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Midterm 1 Study Guide

by: Pittman Notetaker

Midterm 1 Study Guide BIO 002

Pittman Notetaker
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It is mainly textbook based chapters 1 and 2 however it does have diagrams and helpful tables to visualize information. I also included notes from powerpoint, lecture, and previous exams. Best of l...
Dr. Kamal Dulai
Study Guide
Biology, Macromolecules, Models, Organic Chemistry, organelle
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This 12 page Study Guide was uploaded by Pittman Notetaker on Wednesday September 7, 2016. The Study Guide belongs to BIO 002 at University of California - Merced taught by Dr. Kamal Dulai in Fall 2016. Since its upload, it has received 7 views.

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Date Created: 09/07/16
Bio 002 Midterm 1 Study Guide Chapters 1+2 Ch.1 Student Learning Outcomes 1. Describe the 3 tenets of the cell theory 2. List the properties of life exhibited by cells 3. Describe the classification of cells 4. Define the size of cells 5. Compare and contrast eukaryotic and prokaryotic cells 6. List Model Organisms Chapter 1: Cells The Fundamental Units of Life 1. cell: small, membrane enclosed units filled with a concentrated aqueous solution of chemicals. Are the fundamentals unit of life. a. life: What is alive? i. MR. GREy+ 1. M- metabolize (anabolic +catabolic bio chemical reactions) 2. R- respond (to their environment) 3. G- grow (increase in volume) 4. E- evolve (change over time) 5. + all cells contain DNA (molecule of inheritance) and are made of cells (that contain a membrane and cytoplasm) b. The Cell Theory (3 tenants) i. 1839 Schwann’s Cell Theory 1. All organisms consist of one or more cells 2. The cell is the basic unit of structure for all organisms ii. 1855 Virchow 1. All cells arise only from preexisting cells c. Unity and Diversity of cells i. ex of cell: 1. Paramecium found in a drop of pond water is covered with thousands of cilia (hairlike extensions whose sinuous beating sweeps the cell forward) 2. Neutrophil or macrophage: found in animal body crawls though tissues, constantly pouring itself into new shapes, as it searches for and engulfs debris, foreign microorganism etc. ii. cells resemble one another in the details of their chemistry 1. composed of same sort of molecules, which participate in same chemical reactions 2. genes: are genetic info. carried by DNA molecules (in all organisms) 3. The Central Dogma: In all living cells, genetic information flows from DNA to RNA (transcription) and from RNA to protein (translation) 4. Proteins are built from amino acids, all organisms use the same set of 20 amino acids to make protein a. Conformation: 3D shape caused by amino acids that are linked in different sequence. makes protein able to preform an array of tasks 5.Viruses are not living, they contain genetic info incased inside protein but cannot self reproduce, inert and inactive outside host cells, but can control a cell when inside. 1. Mutations: are mistakes in the DNA that change the genetic plan from the previous generation, mistakes can be beneficial/ fatal 2. Evolution: the process by which living species become genetically modified and adapted to their environment in more and more sophisticated ways/ based in the principles of genetic change and selection 3. all cells inherited their genetic instructions from the same common ancestor 4. genome: entire sequence of nucleotides in an organisms DNA it is a genetic program for cell behavior a. leads to differentiated cell types which are generated during embryonic development, genes produce some proteins and not others (express different genes) 5. living organisms require a continual supply of energy to exist because they create order out of disorder insider their cells. ii. 17 Century: first microscope 1. light microscope uses b. Scale and Microscopes i. scale is crucial-our eye visable light to illuminate only permit us to see 200 specimens, and allow m beyond this point we biologist to see for first time need microscopes. intricate structure of living things. 