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Biology Midterm Notes.docx

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Department
Biology
Course
Biology 1201A
Professor
Michael Gardiner
Semester
Fall

Description
Biology Midterm Notes Lecture 1: Characteristics of Living Things 1. Organisms tend to be complex and highly organized. 2. Living organisms have the ability to take energy from the environment and change it from one form to another. 3. Organismstendtobehomeostatic– they regulate their bodies and other internal structures to certain 4. Living creatures respond to stimuli. normal parameters. 5. Living things reproduce themselves by making copies of themselves. 6. Organisms tend to grow and develop. 7. Life adapts and evolves in step with external changes in the environment. Lecture 2: A tour of the Cell Early Microscope Anthony van Leeuwenhoek Single Lens - ca. 1673 Robert Hooke  The Cell: first person to coin the word 'cell' to describe the tiniest components of living systems - plants!  1635 - 1703 The Electron Microscope  Resolution limit of Light Microscope is about 0.2 microns (size of a small bacterium – remember 1 micron is .001mm)  Magnification limit of about 1000 times  In 1950’s the introduction of the electron microscope enabled organelles, viruses, proteins, etc.. to be imaged  The minimum resolution of a light microscope is about .2 microns, the size of a small bacterium  Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen. – At higher magnifications, the image blurs. Cell Fractionation  Take cells apart to study their components  Centrifuge is used to fractionate cells and separate their major organelles  Ultracentrifuges are capable of speeds as fast as 150,000 rpm applying forces over 1 million times the force of gravity The Cell Cell = simplest collection of matter which has all the properties of life 1. Lowesthierarchicallevelwhichis alive 2. Cellisbasicunitoflife 3. Cell performs all functions necessary to live and reproduce Virus  Occur in virtually every kind of organism  Some wreck havoc others cause no disease or outward sign of their presence  Often highly specific to host  Can reproduce only when they enter a cell Prokaryotic Cells  Pro-beforeandkaryote-nucleus – Examples – bacteria, cyanobacteria, mycoplasmas, etc..  Nonucleus (genetic information in area called nucleoid. • Visible components–plasma membrane, ribosomes, nucleoid, cytoplasm, cell wall, pili, flagella, mesosomes, photosynthetic membranes Eukaryotic Cells • Eu - true, karyote - nucleus • Found in four (?) Kingdoms – Protist Fungi – Animalia – Planta Characteristics • True Nucleus (surrounded with nuclear membrane, contains DNA, • Visible Components – Plasma membrane, cytoplasm, nucleus, ribosomes, organelles, endomembrane system, cytoskeleton, cell wall, cell matrix, some organelles, flagella The nucleus Eukaryotic cell’s genetic library  Most of the genes in a eukaryotic cell. – Some genes are located in mitochondria and chloroplasts.  Averages about 5 microns in diameter.  Separated from the cytoplasm by a double membrane. – These are separated by 20-40 nm.  Where the double membranes are fused, a pore allows large macromolecules and particles to pass through. The nuclear side of the envelope is lined by the nuclear lamina, a network of intermediate filaments that maintain the shape of the nucleus.  Within the nucleus, the DNA and associated proteins are organized into fibrous material, chromatin.  Appear as diffuse mass.  However when the cell prepares to divide, the chromatin fibers coil up to be seen as separate structures, chromosomes.  Eacheukaryoticspecieshas a characteristic number of chromosomes.  Inthenucleusisaregionof densely stained fibers and granules adjoining chromatin, the nucleolus.  – In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits.  • Thenucleusdirectsprotein synthesis by synthesizing messenger RNA (mRNA). Cytoplasm  Material between the plasma membrane (cell membrane) and the nuclear envelope  Has a variable viscosity  Main chemical constituents are water (approx. 80%), nucleic acids, proteins, lipids, carbohydrates, pigments, etc.....  Ribosomes build • Ribosomes contain rRNA and protein.  • A ribosome is composed of two subunits that combine to carry out protein synthesis. Cell types that synthesize large quantities of proteins (e.g., pancreas) have large numbers of ribosomes and prominent nuclei. • free ribosomes, are suspended in the cytosol and synthesize proteins that function within the cytosol. • bound ribosomes, are attached to the outside of the endoplasmic reticulum. • Ribosomes can shift between roles Endomembrane System  Many of the internal membranes in a eukaryotic cell are part of the endomembrane system.  