BIO 446L 1st EditionFinal Exam Study Guide Final Exam Study Guide50 multiple choice questions = 1.6 points each5 Short Answer questions = 4 points each – or 4 questions worth 5 points eachExams and scantron sheets will be distributed before the exam starts. No lab sections needed this time, but DO bubble in your name, eID and exam version on your scantron BEFORE the exam startsMA’s are important on this exam, some Blue BoxesFollow all instructions! As you know, 5 points will be deducted from your score for not heeding this adviceDo NOT pull an “all-nighter”Set an alarm clock, or several, if you are a heavy sleeper- Review the tissue processing procedures that we discussed – not the procedural details, but howslides lookoo H and E—basic dye (purple) Typically what we see Hematoxylin-- Nuclei and DNA, GAGs, RNA stain blue/purple Eosinophil-- Acidophillic structures like protein in cytoplasm, mitochondria, secretory granules etc. stain in red/pinko PAS Stains sugars very darkly—distincto Fluorescence and immunofluorescence Nucleic acids stain yellow/orange Actin stains green DNA stains blueo Light microscopy- Important features of the plasmalemmao Functions Physical barrier Selective permeability—regulating ions, nutrients, and waste materials across membrane Electrochemical gradient—establishes and maintains electrical charge differenceacross membrane Communication—via cell to cell junctionso Osmium fixation gives trilaminar appearance Shows 2 electron-dense lines enclosing an electron-lucent band Glycocalyx appears fuzzyo Phospholipid bilayer Amphipathic-- Phosphate head, fatty acid tailso Cholesterol Amphipathic Interspersed throughout to disrupt phospholipids- Affects fluidity and rigidity—a stabilizing moleculeo Glycolipids Outer layer of membrane Extended carbohydrate chains and contribute to the glycocalyx- Glycocalyx= cell surface coating that provides antigenic and functional properties to cell surfaceo Lipid rafts membrane proteins functioning as parts of a large enzyme are located at lipid rafts Higher concentrations of cholesterol and saturated fatty acids—reducing lipid fluidity with scaffold proteins, lipid raft will allow signaling proteins to remain in close proximity with each other to interact more efficientlyo Proteins Integral—incorporated in the membrane, act as receptors for ligands, channels for passive and active movement across the membrane, pump for active transport Transmembrane—span the bilayer completely, function in membrane transport (aquaporins—Peter Agre, carrier/transport proteins) Glycoprotein—extensions of integral proteins that act as receptors participating in cell adhesion, recognition, and response to hormones- Problems—defective growth receptors and pseudohypoparathyroidism/ dwarfismo Caused by nonfunctioning parathyroid and growth hormone receptors Peripheral proteins—looser association with one of the two membrane surfaces,usually the inner *proteins have externally exposed carbohydrate chains and hydrophobic regionsfolded inwardo Movement across membrane Receptor mediated endocytosis- Integral membrane proteins serving as receptors for LDL, protein hormones, etc. at the cell surface- Integral proteins bind ligands with high affinity causing proteins to aggregate in special regions of membrane that they then invaginate and pinch off internally as vesicles Phagocytosis (type of endocytosis—cell eating)- Macrophages and neutrophils are specialized in engulfing and removing matter such as bacteria, dead cells, etc. Pinocytosis (type of endocytosis—cell drinking)- Fluid-filled—some of cytoplasm is sampled and taken with it- How do you determine sex in cytology?o Karyotyping X and Y chromosomes are visible under light microscopy Chromosomal analysis can detect certain genetic anomalies from fetus or amnion (closely covers embryo and amniotic fluid) Missing or extra chromosomes and deletions or translocations can also be seeno FISH (fluorescent in-situ hybridization) used to detect and localize the presence or absence of specific DNA sequences, fluorescing only those sequences showing high complementarity  used for finding specific feature in DNA-- i.e. sexo Barr bodies or gender chromatin permit gender Can be used in patients who don’t have external sex organs or have multiple chromosomes Barr body=a small dense mass of heterochromatin “inactivating” an X chromosome when there is already one present - Sex chromatin has the Barr body Pseudohermaphroditism= external sex organs look intermediate between clitoris and penis or appearance opposite to their sex- Understand meiosiso Two closely associated cell divisions occurring only in cells that will form sperm and egg cells (haploid)o Cells entering meiosis have just completed DNA replication in a typical S phase of the cell cycle (synthesis phase, where DNA is replicated) so that each chromosome contains two copies, sister chromatids (diploid)oo Meiosis I Prophase I—chromatin condenses, the nuclear envelope and nucleoli disappear,spindle starts to form, homologous chromosomes begin to pair and synapse (tetrads), and crossing over occurs- Synapsis—double strand breaks and repairs occur in the DNA with crossing overo Crossing over allows recombination-- DNA exchange and is a large source of genetic variance Metaphase I—tetrads line up along the metaphase plate, the spindle is completely formed, recombination completes Anaphase I—tetrads pull apart and chromosomes with two chromatids move toward the poles Telophase I—chromosomes with two chromatids decondense, nuclear envelopereforms, cells separate, and each is haploido Meiosis II Prophase II—chromosomes with two chromatids condense, same steps as Prophase I  Metaphase II—same as metaphase I Anaphase II—same as anaphase I but now it is a chromosome with one chromatid moving toward each pole Telophase II—chromosomes with one chromatid decondense, same steps as telophase I  End result is now 4 haploid daughter cells that are ready to develop into sperm or eggs- Lateral cell structures on epithelial cellso Tight junctions (occluding junctions) Most apical of junctions, forms a seal between adjacent cells by forming a band encircling cell and linking to band of adjacent cell, connecting their