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[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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Boston University
CAS BI 203
Uwe Beffert

BU CAS BI 203 FINAL EXAM STUDY GUIDE find more resources at 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 find more resources at  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 find more resources at  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 find more resources at 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 find more resources at  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 find more resources at  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 find more resources at 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 find more resources at  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 find more resources at  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 find more resources at  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 find more resources at  Ex. Aquaporins (transport water, very important in plant cells it h
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