These membranes are either in direct contact or connected via transfer of vesicles, sacs of membrane.  The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane. There are two regions of ER that differ in structure and function. – Smooth ER looks smooth because it lacks ribosomes. – Rough ER looks rough because ribosomes (bound ribosomes) are attached to the outside, including the outside of the nuclear envelope. Smooth ER  Smooth ER is rich in enzymes and plays a role in a variety of metabolic processes.  Synthesize lipids, including oils, phospholipids, and steroids.  Smooth ER also catalyzes a key step in the mobilization of glucose from stored glycogen in the liver. Smooth ER  Other enzymes in the smooth ER of the liver help detoxify drugs and poisons. – These include alcohol and barbiturates. – Frequent exposure leads to proliferation of smooth ER, increasing tolerance to the target and other drugs.  Muscle cells are rich in enzymes that pump calcium ions from the cytosol to the cisternae. Rough ER  Rough ER is especially abundant in those cells that secrete proteins. – As a polypeptide is synthesized by the ribosome, it is threaded into the cisternal space through a pore formed by a protein in the ER membrane.  Secretory proteins are packaged in transport vesicles that carry them to their next stage. Rough ER • Rough ER is also a membrane factory.  – Membrane bound proteins are synthesized directly into the membrane.  – Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol.  – As the ER membrane expands, parts can be transferred as transport vesicles to other components of the endomembrane system. Lecture 3: Tour of the Cell 2 The Golgi Apparatus • transport vesicles from the ER  Golgi apparatus for modification of their contents • center of manufacturing, warehousing, sorting, and shipping • extensive in cells specialized for secretion. The Golgi Apparatus • flattened membranous sacs – cisternae – looking like a sac of pita bread • membrane of each cisterna separates its internal space from the cytosol • cis side -- receives material by fusing with vesicles, while the other side, the trans side, buds off vesicles that travel to other sites  During their transit from the cis to trans pole, products from the ER are modified to reach their final state  can manufacture its own macromolecules, including pectin and other non- cellulose polysaccharides  tags, sorts, and packages materials into transport vesicles Lysosomes  • The lysosome is a membrane-bounded sac of hydrolytic enzymes that digests macromolecules.  Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids.  These enzymes work best at pH 5. – Proteins in the lysosomal membrane pump hydrogen ions from the cytosol to the lumen of the lysosomes.  Rupturing one or a few lysosomes has little impact on a cell – Massive leakage from lysosomes can destroy an cell - autodigestion.  Lysosomes can fuse with food vacuoles, formed when a food item is brought into the cell by phagocytosis.  Lysosomes can also fuse with another organelle or part of the cytosol. – This recycling, this process of autophagy renews the cell. Vacuoles • Vesicles (or Microbodies) and vacuoles (larger versions) are membrane-bound sacs with varied functions. – Food vacuoles, from phagocytosis, fuse with lysosomes. – Contractile vacuoles, found in freshwater protists, pump excess water out of the cell. – Central vacuoles are found in many mature plant cells. Plant Central Vacuole  The membrane surrounding the central vacuole, the tonoplast, is selective in its transport of solutes into the central vacuole.  Functions - stockpiling proteins or inorganic ions, depositing metabolic byproducts, storing pigments, and storing defensive compounds against herbivores. Endomembrane system plays a key role in the synthesis (and hydrolysis) of macromolecules in the cell. • The various components modify macromolecules for their various functions. Mitochondria and Chloroplasts Cell Energy Transformers Mitochondria and chloroplasts - main energy transformers of cells • Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work. • Mitochondriaarethesitesofcellularrespiration, generating ATP from the catabolism of sugars, fats, and other fuels in the presence of oxygen. • Chloroplasts, found in plants and eukaryotic algae, are the site of photosynthesis. Mitochondria and Chloroplasts  Like mitochondria, chloroplasts are dynamic structures. – Their shape is plastic and they can reproduce themselves by pinching in two.  