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Week 3 Notes

by: Madison Waterman

Week 3 Notes EXSC 223

Madison Waterman
GPA 4.0

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These notes cover lectures from the week of 9/5 as well as the assigned textbook readings. ********IMPORTANT: I accidentally made a mistake in my notes. Please note in the table comparing DNA and ...
Anatomy and Physiology I
Dr. Raymond Thompson
Class Notes
nucleus, cells, translation, transcription, RNA
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This 9 page Class Notes was uploaded by Madison Waterman on Sunday September 11, 2016. The Class Notes belongs to EXSC 223 at University of South Carolina taught by Dr. Raymond Thompson in Fall 2016. Since its upload, it has received 101 views. For similar materials see Anatomy and Physiology I in Science at University of South Carolina.


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Date Created: 09/11/16
EXSC 223: Week of 9/5/16 Notes from the textbook Ch. 3.9 & 3.11 3.9 The nucleus includes the nuclear envelope, the nucleolus, and chromatin • Nucleus o Average size: 5µm diameter o Larger than any cytoplasmic organelle o Usually spherical or oval o 3 regions § nuclear envelope (membrane) § nucleoli § chromatin • nuclear envelope o double membrane separated by a fluid-filled space (like mitochondria) o outer nuclear membrane: continuous with the rough ER, studded with ribosomes o inner nuclear membrane: lined by nuclear lamina § lamina=network of lamins (rod shaped proteins that form intermediate filaments) that maintains the shape of the nucleus o nuclear pores cover nuclear envelope § nuclear pore complex lines each pore § regulate entry and exit of molecules o selectively permeable • nucleoplasm o jellylike fluid in nucleus o holds nuclear elements like the cytoplasm does o contains dissolved salts, nutrients, other solutes • nucleoli o ribosomal subunits assembled here o not membrane bound o typically 1-2 nucleoli per nucleus o large in growing cells • chromatin o composed of: § 30% DNA § 60% histone proteins • cluster of 8 of them form a nucleosome that the DNA wraps around • package and regulate DNA § 10% RNA chains 3.11 Messenger RNA carries instructions from DNA for building proteins • DNA=master blueprint for protein synthesis • Proteins=made up of polypeptide chains o Polypeptide chains=made up of amino acids • Gene: segment of a DNA molecule that carries instructions for creating one polypeptide chain • Nucleotides bases o A,G,T,C o Triplet: sequence of three of the bases § Ex/ AAA, CGT, TAC o Variations in their arrangement allow the creation of different kinds of proteins • Exons: informational sequences of a gene, coding region • Introns: noncoding regions of DNA • RNA o function: decode and transport the message of DNA because it can’t leave the nucleus but RNA can DNA RNA Sugar: deoxyribose Sugar: ribose Double-stranded Single-stranded Has uracil as a base Has thymine as a base • types o Messenger RNA (mRNA): carries the coded information from the nucleus to the cytoplasm where protein synthesis will occur o Ribosomal RNA (rRNA): with the help with proteins, forms ribosomes (sites of protein synthesis) o Transfer RNA (tRNA): carry amino acids to the ribosomes where they decode the mRNA’s message for the amino acid sequence in the polypeptide to be built • All types are formed in the nucleus, using DNA as the template o DNA unzips o One strand used as a template to form a strand of RNA with complementary bases o RNA moves into the cytoplasm through a nuclear pore (it can fit because it is single stranded vs DNA which is double stranded) • Steps of polypeptide synthesis o Transcription: DNA’s information is encoded in mRNA o Translation: information carried by mRNA is decoded and used to assemble polypeptides Lecture Notes on 9/7 • Microtubules and microfilaments function in cell motility by interacting with motor molecules o Motor molecules can attach to receptors • Chemotaxis: movement of an organism in response to a chemical stimulus Mitochondria • Cellular power plants • Site of oxidative metabolism o ADP + PàATP • Mitochondria density in a cell reflects the energy requirements o Very active cell=more mitochondria • Self replicating • Contains its own DNA o Encodes 13 proteins o Maternal • Enclosed by 2 membranes o Outer=smooth o Inner=folds (“cristae”) o Matrix is site of ATP synthesis Summary • Cells are not just bags with organelles • The cytoskeleton o Maintains integrity of the cell o Aids in movement § Of organelles within the cell § Of the cell itself ****READ section on cellular extensions (p89-91) before the exam**** Cells form tissues and