2. Robert Hook used light microscope to examine a piece of cork and discover cells. iii. Combined work Schlieden in 1838 1. extracellular matrix: a dense material made of protein fibers embedded in polysaccharide gel, that separate closely packed cells 2. Cell sample preparation a. fixed: preserved by pickling in a reactive chemical solution b. embedding: in a solid wax/ resin c. sectioned: into thin slices d. stained: with dyes that color particular components differently e. fluorescent probes: absorb light at 1 wavelength and emit at a longer  iii. Light Microscope 3. see at small as 0.2m (limited by wavelike nature of light not lenses) Figure 1 3 Steps to Cells and 6 steps to proteins3 things are required 1. bright light focused on specimen by lenses in condenser 2. specimen must be prepared 3.needs an objective and eyepiece lenses. 5. fluorescence microscopy: 1. filters lights 2. blocks one and passes another| confocal microscope: iv. Electron microscope builds an image by scanning specimen w/ a laser 1. uses beam of electrons to see distinct cellular organelles, and the different membranes (plasma and internal) 2. transmission electron microscope: used to examine thin sections of tissue; uses magnetic coils to focus beam of electrons, specimen is stained w/ electron-dense heavy metals to locally absorb/scatter electrons, removing electrons from beam as it passes through specimen. Can see up to 1nm 3. scanning electron microscope: scatters electrons off the surface of the sample, tissue also coated w/ heavy metal, and magnetic coils also act as lenses, creates 3-D images with great focus can resolve details from 3nm-20nm. 4. limit of resolution 0.1- 0.2nm 5. cannot visualize individual atoms, X-ray crystallography (used to determine precise 3-D structure of protein molecules c. The Prokaryotic Cell 1. 0.5 m- 20 m 2. organisms whose cells lack a nucleus and nuclear envelop 3. karyotic=nucleus. prokaryotic=before the nucleus 4. contains two domains of life bacteria and archaea a. have a cell wall: surrounds plasma membrane that encloses a single compartment containing cytoplasm and DNA 5. most live as single-celled organisms, can combine to form multicellular structures 6. chemically most diverse and inventive class of cells..other living things depend on the organic compounds that these cells generate from inorganic materials 7. archaea: extremeophiles can live in extreme conditions a. found in the acidic, oxygen-free environment of a vow’s stomach where they break down cellulose and generate methane gas 8. aerobic: uses O to oxidize food molecules 9. anaerobic: killed by slightest exposure to O 10. example: Beggiatoa: lithotrophic bacteria lives in sulfurous environments and oxides H2S to produce sulfur and fix carbon 11. bacteria: typically forms spherical, rod-shaped, or spiral cells typically weighs 10^(- 12)g and can divide every 20mins. a. photosynthetic: uses sunlight energy to produce organic molecules from CO2 b. nitrogen fixers: capture N2 from atmosphere and incorporate it into organic compounds c. can derive energy from chemical reactivity of inorganic substances in the environment d. The Eukaryotic Cell 1. can live as single-celled organisms (i.e. yeast) or multicellular organisms 2. divided into kingdoms: animals, plants, fungi, protists (look at phylogenetic tree of life) 3. may have originated as predators 4. contains a nucleus enclosed by a nuclear envelop (two concentric membranes) and contains polymers of DNA a. DNA becomes visible as individual chromosomes before a cell divides into two daughter cells 5. internal membranes create intracellular compartments w/ different functions a. “membrane enclosed organelles allow for chemistry inside organelle to be different from chemistry in cytoplasm” 6. mitochondria: enclosed in two separate membranes w/ inner membrane extensively folding (to increase surface areas for the proteins responsible for cellular respiration: in which proteins harness energy from oxidation of food molecules (i.e. sugars) to produce adensosine triphosphate (ATP)). a. contain own DNA and reproduce by dividing into…likely evolved from engulfed bacteria that was able to live in symbiosis w/ host cell 7. chloroplast: large, green organelles (plants, algae), photosynethisis: traps energy of sunlight in chlorophyll + uses energy to drive the manufacture of energy-rich sugar molecule, releasing O as by-product. a. likely evolved from photosynthetic bacteria b. contain two surrounding membranes and stacks of membranes containing chlorophyll 8. complex interrelationship between chromatin (chromosomes and associated proteins) 9. cytoskeletal system a. a system of protein filaments, composed of 3 major filament types (AIM), responsible for directed cell movements i. actin filaments: the thinnest filaments, abundant in all eukaryotic cells but especially in muscle cells, responsible for muscle contraction. ii. microtubules: thickest filament, hollow tubes, when a cell is dividing they are reorganized to pull duplicated chromosomes in opposite direction and distribute equally into daughter cells. Stiff structure iii. intermediate filaments: intermediate in thickness serve to strengthen the cell. Do not participate in cell motility 10. Smooth Endoplasmic: responsible for synthesizing carbohydrates, lipids, and steroids. 