Mitochondria and chloroplasts are mobile and move around the cell along tracks in the cytoskeleton. Peroxisomes  Found in Plant and Animal cells  Singlemembraneboundcompartment  Enzymesthattransferhydrogenfrom various substrates to oxygen  Thisproduceshydrogenperoxidewhich is then converted to water • Are made from cytosol not endomembrane system?? Cytoskeleton • The cytoskeleton is a network of fibers extending throughout the cytoplasm. • Thecytoskeleton organizes the structures and activities of the cell. Structural support - cell motility - regulation • mechanical support and maintains shape of the cell • Fibers act like a geodesic dome to stabilize a balance between opposing forces.  anchorage for many organelles and cytosolic enzymes.  Dynamic - dismantling in one part and reassembling in another to change cell shape. Property Microtubules Mifrofilaments Intermediate Filaments Two intertwined Fibrous proteins Structure Hollow tubes strands super coiled Diameter 25 nm 7 nm 8 – 12 nm Protein Tubulin Actin Keratin proteins Subunits Maintain cell shape Cell motility Maintain cell shape Change cell shape Maintain cell Function Chromosome Muscle contraction shape Organelle movement Organelle Cytoplasmic streaming anchorage Cell division movement Microtubules • Hollow tubes • 25 nm diameter • Composed of protein tubulin • Cell shape, cell mobility, chromosome movement, organelle movement Anotherfunctionis as tracks that guide motor proteins carrying organelles to their destination. Microfilaments  Two intertwined actin strands  7 nm in diameter  Cell shape, muscle contraction, cytoplasmic streaming, cell motility, cell division Intermediate filaments • Thick cables • 8–12nm • Different proteins (keratin family) • Anchorage of nucleus and organelles Centrosomes and Centrioles  In many cells microtubules grow out of the centrosome (region locate near nucleus)  Within centrosome of animal cell are a pair of centrioles (9 sets of triplet microtubules arranged in a ring – Not present in plant cells Centrosome  In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring.  During cell division the centrioles replicate. Cilia • Cilia - large numbers on the cell surface. – They are about 0.25 microns in diameter and 2-20 microns long. • One or a few flagella per cell. – Flagella are the same width as cilia, but 10-200 microns long. Flagella • A flagellum has an undulatory movement. – Force is generated parallel to the flagellum’s axis. Dynein • The bending of cilia and flagella is driven by the arms of a motor protein, dynein.  – ATP supplies energy  – Dynein arms alternately grab, move, and release the outer microtubules.  – Protein cross-links limit sliding and the force is expressed as bending. Cilia and flagella have the same ultrastructure.  Core of microtubules sheathed by the plasma membrane.  Nine doublets of microtubules arranged around a pair at the center, the “9 + 2” pattern.  Flexible “wheels” of proteins connect outer doublets to each other and to the core.  Outer doublets are also connected by motor proteins.  Anchored in the cell by a basal body (centriole) Muscle Cells  Thousands of actin filaments are arranged parallel to one another.  Thicker filaments composed of a motor protein, myosin, interdigitate with the thinner actin fibers.  Myosin molecules walk along the actin filament, pulling stacks of actin fibers together and shortening the cell. Cytoplasmic Streaming • In plant cells (and others), actin- myosin interactions and sol-gel transformations drive cytoplasmic streaming. Plant Cell Wall  Much thicker than plasma membrane  pm 0.008 microns (not visible in LM)  Cell wall 0.1 to several microns thick (visible in LM)  Cell walls are strong  Composition – fibres of cellulose (polymer of glucan), embedded in other polysaccharides also pectin (polysaccharide) Intercellular Junctions • Anchoring Junctions (Desmosomes) – Fig. 7.30 – Two cells attached by intercellular filaments – rivet cells together • Tight Junctions – Prevent materials from moving between cells – Form a belt around cell – forms a seal • Gap Junctions – Intercellular connections between animal cells – Like Plasmodesmata, small molecules can pass Lecture 4: Divide and Conquer What do all cells require to survive? •A complete set of genetic instructions • Produce required molecules • direct life processes • Genetic instructions are coded in the DNA of cells Why do cells divide? • Growth • Repair • Development Cell Cycle Activities of a cell from one cell division to the next  Cellgrows,addingmorecytoplasmic constituents  DNAisreplicated  Cell divides into two identical daughter Cells Essential Features of Cell