organs by “holding hands” • Specialized membrane proteins help cells hold onto one another o Cellular adhesion molecules (CAMs): glycoproteins that help cells to bind at junctions • Membrane junctions o Tight junctions § Impermeable junction that encircles the cell § Prevent molecules from passing through the extracellular space between adjacent cells § Ex: blood-brain barrier separates the brain from the body § Interlocking junctional proteins: claudins and occludins o Desmosomes § Anchoring junctions scattered along the sides of cells § Form an internal tension-reducing network of fibers § Parts of a desmosome: • Plaque • Linker proteins • Intermediate filaments • Plaque anchors linker proteins to the intermediate filaments § Linker proteins fit together like a zipper in the extracellular space § Ex: many are prevalent in the heart and skin because they are under constant mechanical stress o Gap junctions § A nexus that allows chemical substances to pass between cells § Communication between cells § Cells connected by channels/pores called connexons § Selectivity of substances varies § Ex/ Cardiomyocytes: synchronize electrical activity and contraction o Membrane junctions allow cells to § Hold onto each other to form sheets § Make water tight seals § Communicate Cell to cell communication • Hormone receptors o Method for the cell to interact with its environment o Ex/ fat cells secrete leptin (signal) to the brain which binds to leptin receptors in the brain which then sends a message to the body that you are full o Very selective (i.e. leptin receptors only bind leptin) o Diverse group of integral proteins and glycoproteins that serve as binding sites (because everything has to have its own binding site) o Response varies for each cell type § Ex/ acetylcholine stimulates skeletal muscle but inhibits cardiomyocytes • Receptor mediated second messenger system st nd o Ligand (1 messenger)àreceptoràG proteinàenzymeà2 messenger o Ligand binds to the receptor o Activates G protein with GTP (similar to ATP) o G protein activates or deactivates effector protein (ex/ an enzyme) by causing its shape to change nd o Effector catalyzes reaction that produces 2 messengers in the cell o 2 messenger carries out instructions Build/remodel/demolish • DNAàRNAàprotein • Cells make proteins for structural or enzymatic reactions • Transcription o mRNA o splicing • Translation o rRNA tRNA o modification o packaging o secretion • Demolish/recycle o When proteins are damaged or no longer needed, they are broken down o Protein degradation o Ubiquitin proteasome pathway • Overview of the path from DNA to protein o Starts in the nucleus § Transcription: complementary RNA is transcribed from DNA § DNA is transcribed to pre-mRNA § RNA processing: non-coding sections (introns) removed § mRNA is able to leave the nucleus now o mRNA travels out of the nucleus through a nuclear pore o in the cytosol § mRNA binds to a ribosome § translation: nucleic acid language translated to amino acid language to make a protein § amino acids link together to make a polypeptide (string of amino acids) • DNA vs. RNA DNA RNA Sugar: deoxyribose Sugar: ribose Double-stranded Single-stranded Has uracil as a base Has thymine as a base • Transcription o Initiation: transcription factors come in, loosen up DNA, and open it up o RNA polymerase binds at the promoter region on DNA o Complementary nucleic acids are added to the template strand to produce a copy of the coding strand § Nothing happens to the coding strand, it is just the strand that is needed so the template strand contains the complementary bases with which the coding strand can be reproduced • Elongation: RNA polymerase aligns and links together incoming RNA nucleotides with complementary DNA bases on the template strand o DNA-RNA hybrid: at any given moment, 16-18 base pairs of DNA are unwound and the new RNA is still bound to DNA • Termination: RNA polymerase detaches when it gets to the terminator region in the DNA o Product: complete pre-mRNA transcript • RNA processing o Introns: don’t code for anything o Exons: part of the code for amino acids o Introns are cut out Notes from the textbook Ch. 3.10 3.10 The cell cycle consists of interphase and a mitotic phase • Cell cycle: changes a cell goes through from when it is formed to when it reproduces • Two major periods for the cell o Interphase: cell grows and carries out normal activities § G1 (gap 1 subphase) • Metabolically active • Synthesizing proteins • Growing rapidly • Most variable in length, can last minutes to years • Cells that permanently stop dividing are in the G0 phase § S phase • DNA is replicated to ensure the two future cells will have