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BIOL 239 Final: BIO 239 FINAL EXAM

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University of Waterloo
BIOL 239
Christine Dupont

SET 11: DNA REPLICATION The Watson-Crick An original double helixes strands will separate, complementary bases model of DNA then align opposite templates, then enzymes line sugar-phosphate replication elements of aligned nucleotides into a continuous new strand; semiconservative Semiconservative One strand is preserved from the parental molecule and the other is newly synthesized Conservative Entire parental strand is duplicated to form a newly synthesized double stranded DNA molecule Dispersive Parental DNA is conserved and specific sections of each of the 2 DNA molecules are newly synthesized Matthew Provided experimental proof in 1958 that DNA indeed was Meselson and semiconservative Franklin Stahl The Meselson- Used E. coli: Isotopically labelled different DNA preparations with N14 Stahl experiment (light) and N15 (heavy), then centrifuged them and saw that they banded in different places (because N14 and N15 had different densities); when DNA was mixed (N15 cells onto a medium containing N14) and allowed to replicate, there was a hybrid density, meaning it was a mix of the two strands (ruled out conservative model), replication to produce a second generation ruled out the dispersive model Prokaryotes Have small circular chromosomes (e.g., E. coli) and a much smaller genome than humans (e.g., E. coli ~ 4 million: humans ~ 3 billion) Origin of Consists of long tracks of AT base pairs since they only have two replication hydrogen bonds and are easier to break apart Helicase A series of enzymes recognizes the AT rich region so that helicase can work on both sides to unwind the double stranded DNA molecule Replication The opening produced when the double stranded DNA molecules have bubble been pulled apart SSBP (Single Once the strand is pulled apart, SSBP’s help to make sure the bases don’t stranded DNA pair back together binding proteins) DNA Primase Makes RNA (makes the RNA primer that DNA polymerase can then use) RNA Primer Need to provide a free 3’ OH (hydroxyl) on which DNA polymerase can add nucleotides for synthesis DNA Polymerase Makes DNA starting from the 3’ hydroxyl at the RNA primer and works III towards the 5’ of the next RNA primer then will stop (CAN ONLY ADD IN THE 3’ DIRECTION) Okazaki Occur as a result of the synthesis on the lagging strand; as the fragments replication bubble opens, DNA polymerase needs access to the 3’ end to extend the DNA, but can only get access in small access because of the orientation of the lagging strand DNA Polymerase I Will remove RNA primers during elongation and then fills in the gap where the RNA primer use to be DNA Ligase When DNA polymerase III comes to a stop when it encounters a 5’ RNA primer, there is a small gap (after the RNA primer is removed with pol I), so ligase seals the 3’ OH and 5’ PO4 nicks by catalyzing the formation of phosphodiester bonds Proof reading During elongation if the wrong base is added, DNA polymerase III can ability biochemically sense that the stability is off once it is put in, so exonuclease will cut it out, and DNA will move backwards (3’-5’) and replace it with the correct one; this correction can only be made as it is copied Topoisomerase 1. Responsible for making transient nicks in circular chromosomes when supercoiling occurs from the widening of the replication bubble 2. Responsible for clipping and separating the newly replicated intertwined chromosomes into separate daughter molecules Telomeres The ends of chromosomes that contain specific sequences (no genes) of repetitive units (250 – 1500) used to safe guard genetic material when it gets snipped Ribonucleases Remove RNA primers Telomerase Recognizes and binds to single stranded overhang DNA, matches RNA to the repetitive sequence of the telomeres, then extends the strands (elongation), so DNA polymerase III can fit inside and fill gap, then the RNA primer is degraded and the DNA overhang is degraded Senescence Occurs <50 generations in culture (Hayflick Limit) when you lose all of your telomeres and then start to lose genetic information SET 12: GENETIC CODE Gene expression The flow of genetic information from DNA to RNA to protein RNA transcript Serves directly as mRNA in prokaryotes; processed to become mRNA in eukaryotes Codon A