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Study Guide

[CAS BI 203] - Final Exam Guide - Everything you need to kn..
[CAS BI 203] - Final Exam Guide - Everything you need to know! (22 pages long)

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School
Boston University
Department
Biology
Course
CAS BI 203
Professor
Uwe Beffert
Semester
Fall

Description
BU CAS BI 203 FINAL EXAM STUDY GUIDE find more resources at oneclass.com Cell Biology Test 1: (Chaps. 1-2, 4-5, 14) I. Lecture I  Fundamental principles: cell has a life of its own, cells are dynamic, living units,  Cells are complex little bags of organic molecules o Outer boundary is flexible o Outer boundary is semi permeable  ~ 20 micrometers (size)  inside contains a vast array of organic molecules o proteins, lipids, carbohydrates  DNA is the same in every cell in our body  RNA is NOT the same in every cell in our body (different mRNA, different proteins, different cell make up)  Cells contain intracellular compartments  Difference between prokaryotic cell and eukaryotic o Cytoplasmic organelles (present in eukaryotic, absent in prokaryotic) o Chromosomes (prokaryotic circular DNA, multiple linear DNA Molecules in eukaryotic)  Advantage of compartments: enable cells to compartmentalize gives order and efficiency  Fundamental features are characteristic of almost every cell type  All cells arise from pre-existing cells  All present day cells are descendants from a common primordial ancestor  Time Scale of Evolution: o First prokaryotes: ~ 4 billion years o Oxidative Metabolism and Photosynthesis: ~ 3 billion years ago  Necessary for an ancestor to develop: o Organic molecules serve as the building blocks of life  H2, CH4, NH3, H2O + electrical spark (lighting) = spontaneous formation of organic molecules  Oxygen was lacking in the beginning  Mille▯’s solutio▯: ▯o▯ditio▯s o▯ ea▯th ▯e▯e at least ▯o▯du▯i▯e to spontaneous formation of organic molecules o Informational molecule that could be replicated & passed on to future generations  ▯▯▯▯’s “id Alt▯a▯ a▯d To▯ Ce▯h  series of experiments: RNA molecules can catalyze chemical reactions  Like DNA, RNA structure enables it to direct its own replication  Alt▯a▯ a▯d Ce▯h’s solution: the primordial ancestor was most likely RNA based o A ▯a▯▯ie▯ to sepa▯ate the ▯i▯side▯ of the ▯ell f▯o▯ its su▯▯ou▯di▯g environment find more resources at oneclass.com find more resources at oneclass.com  First cells came from an enclosure of self replicating RNA within a phospholipid bilayer  The need for energy provided the pressure to evolve metabolic mechanisms to create energy  In more evolved cell types, we develop mitochondria because more energy is required for more complex needs  Ea▯l▯ ▯eta▯oli▯ path▯a▯s ▯e▯e likel▯ p▯i▯iti▯e fo▯▯s of toda▯’s gl▯▯ol▯sis  Glycolysis: glucose -> 2 ATP  Oxidative Metabolism (1 billion years later) glucose -> 36 ATP  Cells in the human body: ~ 50 trillion  Difference between E. Coli and Yeast: E. Coli (Prokaryote), Yeast (Eukaryote)  E. Coli: o Useful because they have a small genome: ~ 4.6 million base pairs, 4200 protein-coding genes o Bacteria are cheap and replicate quickly  Yeast: o Small genome o Unicellular eukaryote  C. Elegans o Relatively small genome o 97 million base pairs o 19,000 protein coding genes o in order to study more complex things o multicellular eukaryote but is simple  Drosophila melanogaster o Relative small genome, but similar # of genes as higher eukaryotes o Easily grown in the lab o Played a major role in our current understanding of molecular mechanisms underlying animal development  Xenopus laevis (large eggs), Zebrafish (transparent embryos) o Studying vertebrate development o Develop outside of the mother -> easily observed o Larger more complex genomes o  Mouse o Most suitable model for human development o Deletion of genes, introduction of genes -> study roles of genes in intact animals  Animal Cells in Culture o Research on cells grown on plastic tissue culture dishes plays a major role in our understanding of cell biology o Advantages:  Individual cells easily observed find more resources at oneclass.com find more resources at oneclass.com  Homogenous population of cells  Easily & quickly maintained o