Division  Transmit a complete copy of genetic information (DNA)  Transmit materials necessary for cell to survive and use genetic information Prokaryotic Cell • no nucleus – genetic material (DNA) in cytoplasm • no membrane-bound organelles • example: bacteria • cell division is called binary fission Prokaryotic Cell Cycle  Prokaryotic chromosome a circular loop  chromosome attaches to one point on plasma membrane  chromosome is replicated – replicated chromosome attached to plasma membrane at a different nearby point • Prokaryotic Cell Cycle cellelongates–new plasma membrane is added between between chromosomes, pushing them towards opposite ends of cell plasma membrane grows in ward at middle of cell parent cell is divided into two identical daughter cells Eukaryotic Cell  membrane-bound organelles, including a nucleus  genetic material (DNA) contained within the nucleus  examples: fungi, protists, plants, animals • cell division of somatic cells called mitotic cell division Eukaryotic Chromosomes • Contain almost all the genetic information – Mitosis only deals with nuclear chromosomes • Mitochondria and Chloroplasts also have some DNA – DNA replication here is handled differently Chromosomes • Chromosomes = long thread like structures  – Highly condensed during Mitosis  – DNA + protein  – Contain most of the organisms genetic information – # varies with species Eukaryotic Chromosome Structure • Strands of linear DNA • Human cells – 46 strands (46 chromosomes) – Average length 4 cm  Each strand coiled up  Human cell approx. 3 metres of DNA  Total length of DNA in an adult human approx. 2 x 1013 metres (distance earth to sun and back) Chromatin • Many proteins are bound to DNA – Protect – Packaging – Duplication – Transcription – Regulation – Modification • DNA + bound protein = chromatin – Chromatin only about 50 % DNA Review the basics of nucleotides and nucleic acids in the text book. F37 – F39 You are responsible for this material. During non-division phase of cell cycle • DNA molecules in extended, uncondensed form = chromatin • cell can only use DNA to produce molecules when in extended state During division phase of cell cycle  DNA molecules condense to form chromosomes prior to division  eachchromosomeisasinglemolecule of DNA  easier to sort and organize DNA into daughter cells What is Mitotic Cell Division?  Division of somatic cells (non reproductive cells) in eukaryotic organisms  A single cell divides into two identical daughter cells (cellular reproduction) Ploidy • Organisms have a specific number of sets in diploid and haploid cells • Mitosis and Meiosis lead to different ploidy outcomes Chromosome ploidy of cell Ploidy – refers to the number of pairs of chromosomes in cells • haploid–onecopyofeach chromosome – designated as “n” • diploid–twocopies(=pair)ofeach chromosome – designated as “2n” Ploidy • Haploid = 1 set (n) • Diploid = 2 sets (2n) • Triploid = 3 sets (3n) • Polyploid = more than two complete sets – Common in plants, not animals Eukaryotic Cell Cycle • 2 major phases: • Interphase (3 stages) – DNA uncondensed (= chromatin) • Mitotic cell division (5 stages) – DNA condensed (= chromosomes) G1 – First Gap Size Increases, Organelles may replicate Normal Growth and Development S – DNA synthesis DNA is replicated, synthesis of proteins associated with DNA ploidy does not change G2 – Second Gap cell prepares for division, synthesis of proteins associated with Mitosis cell committed to divide Interphase Occurs before stages of mitosis Genetic material is called Chromatin DNA replication occurs during this phase Interphase •Nucleus well defined •Nucleoli present •Centrosomes replicated (replicated centrioles in animal cells only) •Microtubules extend from centrosomes (called aster [star]) •Chromosomes have duplicated but not condensed Mitosis in Eukaryotic Cells has five stages: 1. Prophase 2. Prometaphase 3. Metaphase 4. Anaphase 5. Telophase (cytokinesis also occurs during this phase) Prophase •Chromatin fibres become tightly coiled chromosomes •Nucleoli disappear •Mitotic spindle begins to form •Centrosomes move away from each other Prometaphase •Nuclear envelope fragments •Microtubules connect to chromosomes •Kinetochores have formed •Some microtubules connect with those from the opposite pole Metaphase •Centrosomes now at opposite poles •Chromosomes at metaphase plate •Centromeres of the chromosomes are on the metaphase plate •Kinetochores of each chromatid connected to microtubules from different pole Anaphase •Begins when paired centromeres separate •Chromosomes (1/2 of each s
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