nucleotide triplet that codes for an amino acid; the 4 nucleotides in different triplet combinations encodes for 20 amino acids Start codon Signifies the beginning to the open reading frame, sequence is AUG (methylamine); when these codons appear in frame, translation stops and the polypeptide chain is terminated Reading frame The partitioning of groups of 3 nucleotides such that the sequential interpretation of each succeeding triplet generates the correct order of amino acids in the resulting polypeptide chain Open reading The triplet codons in between the stop codon and the start codon; the frame start triplet must be in frame with the stop triplet Stop codon Signifies the end of the open reading frame, sequences can be UAG, UAA, or UGA Frameshift Changes that alter the grouping of nucleotides into codons; a deletion or mutation insertion that causes everything from the mutation onward to be read in a different set of triplets (thus coding for different amino acids) Intragenic The restoration of gene function by one mutation canceling the other in suppression the same gene (e.g., adding 3, subtracting 3, add 1 & subtract 1) – restores the reading frame after the mutation (the protein should still be able to function as long as the mutation did not affect the majority of amino acids) Ribosome Very large complexes of several different proteins; consists of the small ribosomal unit (30s) and the large ribosomal unit (50s); houses the tRNA and synthesizes polypeptide chains tRNA Responsible for matching up the codons on mRNA to their corresponding amino acid, and then they get joined up In vitro Had cellular extracts that contained ribosomes, tRNAs and amino acids translation (labeled), then added artificial/synthetic mRNA of a known sequence to experiments see which codons corresponding to which amino acids Ribosome binding From in vitro translation, couldn’t tell, for example, is Leu was CUC or assay UCU so they radioactively labelled Ser tRNA and Leu tRNA to see which was not filtered through when they added CUC; tRNA Leu was CUC because it did not filter through – only those tRNAS carrying the corresponding amino acid for the triplet would bind to the ribosome and stick to the filter Coding strand In the 5’  3’ direction, mRNA will be the SAME as the coding strand (but have U instead of T); also known as sense strand Template strand In the 3’  5’ direction, mRNA will be COMPLEMENTARY to the template strand (but have U instead of T ); also known as sense strand Non sense codons Nucleotide triplets that do not correspond to any amino acids (e.g., stop codons) SET 13: TRANSCRIPTION Transcription The process by which the polymerization of ribonucleotides guided by complementary base pairing produces an RNA transcript of a gene RNA polymerase The enzyme that catalyzes transcription Promoters DNA sequences near the beginnings of genes that signal RNA polymerase where to begin transcription (promote the transcript) Terminators Sequences in the RNA products that tell RNA polymerase where to stop (encoded by DNA); (terminate the transcript) – also known as transcriptional terminator ~ TT Sigma factor Recognizes the sequences in the promoter region (once used, can be recycled) Holoenzyme The complex of the sigma factor and RNA polymerase core enzyme Rho-independent A type of transcription termination which does not depend on the rho (bacteria only) protein; (intermolecular base pairing in mRNA causing termination) sequences near the end of the mRNA will be complementary and base pair with each other, forming a hairpin loop which causes polymerase to detach and ends transcription Rho-dependent Rho factor (protein) will recognize and bind to a sequence, then (bacteria only) destabilizes the polymerase and then the polymerase will fall off Post Modifications of eukaryotes done after transcription – 5’ methyl cap, transcriptional Poly-A tails, and sometimes splicing; these post transcriptions modifications modifications transform a transcript  mature mRNA 5’ Methylated A special capping enzyme that adds a guanidine triphosphate in reverse cap orientation to the 5; end after polymerization of the transcripts first few nucleotides; the G is not encoded by the gene – next methyl groups are added to the backwards G an to one or more of the succeeding nucleotides in the RNA; CRITICAL because it is needed so the ribosome can recognize and translate Poly-A tail The addition of 100-200 Adenosines