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INTRO BIOLOGY A Midterm 2 Notes - I got a 4.0 on the Midterm!

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University of Pennsylvania
BIOL 101

mt2sg LECTURE 11-12 • RNA WORLD- transcription and translation • Different types of RNA And RNA Ps • • Which ones do proks and euks have? Wut does each make • Sigma factor (what is it) • RNA Transcription • What is it • promoter/terminator • Initiation, elongation, termination • primary transcript (example) What is the difference b/t the polynucleotide made by RNAP vs DNAP • • What makes the transcription process more simple in proks LECTURE 12 • Transcription to translation • Codons (what are they) • Reading frames Info: amount of possible codons, redundancy/ambiguity • • What are the letters of the start/stop codon triplets • What is translation (what happens, using what) • where does it occur • tRNA • Two things that make different tRNAs different • components and how it attaches to them (enzyme name) • The reaction that makes the AANtRNA • anticodons • AANtRNA • How its synthase recognizes its cognate tRNA • How many different synthases are there? how many different tRNAs? • Ribosomes/tRNA • Subunits • tRNA binding sites • Initiation, elongation, termination • Protein factors that aid in processes • Initiation • What comes together first • what is the first/initiator tRNA • Order of what happens next to reach translation initiation complex • Purpose of IFs, what they use to do their job • Where is the mRNA binding site • And its relation to the start codon on the mRNA •Elongation • Two energy-requiring steps: • HOw much does each “cost” •Termination • What comes in the A site for stop codon • What it does instead of peptidyl transferase • Disassembly of translation complex •TOTAL ENERGY COST OF TRANSLATION (include charging of tRNA) • Consider *per peptide bond and the other costs for 1 polypep translation •draw out this process •Polysomes/polyribosomes •In prokaryotes, transcription and translation occur simultaneously (there is no need for a intermediate stage) LECTURE 13 • Signal peptide • When the signal peptide _____________ , it is recognized by the _________ which docks it to the _____________. This process allows ____________ •Upon completion of synthesis, signal peptide_________ • draw out this process • Changes in DNA Sequence: Mutations • Are the basis of evolution • Single basepair changes mutations •Point mutation (SNP) • What does it stand for • Types of mutations they can lead to • (Example of sickle-cell v wild type RBC) •Basepair indels • Why can they be more disastrous • Type of mutations •LARGE changes • IS and Tn elements; translocations • difference b/t IS and transposon • Transposons/ transposable elements • what they are • Enzyme they use •Effects of these mutations • Regulation of gene expression • The difference: Activity regulation and gene regulation • Prok and euk regulate gene expression in response to changing environment • __________ gene makes ________ or ________ protein which binds to the _____ • Promoter • Operon • ORF • Types of regulation • Negative __________ binds to _________ to _________ • • Repressor can be both active or inactive •***In respect to its ability to bind an operator • Depending on other molecules around it • Inducible and repressible operons (e.g. lac and trp Inducers • •Aporepressors and corepressors •Why are both inducible and repressible operons part of negative regulation? • Positive •_________ binds to _________ to facilitate ___________ of _________ Example with lac operon, cAMP, CAP, glucose/lactose • LECTURE 14 • RNA transcription-translation-- how it is simpler for proks than euks Eukaryotic gene structure • • chromatin, nucleosome, histones •histone tail • To be transcribed - genes in histone cmplx •What can happen to allow histone to be transcribed Types of modification (and purpose) • • epigenetic; how long does the modification last • Eukaryotic gene structure and transcription • distal control elements •what are they called • what binds there • promoter region •TATA sequence • _______ and _______ bind there • __________ proteins bring together the __________ and ___________ to form the __________ complex LECTURE 15 • Pre-mRNA Processing • Addition of _______ and ________ • Introns v Exons • Splicing done by large protein complex called What’s its makeup • • snRNPs, snRNA • UTRs • Mature mRNA, primary transcript, pre mRNA • parts of mRNA Alternative splicing • • benefits (economical) • Introns: why are they there? • Global regulation of gene expression • Transcription/translation can be regulated at all levels in the cell What ways in the nucleus? • • Cytoplasm? • mRNA degradation • Post-transcriptional events • mediated by What can they do to RNA • • Primary miRNA transcript • process of how it’s made (p365) • Protein processing and degradation • Proteasome, ubiquitin Describe process • • Cell communication; signal transduction pathways • Three major steps • Signaling molecule (often water soluble) and receptor is usually a _________ • Transduction (when as a series of steps) happens as a __________ of _________ of the components of the chain • Relay of the signal done as ________________ of relay molecules • The parts of this signal transduction pathway are called _________________ (see main diagram) LECTURE 16 (still signal transduction) • List the three main types of membrane receptors • GPCRs • Describe process • DRAW OUT THE SIGNAL TRANSDUCTION PATHWAY • Signaling and Apoptosis • What happens in apoptosis • How does it differ from autophagy • Can be triggered by... (4 things) - explain each step (details in notebook) • Proteases that carry out apoptosis: ____________ • Apoptosis has planned uses (not just emergency). Example? • Embryonic development and cell differentiation • Cytoplasmic determinants and induction: explain the two factors •Cyt determinants • Only in one type of cell. Why? • Draw this out •Induction •
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