11. Rough endoplasmic reticulum: contains ribosomes (translate RNA in proteins) specialized for secretion of protein. site where most cell-membrane components and materials for export are made 12. Golgi-apparatus: flattened- membrane enclosed sacs; responsible for modifying and packaging molecules made in ER destined to be secreted from cell or transported to another cell compartment 13. lysosomes: small, odd shaped organelles responsible for intracellular digestion (releases nutrients from ingested food and breaks down unwanted molecules for recycling or excretion) 14. transport vesicles: transports material between membrane enclosed organelles 15. cytosol: part of cytoplasm, not contained w/ intracellular membranes, site of chem reaction, concentrated aqueous gel of large and small molecules 16. vacuoles: fluid or water (similar to vesicles) but carry lighter fluid like water 17. protoplasm is everything inside a cell 18. complex flagella and cilia 19. endocytosis and phagocytosis a. endocytosis: import extracellular materials, portions of plasma membrane tuck inward and pinch off to form vesicles that carry material captured from external medium into the cell. Animal cells can engulf very large particles or foreign cells b. exocytosis: secrete intracellular materials, vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium i.e. how membrane-enclosed organelles move proteins and other molecules from place to place intracellular c. phagocytosis: process by which particular material is engulfed “eaten” by a cell. i.e. predatory cells, and in cells of the vertebra immune system. 20. cellulose-containing cell walls 21. cell division utilizing spindle fibers 22. 3 RNA polymerases 23. protozoans: free-living, actively motile microorganisms a. Didinium: large carnivorous protozoan, i. 10x size of avg. human cells ii. globular body surrounded by two fringes of cilia (that allow it to swim at high speeds) iii. when finds prey it releases small paralyzing darts from its snout and attaches to and engulfs its victim b. although single-celled can be as intricate and versatile as many multicellular organisms e. Model Organisms 1. representative organisms that are studied because all cells are descended from a common ancestor, whose fundamental properties are conserved through evolution 2. comparing genome sequences reveals life’s common heritage a. E. coli: small, rod-shaped cell that inhabits the guts of vertebrates, helped biologist understand how cells replicate DNA b. S. cerevisiae: yeast, rigid cell-wall, immobile, possesses mitochondria, no chloroplast, helped biologist understand cell-division cycle c. Arabidopsis: simple weed that contain genes whose counterparts are found in agricultural species, helps us understand development and physiology of crop plants d. Drosophila melanogaster: small fruit fly, foundation of classical genetics, that proved genes are carried by chromosomes, demonstrates how genetic instructions encoded in DNA molecules direct the zygote’s development, also studied for human development and disease. e. Caenorhabditis elegans: nematode worm, 70% of humans genes have a counterpart in this model, it helped biologist study many developmental processes that occur in human bodies, in particular the details of apoptosis: a form of programmed cell death by which surplus cells are disposed of in all cells. f. Zebrafish: popular models for studies of vertebrate development, transparent embryos make it easy to observe development 3. the world of animals is represented by: fly, worm, zebrafish, mouse, and humans 4. factors that go into selecting a model are speed, cost, numbers (grow large quantities) 5. genetic engineering: we can use the property (mutant yeast that can divide at cool temperature) to select for those fungi that have picked up mutant gene and can grow at warmer temperature Chapter 2: Chemical Components of Cells Student Learning Outcomes 1. List the four main molecular forces 2. Describe macromolecules 3. Define condensation and hydrolysis 4. Draw the structure of macromolecules 5. Panel 2-1 1. chemistry of life is dominated and coordinated by enormous polymeric molecules (chains of chemical subunits, whose unique properties enable