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Cell Bio-Exam 1 study guide

by: Michelle Notetaker

Cell Bio-Exam 1 study guide BIOL 3510

Marketplace > University of North Texas > Biology > BIOL 3510 > Cell Bio Exam 1 study guide
Michelle Notetaker
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This study guide is comprised of all the notes over exam 1 material. It covers everything on the study guide uploaded to blackboard.
Cell Biology
Dr. Amanda Joy Wright
Study Guide
Cell, Biology
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This 8 page Study Guide was uploaded by Michelle Notetaker on Tuesday September 20, 2016. The Study Guide belongs to BIOL 3510 at University of North Texas taught by Dr. Amanda Joy Wright in Fall 2016. Since its upload, it has received 146 views. For similar materials see Cell Biology in Biology at University of North Texas.


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Date Created: 09/20/16
Cell Biology Exam #1 Study guide (Answers) Intro to Cells 1)What technological development and subsequent observations led to the birth of cell biology? -Better lenses and invention of the microscope. -Hooke (cork cells), Schleiden (plant cells), Schwann (animal cells). What is the cell theory? -all living things are formed by division of existing cells. What are the average sizes of prokaryotic and eukaryotic cells and organelles? -Prokaryote (0.1-5.0 micrometer), Eukaryote (10-100 µm): mitochondria (1 µm), ribosome (30 µm). What are the resolution limits of the different types of microscopy? -Light: all types (0.2 µm), Electron Microscopy: TEM (2 nm), SEM (3-20 nm). Compare and contrast bright field light microscopy, differential interference contrast light microscopy, fluorescence microcopy, confocal fluorescence microscopy, transmission electron microscopy, and scanning electron microscopy. What do images produced by the different types of microscopy look like? (Check out the relevant figures in your book). -Light: Bright Field-transparent image. Diff. Int.-3D image. Fluorescence: 2 steps (1. excited fluorescent molecules-blue, 2. different wavelength emitted-green), Confocal fluorescence-clearer, more detailed image than fluorescence. -Electro: TEM-beam of electrons transmitted through sample, gray contrasted image. SEM-electrons scattered over surface of heavy metal-coated sample, 3-D image. What are the differences and similarities between prokaryotic and eukaryotic cells? -Prokaryotes: no nuclei or membrane-bound organelles, smaller, single- celled. -Eukaryotes: membrane-bound organelles and nuclei, single-celled or multicellular. What are the main organelles and cell parts found in a eukaryotic cell? -Mitochondria(ATP synthesis), ribosomes(protein synth.), nuclei(DNA&RNA), Golgi apparatus(packages molecules made in ER), ER(folds proteins), Lysosomes(digest unwanted material), Peroxisomes(inactivate toxins), Cytosol(gel b/w organelles). Proteins I Be familiar with the general structure of amino acids, peptide bonds and polypeptide chains (or proteins). While I don’t expect you to memorize the amino acid side chains, I do expect you to be able to tell if they are nonpolar, acidic, basic, or uncharged polar if the structure is provided: What are the four levels of structural organization of a protein and what characterizes each level? -1)Primary-single amino acid sequence. -2)Secondary-��� helix & ��� sheet. -3)Tertiary-single polypeptide w/ secondary proteins attached. -4)Quaternary-multiple folded subunits of polypeptides. What are covalent bonds (both polar and nonpolar)? What is a dipole? -Covalent bonds: sharing of electron pairs creates a strong bond (90kcal/mol to break). Polar-unequal sharing, Non-polar-equal sharing. (Peptide bonds are covalent bonds that hold amino acids together, created by a dehydration reaction). -Dipole: unequal sharing of electron pair causes a partial (-) and a partial (+) part of the molecule (e.g. H₂O) What are the 4 types of non-covalent bonds/forces relevant to cells? Be able to describe them. -1)Electrostatic interactions-attract oppositely charged atoms(ions), dissociate in water. -2)Hydrogen bonds-electronegative atom + H atom bind to another electronegative atom (e.g. H₂O). -3)Van der Waals interactions-a dipole is created due to fluctuations of electron cloud around an atom. Dipoles induce other dipoles in nearby molecules. -4) Hydrophobic forces-excludes non-polar