to the 3’ end of the transcript – not encoded by the gene; first ribonucleases cleaves the primary transcript to form a new 3’ end then Poly-A polymerase adds A’s onto this new 3’ end (Poly-A tails help stabilize the transcript, preventing degradation) Exons Sequences found in both a gene’s DNA and in the mature mRNA; exons are coding sequences for the protein produce (Ex = EXPRESSED SEQUENCES) Introns Sequences found in gene’s DNA but NOT in the mature mRNA – they are removed from the primary transcript (IN = INTERVENING SEQUENCES) RNA Splicing Takes exons and brings them together through the removal of introns; splicing is usually carried out by a complex known as the spliceosome, although some RNA transcripts are self-splicing Alternative Splicing induced to certain introns due to stimuli; splicing may occur splicing between the splice donor site of one intron and the acceptor side of a different intron downstream – this produces different and mature mRNA molecules that may encode related proteins with different, though partially overlapping amino acid sequences Trans-splicing Splicing coming from different places (genes) and then exons from two completely different genes gets put together SET 14: TRANSLATION Translation The process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids; requires mRNA and tRNA (with an attached amino ribosomes) Transfer RNAs Short, single stranded RNA molecules 74 – 95 nucleotides long that (tRNAs) carries one particular amino acid (when it is charged); tRNAs of the end products of a gene, they are a functional molecule right after transcription and don’t need to be transcribed; some tRNAs may carry modify bases in their anticodons (e.g., inosine) that allow for wobble Aminoacyl-tRNA Responsible for catalyzing the attachment of a tRNA to its conjugate syntheses amino acid – once this happens, the tRNA is considered to be charged Wobble Some tRNAs recognize more than one codon for the amino acid they carry; (e.g., CPW = can pair with: G CPW U or C & C CPW G & A CPW U & U CPW A or G & I CPW U or C or A); thus only ~2 tRNAs are required to recognize an amino acid that can be made from 4 different codons Inosine A base found in tRNA anticodon sequences that can bind with U, G and A Ribosomes Big complexes made up of protein & mRNA and are the sites of protein synthesis Prokaryotic Has a large ribosomal subunit of 50S and a small ribosomal subunit of ribosome 30S and total size is 70S Eukaryotic Has a large ribosomal unit of 60S and a small ribosomal unit of 40S and ribosome total size is 80S 16S rRNA Prokaryotic ribosomal RNA (smaller than eukaryotic rRNA) – composed of 1700 nucleotides; needed to direct translation 18S rRNA Eukaryotic ribosomal RNA (larger than prokaryotic rRNA) – composed of 2000 nucleotides; needed to direct translation Peptidyl A catalytic domain that forms peptide bonds (top middle part of the transferase ribosomal complex) Aminoacyl (A) Where new charged tRNA comes in (right) site Peptidyl (P) side Where the peptide bond gets made (middle); chain will be synthesized (grow) from this site Exit (E) site Where the uncharged tRNA is pushed to before it is released (left) Shine-Dalgarno A sequence that is specifically recognized in the 16S rRNA of the 30S sequence subunit (ONLY FOR PROKARYOTES) and is typically located 6 – 10 base pairs upstream of the start codon (so before the start codon); the SDS in E. coli is 5’AGGAGG 3’ fMet ONLY FOUND IN PROKARYOTES; modified methionine (tRNA FMe) 50S Ribosomal The large ribosomal unit (part of the ribosomal complex) that binds such FMet unit that the tRNA is placed in the P site of the ribosome thus completing the initiation of translation Elongation Responsible for escorting the tRNA into the A site of the ribosome; this factors (EF) causes the release of fMet from its tRNA, then the free tRNA is shifted to the E site so the P site is available for the next incoming amino acid Release factor Recognizes a stop codon when the ribosome encounters it; the release factor then moves into the A sire and the polypeptide is released from the C terminal of the tRNA Ribosomal IN PROKARYOTES consists of the Shine-Dalgarno sequence (SDS) AND binding site the start codon (prokaryotes) Ribosomal IN EUKARYOTES the 40S ribosome subunit recognizes and binds to the 5’ binding site methylated cap and scans along the mRNA until it finds the start codon (eukaryotes) Polyribosome A complex of