cells and organisms to preform life’s requirements a. predominately the chemistry of lighter elements 2. Chemical Bonds a. are forces which hold (glue) atoms together either transiently or more permanently b. Atoms: smallest particle of an element that still retains its unique chemical properites i. contains a dense, positively charge nucleus ii. nucleus is composed of protons (positive charge) and neutrons (neutral, electron +proton, contribute to structural stability of a nucleus, if extra or insufficient it may radioactively decay) iii. nucleus is surrounded by a cloud of negatively charged electrons held together by electrostatic attraction to nucleus iv. #of protons= atomic number #of ps+ns= atomic mass v. isotope: physically distinguishable but chemically identical form of an element has same # of protons not # of neutrons c. Avogadro’s number: relates everyday chemical quantities to numbers of individual atoms or molecules 6.022 *10^(-23)- one mole of a substance i. one molar solution =1 mole of substance in 1 L of solution d. electron orbitals: energy levels that a specific # of electrons can be found in. Electrons closest to nucleus are attracted most strongly to it and occupy inner shell. i. the arrangement of electrons in an atom is most stable when all the electrons fill the innermost shell possible ii. noble gases: have their outmost shell entirely filled and are unreactive e. ionic bond: between a metal and non-metal, is formed when eletrons are donated from one atom to another, it is omni-directional f. covalent bond: usually between two nonmetals, formed when two atoms share a pair of electrons i. strongest bond ii. takes the most energy to make and to break iii. it is directional iv. single bond- molecule shares 2 electrons 1. Can change shape since it can rotate 2. |double bond= 4 electrons, no rotational freedom, shape doesn’t change v. nonpolar covalent bond: the electron pull on all sides of the molecule is even and therefore charge distribution is even, weak but in sums energies create an effective force vi. polar covalent bond: electrons are shared unequally the molecule has charge poles ex H2O vii. electronegativity: “pull” factor Oxygen is most electronegative inside cells, fluorine is most electronegative element viii. bond strength: measured by amount of energy need to break bond (1kilocalroie of energy is needed to break 1 mole of bonds) ix. bond length: goldilocks principal (not too close or nuclei repel each other) (not too far or no attract) x. electrostatic attractions: strongest when atoms are fully charged, weaker in polar covalent bonds (allows molecules to interact through electrical forces), very reactive in aqueous environments xi. help bring molecules together in cells ex a large molecule (protein) can bind to another protein through complementary charges on surface of a molecule g. hydrogen bonds: weak and easily broken by thermal reactions; responsible for many of water’s life sustaining properties i.e. liquid at the temperature inside a mammalian body i. hydrophilic: “water loving” polar molecules, alcohol, that dissolve readily in water ii. hydrophobic: “water fearing” are uncharged molecules that are unreactive in water, ex hydrocarbons have nonpolar covalents bonds h. Van der Waals forces: form of electrical attraction caused by fluctuating electric charges whenever 2 atoms are in proximity 3. Polar Molecules in aqueous solutions form acids or bases a. H3O+ hydronium ion when proton is attract to O- on nearby H2O molecule b. acids: substance that release proton in H2O c. bases: molecules that accepts H+ d. pH scale: is based on concentration of H+ in solution e. buffers: a mixture of weak acids+bases to keep cell pH level constant f. organic molecules contain carbon. all other compounds are said to be inorganic g. every metabolically active cell uses water as a solvent. The polar nature of water can cause other polar molecules to dissociate, constant movement of protons 4. Aging and Free Radicals a. free radicals destroy other neighboring molecules by stealing electrons. b. cells has a # of mechanisms to contain and eliminate radicals-hydrogen peroxidase 5. Organic Molecules a. all are synthesized from- and are broken down into- the same set of b. macromolecules: are made by monomers (proteins, nucleic, acids, polysaccharides) Monomers Polymers c. lipids are not polymers do not form huge molecules d. isomers: sets of molecules w/ same chemical formula but different structures i. optical isomers: mirror-image pairs help generate enormous varieties of