surfaces from a H-bonded water network. Hydrophobic side chains of a folded protein are contained in the center-. How do proteins fold? -through a combo of the 4 types of non-covalent bonds. What are α helices and β sheets? How are they formed? -folded secondary structures. -H-bonds b/w polypeptide backbone. What are a protein domains, chaperones, intrinsically disordered sequences, disulfide bonds, and protein families? -Protein domains: regions of polypeptide chain that fold independently into stable structures. -Chaperones:proteins that improve the efficiency of protein folding. -Intrinsically disordered sequences: correspond to unstructured regions of some proteins. -Disulfide bonds: covalent bonds between cysteines that act as “atomic staples” to stabilize extracellular proteins. -Protein families: proteins with similar 3D sequences. How do X-ray crystallography and nuclear magnetic resonance spectroscopy work? -X-ray crystallography: X-rays diffract through a protein crystal and create a pattern. -Nuclear magnetic resonance spectrometry: magnets determine 3D structure of small proteins. Proteins II What are binding sites, active sites, ligands, substrates, active sites, catalysts, and enzymes? -Binding sites(active site): area of protein that interacts w/ a ligand. -Ligand(substrate): anything bound by a protein. -Catalysts: increase the rate of a chemical reaction. -Enzymes: proteins that increase the rate of a chemical reaction & are not altered by the reaction. What does lysozyme do? -cleave polysaccharide chains found in bacterial cell walls. What do small molecules covalently attached to protein often do? -increase protein functionality. How does feedback inhibition work? -product of a pathway inhibits an enzyme that acts earlier in the pathway. What is an allosteric protein? -undergo conformational changes that alter their activity upon binding to a ligand. What are some of the ways protein activity is modulated in a cell? -Protein phosphorylation, GTP-binding, other covalent modifications. What do conformational changes have to do with protein activity? -can change the function, activate, or inactivate. What are kinases, phosphatases, and GTPases (GTP binding proteins)? How do these regulate protein activity? -Protein phosphorylation: Kinases-attach phosphates, Phosphatases- remove phosphates. -GTPases-activates a protein (inactive when bound to GDP) What are antibodies and antigens? -Antibodies: recognize specific antigens. -Antigen: foreign “invader” in the body. How are antibodies used as molecular tags? -dye and particles can attach to the antibody, which seeks out the protein of interest, and can then be seen under the microscope. What is GFP and how is it used to track proteins in cells? -Green Fluorescent Protein-a reporter used to determine where a protein is expressed. DNA and chromosomes Be familiar with the general structure of nucleotides, phosphodiester bonds, and nucleic acids. -Nucleotides: base, sugar, & phosphate group. -Phosphodiester bonds: link nucleotides, formed by dehydration. -Nucleic acids(DNA, RNA): linked nucleotides. Compare and contrast: Purines vs pyrimidines, ribose vs deoxyribose, RNA vs DNA, heterochromatin vs euchromatin. -Purines: (G/A), Pyrimidines: (T/C). -Ribose: sugar in RNA, Deoxyribose: sugar in DNA. -DNA: double-stranded, polarity 5’vs3’, negatively charged, (T binds to A). - RNA: single or double-stranded, polarity 5’vs3’, (U binds to A). 2 levels of interphase chromatin condensation: -Heterochromatin: most condensed, at centromeres & telomeres (gene poor regions). -Euchromatin: least condensed, at gene rich regions. How are the following terms applied to the structure of double stranded DNA: hydrogen bonds, complementary base pairing, anti- parallel, and polarity. Ponder how complementary sequences are written with respect to polarity. -Hydrogen bonds: hold DNA strands together. -Complementary base pairs: (A-T), (G-C). -Anti-parallel: strand ends are opposite of each other (5’ & 3’). What are genomes, karyotypes, chromosomes, homologous chromosomes, and chromatin? -Genome: all info contained within an organism’s DNA. -Karyotype: display of mitotic chromosomes (most condensed form). -Homologues: 1 pair of chromosomes (1 paternal, 1 maternal). -Chromatin: DNA and its associated proteins. What three sequence elements are needed for chromosome replication and segregation? -Replication origin and telomere, centromere. What