several ribosomes translating from the same mRNA Posttranslational Modifications that occur to the protein after translation (e.g., meth processing often gets cleaved of so the chain really begins with the second amino acid) Silent mutation A silent mutation swaps out one base in a codon, but the new codon sequence still codes for the same amino acid as it did previously (typically the 3 base in the triplet is changed) thus the protein doesn’t change Missense Swapping out a base in a codon that changes the amino acid it codes for mutation and thus may alter the protein Nonsense Swapping out a base (typically the first one) so that the codon becomes mutation a stop codon Sickle cell anemia Caused by a single missense mutation in the beta-globin polypeptide chain SET 15: GENE REGULATION IN PROKARYOTES RNA Polymerase Tetramer responsible for recognizing the promoter in transcription Phosphorylation A posttranslational modification that rags a protein for destruction; a way to control protein expression and how long it lasts in the cell -10 sequence Also known as the TATA box (known as a consensus sequence because its mostly commonly TATA but there is some variation); found 10 nucleotides before +1 Sigma factor Recognizes the -10 and -35 and loads the polymerase on before starting transcription at +1 Regulatory Binds to DNA targets to control transcription by inhibiting or enhancing proteins it Operon A unit of DNA composed of specific genes, plus a promoter and an operator, which act in unison to regulate the response of the structural genes to environmental changes Structural genes Genes that have been made into proteins Non-structural Genes that are not translated; their final product is the mRNA (e.g., genes tRNA, rRNA) Induced The presence of lactose induces the expression of genes required for expression lactose utilization Beta- Breaks the glucalytic bond OR changes the bond; break = make glucose galactosidase and galactose, change = allolactose Lac Z Encodes for beta-galactosidase Lactose Broken down in the cell so energy from glucose can be used; Glucose + galactose  lactose Allolactose Results from beta-galactosidase changing the bond of lactose; acts as an inducer Permease A channel in the membrane that allows transportation of lactose into the cell Lac Y Encodes permease Lac A Encodes transacetylase that adds an acetyl (CH 3O) group to lactose (not required for lactose breakdown, no one really knows what Lac A does but it’s there in the operon) Promoter Promotes transcription; if there is a mutation here then none of the downstream genes of ZYA can be transcribed for Lac I The repressor gene is the most upstream in the lac operon and is not part of the lac operon; it codes for the repressor protein Repressor protein Can bind to the operator to repress its function; although if allolactose (inducer) is made and binds to the repressor protein, it can be turned off Constitutive A mutation that results in protein synthesis regardless of environmental mutants conditions (e.g., the presence of absence of lactose) Derepression When protein synthesis is not being repressed Operator Allows for protein synthesis of Z, Y, and A Polycistronic Two or more genes transcribed together at the same time on the same (prokaryotes) mRNA; when one gene is repressed or induced, the same effect is observed for the others (in lac operons, all 3 proteins are translated simultaneously and at the same amounts) Monocistronic Each transcript codes for only one protein (eukaryotes) Cis DNA sites such as the promoter and operator act in cis Trans Proteins, such as repressor proteins, permease, and beta galactosidase can act in trans – able to transport around the cell (e.g., to a plasmid or chromosome) Mirodiploid A partial diploid cell, also known as a miroploid, that can contain a plasmid and a chromosome Corynebacterium Colonizes throat bacteria, regulation and action of diptheria toxin and diptheriae causes death when it travels through the bloodstream and gets into organ systems; when iron is present, the operator is turned off; the toxin sticks a ribose on the tRNA escort factor which stops the growth of the polypeptide chain. SET 16: EUKARYOTIC EXPRESSION Non-structural Genes that aren’t translated; the RNA is the final product (e.g., mRNA, genes tRNA, rRNA) Core promoter Always very close to the genes coding region; includes a TATA box
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