sugar e. Sugars: energy sources for cells and subunits of polysaccharides i. monosaccharides: simplest sugars, are compounds general formula (CH2O)n 1. glucose: central role as cell energy source, cells use simple polysaccharides composed only of glucose units (animals-glycogen, plants-chitin) as long term energy stores ii. carbohydrates: have same formula as sugar, monosaccharides that are linked by glycosidic bonds (covalent bonds) iii. disaccharide: 2 monosaccharides iv. oligosaccharides: larger sugar polymers (oligo-refer to molecules made of small #of monomers) 1. can be covalently linked to proteins =glycoproteins 2. can be covalently linked to lipids =glycolipids v. polysaccharides: largest polymers f. Biochemical formations i. condensation: two molecules join together and expel H2O. all monomers come together to form dimers using same exact interaction, releasing water molecule ii. hydrolysis: when cells digest dimers, they cut the dimers in the exact reverse reaction, to release monomers and require water molecules to donate required atoms. g. Fatty Acids: i. two chemically distinct regions, amphiphatic, lipids 1. long hydrocarbon chain, hydrophobic and unreactive, tail a. saturated: when the tail has no double bonds and max # of hydrogen b. unsaturated: has double bond(s) which structurally appear like a kink. i. monounsaturated: one double bond ii. polyunsaturated: multiple double bonds 2. carboxyl group (-COOH), extremely hydrophilic, behaves like an acid in water, head ii. serve as a concentrated food reserve in cells iii. stored in cytoplasm in form of fat droplets composed of triacylglycerol (made of 3 fatty acid chains covalently joined to a glycerol molecules) 1. when cell needs energy the fatty acid chains can be released from triacylglycerol and broken down into 2 C units, just like glucose. iv. lipids: loosely defined as molecules, insoluble in water but soluble in fat and organic solvents such as benzene 1. phospholipids: are composed of two hydrophobic fatty acid tails joined to a hydrophobic head a. lipid bilayer: is formed in aqueous solution the hydrophobic tails pack together to exclude water, and hydrophilic heads are facing aqueous environment b. these triglycerides are basic building materials of all living membranes h. Amino Acids : small organic molecule, composed of an amino group, carboxyl group, and side chain (R), attached to a carbon group i. in cell: free amino acids exist in ionized form ii. incorporated into polypeptide chain charges on amino and carboxyl group disappear iii. building blocks of proteins 1. in a protein amino acids held together by covalent peptide bonds (formed in condensation reactions) 2. a long chain that folds into unique 3D structure iv. polypeptide chain: chain of amino acids. ends are chemically distinct giving it structural polarity 1. N-terminus: is capped by an amino group 2. C-terminus: ends in a carboxyl group v. chemical versatility of 20 standard amino acids provide is important to function of protein i. Nucleotides : subunits of DNA and RNA i. can act as short term carriers of chemical energy ii. fundamental role in storage, and retrieval of biological info iii. nucleosides: are made of a nitrogen-containing ring compound linked to a five carbon sugar (either ribose or deoxyribose) 1. are nucleotides that contain one or more phosphate group attached to sugar 2. ribonucleotides: contain ribose 3. deoxyribonucleotides: contain deoxyribose iv. bases 1. pyrimidines: derive from 6-membered pyrimidine ring cytosine (C), thymine (T), uracil (U) 2. purines: 5-membered ring fused to 6-membered ring: guanine (G), adenine (A) v. ATP: adenosine triphosphate is crucially important energy carrier in cells. 1. is formed through reaction that are driven by the energy released by the breakdown of food. Its 3 phosphates are linked by two phosphoanhydride bonds. Rupture of phosphate bonds release large amounts of energy vi. building blocks of nucleic acids (long polymers in which nucleotide subunits are linked by the formation of covalent phosphodieester bonds) (formed by condensation reactions between subunits) j. Macromolecules i. specific sequence of subunits ii. noncovalent bonds specify precise shape and allow macromolecules to bind to other molecules iii. chemistry of a cell operates at the level of random motion. when molecules need to be held together for long periods of time –covalent bonds are used. when molecules need to be held together temporarily- non- covalent bonds. +page 66-67


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