are the levels of chromatin organization and what proteins and interactions led to their formation? -Mitotic: histones., Interphase. What three ways can DNA binding proteins access nucleosome wrapped DNA? -1)Nucleosome structure is fluid and dynamic, 2)Chromatin remodeling complexes slide DNA in nucleosomes, 3)Histone tails are modified. What is the relationship between the amount of DNA condensation and the level of transcription? -transcription occurs in areas of least condensation. What is X inactivation? -one X chromosome in females is inactivated. What are the main structural components of the nucleus? -nuclear envelope, nuclear pores, nuclear lamina, nucleolus. What is a biochemical neighborhood? What happens in the nucleolus? -areas where specific genes congregate. -genes are pulled into different neighborhoods when needed. Central Dogma I What is the central dogma? -DNA-{transcription}-RNA-{translation}-Proteins What do polymerases do? Remember 5’ to 3’. -catalyze formation of phosphodiester bonds. What are the main steps in prokaryotic transcription? What is the role of the promoter (-10 and -35 sequences), sigma factor, RNA polymerase, and termination sequence? -Sigma factor of RNA polymerase: recognizes the promoter. -DNA is unwound and transcription begins. -RNA Polymerase: transcribes the genes (5’->3’). -Terminations sequence: ends transcription. How does prokaryotic and eukaryotic transcription differ? What are the main steps in eukaryotic transcription? What are the roles of the promoter (TATA box), the general transcription factors (especially TFIID and TFIIH), RNA pol II, and the CTD of RNA pol II? -Promoter (AUG): tells RNA polymerase where to start. -Transcription factors: needed for RNA pol II initiation. TFIID-distorts DNA double helix, TFIIH-unwinds DNA at start site & phosphorylates RNA pol II CTD. How are eukaryotic transcripts processed prior to exiting the nucleus? Why? -proteins that recognize mRNA modifications bind to RNA & interact with nuclear pore complex. What is the role and composition of the spliceosome? What are snRNPs and snRNAs? -to remove introns. -snRNPs- small nuclear ribonucleoproteins. -snRNAs-small nuclear RNAs. What is the advantage of alternative splicing? -increases protein diversity. Central Dogma II What are codons, the genetic code, redundancy, and reading frames? -Codons: groups of 3 nucleotides that encode for individual amino acids. -Genetic code: nucleotide triplets of DNA and RNA that carry genetic info to cells. -Redundancy: a single amino acid sequence may be coded for by more than 1 codon. -Reading frames: way of dividing the sequence of nucleotides. 3 ways: can start from the 1st letter, 2nd letter, or 3rd letter. What are the important structural features of a tRNA? What is tRNA charging? -link codons to amino acids to 3’ end, anticodon loops (unattached to other codons). -tRNA charging: aminoacetyl-tRNA synthetases connect amino acids. What is the enzyme responsible for tRNA charging? How is the charging checked within the enzyme? -aminoacetyl-tRNA synthetase. -1)amino must fit synthesis site, 2)amino acid must be excluded from editing site. What are ribosomes made of? What are the roles of the large and small subunit? What are the E, P, and A sites? -Ribosomes: made of proteins & rRNAs. -Small subunit: matches tRNA to codons. -Large subunit: catalyzes peptide bond formation. -E=exit, P=peptidyl-tRNA, A=aminoacetyl-tRNA. What are the steps in translation including initiation, elongation, and termination? -1)new tRNA binds to A site. (initiation at start codon using eIFs) -2)peptide bond formation. (elongation using EFs & peptidyl transferase) -3)large subunit shift. -4)small subunit shift. -5)release factor binds to A site and releases an H₂O molecule (termination at stop codon). What are the roles of the initiator tRNA, eIF2, EF-Tu, EF-G, release factors, and GTP hydrolysis in translation? -Initiator tRNA: starts translation. -eIF2: binds GTP-binding protein to ribosome. -EF-Tu: binds tRNA to GTP. -EF-G: hydrolyzes GTP causing shifts in sites. What is a polysome? -single mRNA with multiple ribosomes attached, all translating at the same time. What do proteasomes, ubiquitin, and proteases have to do with protein degradation? -abnormally folded & short life-span proteins are tagged with ubiquitin and are targeted to the proteasome.


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