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BIOL 302 3/1/16 and 3/3/16

by: Michaela Sanner

BIOL 302 3/1/16 and 3/3/16 BIOL 302

Marketplace > University of South Carolina > Biology > BIOL 302 > BIOL 302 3 1 16 and 3 3 16
Michaela Sanner
GPA 3.5

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About this Document

These notes cover the material that was presented in class on 3/1/16 and 3/3/16.
Cell and Molecular Biology
Erin Connolly
Class Notes
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This 7 page Class Notes was uploaded by Michaela Sanner on Friday March 4, 2016. The Class Notes belongs to BIOL 302 at University of South Carolina taught by Erin Connolly in Spring 2016. Since its upload, it has received 36 views. For similar materials see Cell and Molecular Biology in Biology at University of South Carolina.


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Date Created: 03/04/16
3/1/16 Practice exam posted today Answers posted ­ Friday  Exam 2 ­ chapters 6, 7, 8 Steps of translation elongation         ­start with chain of 3 amino acids                  ­>add amino acid #4         1) amino acyl tRNA binds in A site (carrying amino acid #4)          2) a new peptide bond is formed between amino acid #3 and amino acid #4                 ­catalyzed by peptidyl transferase activity of large subunit          3) accompanied by a shift of large subunit forward (towards 3' end of mRNA) while  small subunit stays in place                  ­> moves tRNAs from A+P sites into P+E sites          4) the small subunit moves forward a distance of 3 nucleotides (towards 3' end of  mRNA)                 ­> ejects spent (uncharged) tRNA from E site                  ­> resets the ribosome so that the next amino acyl tRNA can bind the A site (amino acid #5) What's next for the polypeptide chain?         ­most proteins will spontaneously fold to acquire final 3­D shape (tertiary structure)                  **some proteins require chaperones to aid in folding          ­some proteins are subject to processing                  ­trimmed                 ­post­translational chemical modification                          Ex: phosphorylation                                  ­add phosphate­may activate or inactivate a protein         ­some proteins need to be transported to final destination (various organelles,  extracellular) **ch 15­protein sorting**          CHAPTER 8 Control of Gene Expression          *control of transcription*  ­organisms use DNA (genes) selectively          ­>switch genes "on" or "off"         ­> make certain proteins only when needed  Question: How do cells switch genes "on" or off"? (Dial up or down gene expression)  Differentiation: process by which cells acquire their unique characteristics          **depends on sets of genes that are expressed in a cell at each step in process**         ­>multicellular organisms mostly  Do differentiated cells retain all genetic information ?         ­>nuclear tranplantation                  ­yes, they do; cells retains all of their genetic information  2 major classes of genes/proteins**         ­housekeeping genes­ genes that are expressed in all cells in an organism                  ­ex: enzymes in glycolysis, DNA polymerase, RNA Polymerase, actin          ­specialized genes ­ only expressed in a subset of cell types; contribute to unique  characteristics of differentiated cells                  ­ex: hemoglobin, antibodies,          ­a typical differentiated cell will only express ~1/3 to 2/3 of total possible proteins  Signals that alter gene expression          ­developmental signal ­endogenous (internal)         ­external signals­temperature, nutritional signals, chemical signals         ­Circadian signals­ 24 hour period, day/night signals           Eukaryotic Gene Expression can be controlled at many different levels          1) transcriptional control          2) RNA processing control         3) RNA export and localization control          4) mRNA degradation          5) translation         6) protein degradation         7) protein activity ­ ex phosphorylation  Regulation of Transcription          ­sequences that regulate transcription                 ­> can be long or short (10bp­>10000bp)                  ­bacteria: sequence are usually shorter; usually respond to single signal                  ­eukaryotes: sequence can be much longer, can respond to multiple signals  ­transcriptional regulators/transcriptional regulatory proteins: proteins that bind specifically to  certain DNA sequences          ­fit very tightly against special features of DNA helix          ­make a series of molecular contacts with base pairs (H bonds, ionic interactions, etc,  non­covalent)          ­strong + specific          ­most DNA­proteins interactions occur in the major groove          ­usually contain 1 or more of a few common DNA binding motifs                  1) homeodomain                 2) leucine zipper                  ­alpha helices contact major groove of DNA                  ­often bind to DNA as dimers (heterodimers or homodimers)          ­Homeodomain: 3 linked alpha helices; helix #3 makes contacts with DNA in major  groove via H bonds          ­Leucine zipper: formed by 2 alpha helices, each from a different polypeptide chain;  binds to DNA as a dimer                  ­leucine zipper grip DNA like clothes pin                  ­leucine residues are hydrophobic and interact and stabilize interaction between 2  alpha helices     Bacterial transcriptional regulators:         ­repressors: proteins that switch expression "off"                  **ex tryptophan repressor         ­activator: proteins that switch gene expression "on"                 ­often work by binding to DNA sequences, adjacent to RNA polymerase binding  site, and interact with RNA polymerase to help initiate transcription more efficiently                  **ex CAP         Ex. Transcriptional Repressor­ Tryptophan Repressor                 ­E.Coli­ ~4300 proteins but only a fraction made at any given time                  ­Genes are often arranged in operons                          1) genes in operons are co­regulated  3/3/16 Announcements: ­Practice exam posted ­key post tomorrow ­review session Monday 3/14 