epidermis, nervous system o Mesoderm § Skeletal and circulatory system § Reproductive system § Excretory system § Muscles § Notochord o Endoderm § Thymus, thyroid, pancreas, liver § Epithelial lining of digestive tract, respiratory and reproductive and e xcretory system • Be able to explain the role of the grey crescent and the dorsal lip of the blastoporein organizing the the frog embryo o The gray crescent forms near the dorsal lip and determines where the future dorsal side of the tadpole is o The gray crescent is where cells invaginate to begin gastrulation, forming the dorsal lip of the blastopore § This determines the dorsal -ventral axis of the embryo § Cell determinants in gray crescent cells have positional info for the embryo and induce differentiation accordingly § Without these CDs, a proper organism will not form § 2 gray crescents will form 2 dorsal regions in an organism if induced experimentally • Be able to explain how morphogens work o Morphogens are gradient substances that establish an em bryos axis and other features § morphogens encoded by maternal effect genes determine body axis § The physical process that gives an organism shape is morphogenesis • Example is formation of neural tube § Actin filaments (microfilaments) facilitate the movement of the cells o Convergent extension - morphogenic movement that is a rearrangement that causes sheets of cells to be narrower and longer (important in gastrulation) Terminology - Notochord, neural fold, groove and tube, neural plate, somite, neural crest c ells Lecture 9 • Be able to explain how hormones act over the entire body and be able to explain how hormones control the timing of developmental changes o Hormone- substance produced by a tissue or organ that travels and causes changes in target cel ls that have specific receptors, helps organize all the development happening (transported over the entire body) o Different tissues respond differently to the same hormone (degenerate/develop/differentiate) o Tissues respond to different threshold levels of a hormone o Development- gradual and progressive loss of cell potential by a series of induced determination events that ultimately lead to the final differentiation of cells at their proper times and locations in the fully developed embryo o Lateral development requir es coordination of changes § Insects-need dormancy because entire body is completely reorganized § Other larvae- transition is more gradual, organism remains active, requires coordination of events o Example: epinephrine- fight or flight § Triggers different thin gs to happen in different cells § Liver cell breaks down glucose § Skeletal muscle blood vessels dilate § Intestinal blood vessels constrict o A single hormone can cause a cascade of gene expression • Know that thyroxin controls the transformation of tadpoles into frogs o Thyroxin gland produces thyroxin which signals target cells and binds to cell receptors o Activated receptors set up a signal transduction pathway that activates or represses genes o Different tissues respond at different times and differently to the sam e hormones § Some things develop before others ( legs before tail is lost and lungs so that it can move onto land when ready) o As thyroxin levels increase, tissues with decreased sensitivity to thyroxin respond in a coordinated pattern=coordinated gene express ion=developmental changes o Experiments § If thyroid is removed= no metamorphosis = huge tadpole § If inject thyroid early= premature mini frog • Understand morphogens vs hormones but how they work together to get cells to differentiate at the appropriate place and time • Gene expression can be affected by environment o Plant in dark place grows tall o Plant in bright light, shorter and many more leaves o Think of an environmental trigger to being an omnivore End of document


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