identical copies of genetic material • New histones made and assembled into chromatin § G2 (gap 2 subphase) • Enzymes and other proteins needed for division are synthesized and moved to their proper sites • By the end, centriole replication is complete o Cell division (mitosis): cell divides into two cells § Prophase § Metaphase § Anaphase § Telophase § Cytokinesis Lecture Notes on 9/9 RNA is made of nucleotides • Every 3=1 codon o Each codon=1 amino acid o Multiple different codons can code for the same amino acid • AUG= start codon • UAA, UAG, UGA= stop codons How to read RNA to make a protein • tRNA=transfer RNA o binds with aminoacyl tRNA synthetase (an enzyme) which catalyzes the addition of an amino acid to the tRNA o tRNA has the anticodon • initiation o a small ribosomal subunit binds to an initiator tRNA and scans the mRNA until it identifies the start codon o large ribosomal subunit unites with the small one, forming a functional ribosome • elongation o codon recognition § incoming aminoacyl tRNA binds to a complementary codon in the A site of the ribosome o peptide bond formation § an enzyme catalyzes the peptide bond formation between the amino acid of the tRNA in the P site to that of the tRNA in the A site o translocation § the ribosome moves, shifting its position one codon along the mRNA § this shifts moves the tRNA in the A site to the P site § the unloaded tRNA is transferred to the E site, where it is released o summary of the sites § A site: tRNA recognizes and reads the codon § P site: peptide bond forms, amino acid added § E site: tRNA exists the ribosome • termination o mRNA strand continues to be read until it gets to the stop codon and then the ribosome releases the strand • polyribosome: one strand of mRNA being read by several ribosomes simultaneously • when translation is done, you have a single polypeptide chain in the cytoplasm o this protein will be used WITHIN the cell • for secreted or plasma membrane proteins… o they are made in the rough ER § large organelle continuous with the nuclear membrane • well developed in secretory cells § involved in protein synthesis • surface covered with ribosomes o free ribosomes: synthesis of soluble proteins o bound ribosomes: synthesis of membrane and secretory proteins § involved in phospholipid synthesis for membrane formation Processing function of rough ER • signal-recognition particle (SRP) guides proteins with signal sequence to rough ER receptors so protein can enter rough ER lumen • processing in rough ER lumen o signal sequence removed o protein folding to activate structure o enclosed in vesicles for transportation to the Golgi Golgi Apparatus • stacked membranous sacs o cis face: receiving side from the rough ER o trans face: exiting/shipping side • functions o cell traffic director o modify proteins o concentrate proteins o package proteins/membranes • post-translationally modifies proteins Smooth ER • continuation of rough ER but plays no role in protein synthesis • functions vary by cell types o lipid metabolism: absorption, synthesis, transport o cholesterol synthesis o steroid hormone synthesis o drug/alcohol detoxification o breakdown of stored glycogen o in muscle, Ca storage and release (sarcoplasmic reticulum) Protein demolition • protein degradation: when proteins are no longer useful, they are destroyed • proteolysis: degradation of soluble cytosolic proteins • ubiquitin is the tag for protein degradation. It tags the following: o incorrectly folded proteins (processing error) o damaged proteins (free radicals) o aged/unneeded proteins (cyclins) • tag allows them to enter a proteasome where they are degraded into peptides • proteasome o complex of protein digesting enzymes o proteins degraded to small peptides and amino acids o proteasome and ubiquitin are recycled • cytosolic protein: protein stays in the cell Nucleus • 3 main parts o nuclear envelope: membrane with nuclear pores o nucleoli: dark staining regions where ribosomes are assembled o chromatin: DNA and histones form nucleosomes • there are single and multinucleated cells o multinucleated cells have larger than usual cytoplasm o nuclear domain theory: nucleus/ cytoplasm ration • chromatin= DNA + histones • nucleosome=fundamental DNA packing unit • histone proteins: bind DNA and wrap into chromosomes • chromosome: bodies of tightly coiled chromatin • eukaryotic DNA is packaged into manageable chromosomes o humans have 23 pairs of chromosomes § 22 autosomal, 1 sex § diploid o to replicate itself, each chromosome contains: § telomere: region of DNA at each end of a chromosome § end cap that protects against deterioration


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