Common sources of tissue:  Tumors  Normal tissues of different organs  Tissue from genetically-modified organisms II. Lecture II  FRAP (Fluorescence recovery after photobleaching) o Bleaching a particular part of a cell o Provides measure of the rate of protein movement in a cell  FRET (Fluorescence resonance energy transfer) o Provides a measure of whether two proteins interact in a cell o Excitation through one and emission through the other  Electron Microscopy o Positive Staining o Difficult to portray colors, much more labor intensive technique o Freeze Fracture (combination with EM): it was used for looking at cell membranes, see proteins that go through the boundaries of the cell o Scanning electron microscopy  Super-Resolution light microscopy (STORM) o Random activation of individual fluorescent molecules results in a composite super-resolution image  Subcellular fractionation o Break down cells into fractions based on their densities o Different parts of the cell will separate at different speeds  Velocity centrifugation in a density gradient o The sample is layered on top of a gradient of sucrose o Particles of different sizes sediment as discrete bands o Collect fractions of gradient  Cells a▯e ▯▯o▯ple▯ little ▯ags▯ of o▯ga▯i▯ ▯ole▯ules o The interior of cells contains a vast array of organic molecules o Virtually all aspects of cell behavior and function are dictated by how these molecules interact  Water o > 70% of total cell mass is water o chemical properties of water influence virtually all aspects of cell biology charged, polar molecule that forms hydrogen bonds  Inorganic Ions o Na, K, Mg, Ca, Cl, PO4 o Although lower in quantity than water, highly important in different functions  Carbohydrates o Simple sugars (monosaccharides) find more resources at oneclass.com find more resources at oneclass.com o Polysaccharides  Polymers of simple sugars o Carbon, hydrogen and oxygen o ▯CH▯O▯▯ ▯h▯d▯ated ▯a▯▯o▯s▯ o oligosaccharides (short)  Glycosidic bonds o How simple sugars are joined together into polymers to form polysaccharides o Dehydration reactions in order to join sugars  Carbohydrates o Polysaccharides exist in both unbranched and branched forms  Branched: amylopectin, glycogen  Unbranched: amylose, cellulose o Biological Roles  Simple sugars: major nutrient of cells  Building blocks for other classes of organic molecules  Polysaccharides  Storage  Structural components of the cell  Protein modification, cell recognition, and cell-cell interactions in multicellular organisms  Nucleic Acids o DNA and RNA o Exist and function as monomers (nucleotides), oligomers (oligonucleotides) and polymers (polynucleotides) o Composed of: sugar, base, and phosphate o Five bases: thymine (DNA only), uracil (RNA only), cytosine, adenine, guanine o Nucleoside: sugar + base o Nucleotide: sugar + base + phosphate group o Purines (two rings): Adenine, Guanine o Pyrimidines (one ring): Cytosine, Thymine and Uracil o Phosphodiester bonds: how nucleotides are joined together to form polynucleotides  Fo▯▯ed ▯/▯ ▯’ h▯d▯o▯▯l a▯d ▯’ phosphate  “▯▯thesized i▯ the ▯’ to ▯’ o Nucleotides:  Building blocks for oligo and polynucleotides  ATP= the principal form of chemical energy within cells  Cyclic AMP: Important signaling molecules o RNA oligonucleotides  Regulation of gene expression (siRNA, miRNA) o Polynucleotides find more resources at oneclass.com find more resources at oneclass.com  Informational molecules  Poly-DNAs are uniquely genetic material of cells  Double stranded  Sugar-phosphate ▯▯a▯k▯o▯e▯ is situated at the e▯te▯io▯ od the sdDNA, with the bases on the inside  The two chains are held together by hydrogen bonds between complementary base pairs  C-G: three bonds  A-T: two bonds  Complementary base pairing: enables DNA to o Direct its own replication o Direct RNA synthesis  Poly-RNAs function in the expression of the genetic information  mRNA: carries sequence information from DNA to ribosomes  rRNA and tRNA: facilitate translation of genetic sequence  single stranded  Proteins o The most diverse and complex group of macromolecules o Composition  Polymers of 20 different amino acids, each with a common core chemical makeup  Amino, side chain, o Peptide bonds  Join amino