at 3:30 CLS102 ­CH 6, 7, 8, maybe CH 11? Ecoli­~4300 proteins but only a fraction are made at any given time Genes often arranged in operons         1) genes in operons are coregulated         2) in an operon, a set of genes is transcribed as a single RNA                  Ex: tryptophan operon                         ­contains genes involved in synthesis of tryptophan                          ­controlled by tryptophan repressor                                  ­transcriptional regulatory protein  Operon in figure: is a 15bp sequence within promotors Tryptophan repressor in figure: is a protein that binds to operator to turn off transcription by  blocking RNA Polymerase          ­­> tryp repressor only binds to DNA when tryptophan is abundant  +tryp ­­> tryp binds to repressor ­­> complex binds to operator ­­> blocks RNA Polymerase  ­­> transcription is off  ­tryp­­> tryp repressor is unbound ­­> tryp repressor can't bind to operator ­­> RNA  Polymerase not blocked ­­> transcription is on  Ex: CAP Activator (transcriptional regulator)          ­CAP activator is protein that binds to nucleotide cAMP                  ­CAP+cAMP binds DNA                  ­CAP+cAMP complex interacts with RNA Polymerase to aid in efficiency of  transcriptional initiation  Transcriptional Regulation                          Bacteria/Prokaryotes                                v                                Eukaryotes ­operons                                                                                      ­single gene­­>single  transcript ­1RNA polymerase                                                                      ­3 RNA Polymerases  ­bacterial RNA Polymerase initiate                                             ­RNA Polymerase II requires  general transcription on own                                                                    transcription factors ex: TF II  D ­genes are often controlled by single                                          ­genes can be controlled by  more  simple regulatory sequence near/in                                              complex regulatory  sequences promotor                                                                                        **can be distant  ­DNA is more accessible                                                             ­DNA is packed in  nucleosomes; DNA                                                                                                        less accessible **can  regulate                                                                                                         accessibility  Eukaryotes         ­basic transcriptional machinery needed (for every gene transcribed by RNA Polymerase II)                  ­need RNA Polymerase II                  ­need general transcription factors (TF II D, TF II H)                  ­need TATA Box         ­many eukaryotic promoters also require:                 ­specialized transcriptional regulators                          ­> proteins that bind to DNA to activate or repress initiation of transcription         ­eukaryotic transcriptional regulators can bind to *enhancer sequences* to influence the rate of transcription  Enhancers (DNA sequences)         ­bound by transcriptional regulators          ­can be 1000s of base pairs away from transcriptional start site                  ­­> either 5' or 3' of start site          ­thought is that DNA between enhancer and start site loops out to allow physical contact between protein bound to enhancer and transcriptional initiation complex  Mediator Complex: ­large protein complex that serves as an adapter: it links          1) transcription initiation complex (RNA Polymerase II + General Transcription Factors)         2) activator bound at enhancer site OR repressor bound at distant DNA sequence  Transcription Initiation:         ­can be influenced by chromatin structures                   ­nucleosomes can inhibit transcription initiation if they are positioned over a  promotor                  Activators**­ can attract chromatin remodeling complexes, can recruit histone  modifying enzymes                 Activators* can alter chromatin structure to make DNA more accessible                  Repressors** can recruit histone modifying enzymes to make DNA less accessible  Combinatorial Control: groups of proteins that work together as a team to determine the  **expression level ** of a certain gene(s)          Expression level: rate of transcription initiation          Ex: typical human gene ­ expression can be controlled by dozens of transcriptional  regulators (activators + repressors)  Coordinate Regulation: the expression of a suite/set of genes can be controlled by a single  transcriptional regulator          ­cells need to switch sets of genes "on" or "off"          ­a single transcriptional regulator that functions as a master switch  Ex: cortisol receptor protein (transcriptional regulator)                  ­binds the hormone cortisol                         ­> protein + hormone­> binds DNA (regulates expression)                          ­> protein ­ hormone ­> cannot bind DNA  CHAPTER 11 (will not be on exam 2 will b e on exam 3) : MEMBRANE STRUCTURE ­plasma membrane­separates the cell from its environment  ­eukaryotic cells­ internal membranes: divide cells up into different compartments (sub  cellular compartments)          ­mitochondria­ outer + inner membrane         ­chloroplasts­ outer + inner + thylakoid membrane         ­nuclear envelope­ 2 membrane         ­Golgi, ER, etc­ 1 membrane  Lumen­ refers to "inside" of membrane (organelle)          ­each membrane is unique                  ­different sets of lipids                  ­different sets of proteins  Plasma membrane:          ­Thin sheet of lipid molecules with proteins interspersed amongst the lipids (Harvard  vid. From first week of class)         ­~50nm thick  (50 atoms)          ­provides a barrier:                 1) selective: allows nutrients to enter cells and allows waste to exit cell                 2) sensing: changes in environment (usually through proteins)                  3) cell growth: and changes in cell shape  **dynamic structure***­constantly changing 


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