acids  Amino terminus and a carboxyl terminus  Dehydration reaction  Synthesized in the amino to carboxyl terminus directions o R Groups  Side chains different greatly o Nonpolar  Mostly hydrocarbons  Note that met and cys contain sulfur  Very hydrophobic  Buried inside 3-D structure of protein to void water  Glycine (Gly) G  Alanine (Ala) A  Valine (Val) V  Leucine (Leu) L  Isoleucine (Ile) I  Polar groups  Hydroxyl and amide groups  Uncharged find more resources at oneclass.com find more resources at oneclass.com  Proline (Pro) P  Cystein (Cys) C  Can make bonds with itself  Disulfide bonds  Methionine (Met) M  Always start amino acid  Phenylalanine (Phe) F  Tryptophan (Trp) W o Polar  Polar groups  Hydrophilic o Basic  Charged  Lysine (Lys) K  Arginine (Arg) R  Histidine (His) H  Basic due to protonated N  Positive charge inside the cells  Very Hydrophilic  Will form ionic bonds with other AA o Acidic  Charged  Aspartic acid (Asp) D  Glutamic acid (Glu) E  Acidic due to carboxyl groups  Negative charge inside the cell  Very Hydrophilic  Will form ionic bonds with other AA o Structure  Primary  Sequence of amino acids in the polypeptide chain  Written amino to carboxyl  Start with Met  Secondary  The arrangement of amino acids in localized regions  Alpha helix o Stabilized by hydrogen boding b/w CO and NH groups o Localized region coils around itself o CO of one AA forms a hydrogen bond with NH of AA 4 residues downstream  Beta sheet find more resources at oneclass.com find more resources at oneclass.com o ▯ li▯ea▯ st▯et▯hes of AA’s lie side-by-side with hydrogen bonds between them o either parallel or anti-parallel o Stabilized by hydrogen boding b/w CO and NH groups  Tertiary  Folding of entire polypeptide into its functional 3-D structure  Folding is driven by the chemical properties of the side chains  No▯pola▯ AA’s ▯epelled ▯▯ ▯ate▯ a▯d ▯u▯▯ i▯side  Pola▯ a▯d ▯ha▯ged AA’s o▯ su▯fa▯e i▯te▯a▯ti▯g ▯ith ▯ate▯, each other, and other ions  Often contain both alpha helices and B sheets looped in  Multiples domains o Specific function/activity for each domain o Region between domains: loop region  Quaternary  The association of different polypeptide chains  Ex. Hemoglobin (4 different polypeptide chains)  Held together by non covalent interactions between the respective AA side chains o Function  Execute nearly all cellular tasks that are dictated by that information  Many proteins act as enzymes: catalyze nearly all chemical reactions inside and outside cells by reducing the activation energy o Two Models of enzyme-substrate interaction  Lock and key model  Induced fit model  Substrate and enzyme distorted to transition state conformation o Phosphorylation: common mechanism of enzyme regulation  Phosphate groups are added to the side-chain of OH groups of serine, threonine, or tyrosine  The phosphate comes from ATP that turns into ADP  Ex. Phosphorylase kinase: activates  Lipids o Simplest lipids: fatty acids  Polar carboxyl group  Long nonpolar hydrocarbon chains  Satutared find more resources at oneclass.com find more resources at oneclass.com  Unsaturated: double bond (kink)  Has a bend  Helps the membrane create space in between the molecules  Flexibility to the membrane  Source of energy  Building blocks for more complex lipids o Triacylglycerol (fats): cellular storage form of fatty acids o Phospholipids: 2 fatty acids + phosphate group linked to a glycerol group  Phosphatidylserine o Phospholipid bilayers: provide a semi-permeable barrier  Semi-pe▯▯ea▯le: so▯ethi▯g gets i▯ so▯ethi▯g do▯’t  ▯fluid▯ st▯u▯tu▯es o Glycolipids  Ex. Blood Groups / on the surface of red blood cells and helps distinguish them o Cholesterol:  Affects membrane fluidity  Rings are hydrophobic, but OH group weakly hydrophilic, therefore cholesterol is amphipathic  Precursor for steroid hormones (ex. testosterone and estradiol)  Interactions between the hydrocarbon rings and fatty acid tails makes the membrane more rigid  Reduces interaction between fatty acids, maintaining membrane fluidity at lower temperatures  Fluid mosaic model o Model of membrane structure was proposed by Singer and Nicolson in 1972 o Integral membrane proteins inserted into the phospholipid bilayer, with nonpolar regions in the lipid bilayer and polar regions exposed to the aqueous environment.  Integral Membrane Proteins o Embedded directly in the lipid bilayer  Peripheral membrane proteins o Associated with the membrane indirectly, generally by interactions with integral membrane proteins  Lipids bilayers o 2-dimensional fluids in which molecules are free to rotate and move laterally  Membrane fluidity: is determined by temperature and lipid composition  Unsaturated fatty acids o Double bonds that result in kinds. This reduces packing and increases membrane fluidity find more resources at oneclass.com find more resources at oneclass.com  Channel Proteins o Ions and other polar molecules across the membrane  Carrier Proteins o Ions and other polar molecules across the membrane o Changes shape in order to pass molecules from one side to the other o Typically based on a concentration gradient III. Lecture III  The Plasma Membrane o Selective barrier that regulates the internal composition of the cell  Structure and Composition of the Plasma Membrane o Fundamental membrane structure: phospholipid bilayer o Hydrophilic and hydrophobic fatty acid cells o Impermeable to most water-soluble molecules o Phospholipids (5):  Phosphatidylcholine (outside)  Phosphatidylethanolamine  Phosphatidylserine (negative charge headgroup)  Sphingomyelin  Phosphatidylinositol (negative charge headroup) o Phospholipids are asymmetrically distributed between the inner and outer leaflets o Inner leaflet has a NET negative charge because of negative head group of Phosphatidylinositol and phosphatidylserine o Lipid rafts: Sphingomyelin and cholesterol tend to cluster into semisolid patches  Enriched in proteins involved in cell signaling and endocytosis o GPI a▯▯ho▯s: added i▯ the ER a▯d ▯a▯▯ho▯▯ the▯ to the ER ▯e▯▯▯a▯e  Contain two fatty acid side chains, an oligosaccharide and ethanolamine.  Assembled in the ER and added to proteins anchored in the membrane  Membrane-spanning region is the cleaved and joined to the amino group of ethanolamine, leaving the protein attached to the membrane by the GPI-anchor o The plasma membrane are ~50% proteins and ~50% lipids o Two classes of membrane proteins  Peripheral and Integral o Integral Membrane Proteins  Two mechanisms of insertion:  Transmembrane proteins  Ex. Bacterial photosynthetic reaction center of R. viridis find more resources at oneclass.com find more resources at oneclass.com  Ex. B-barrels = transmembrane domains formed by B sheets o Mito▯ho▯d▯ial oute▯ ▯e▯▯▯a▯e’s pe▯▯ea▯ilit▯ due to porins  Vast majority of TM proteins have a-helical domains  Covalent attachment to glycolipid or lipid anchors  Attachment of lipids anchors proteins in the inner leaflet  Lipid Anchors: recruitment to the plasma membrane by lipid anchors regulates activity of many proteins  Myristic acid: N terminus  Prenyl groups and Palmitic acid: Cysteine residues o Glycosylated proteins / domains are most often extracellular o Glycosylation:  Proper folding  Stability  Cell-cell adhesion o Mobility of membrane proteins  Lateral movement of proteins and lipids in the membrane was first demonstrated in 1970  Human and mouse cells were fused in culture, then analyzed for membrane proteins using fluorescent antibodies  After incubation, proteins were intermixed on the cell surface, indicating that proteins moved within the membrane  Ex. Polarized intestinal epithelial cell o  Transit of Small Molecules across the Plasma Membrane o Passive Diffusion  Fundamental membrane structure: phospholipid bilayer  Some types of molecules can transit directly through the plasma membrane  NET flow of a molecule is always down its concentration gradient o Facilitated Diffusion  Flow of molecules down their concentration gradient via transmembrane proteins  Carrier proteins  Go a conformational change to execute transport  Transport can go both directions as long as it is down the concentration gradient  Channel Proteins  Form open channels through which molecules of appropriate size and charge can pass through find more resources at oneclass.com find more resources at oneclass.com  Ex. Aquaporins (transport water, very important in plant cells it h
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