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genetics 2
| Term | Definition |
|---|---|
| transmission | the passage of information from cell to cell, or parent to offspring |
| replication | the copying of genetic material with low amount of error for transmission to cell lineages across generations |
| variation | genetic material must contain some variation that creates phenotypic differences and allows for natural selection |
| purines | have 2 cyclical rings; adenine and guanine |
| pyrimidines | have 1 cyclical ring; thymine and cytosine |
| thymine-adenine | pairs have 2 H-bonds |
| cytosine-guanine | pairs have 3 H-bonds |
| double helix structure | minor groove and major groove where proteins bind, formed by tightly stacked bases and twisting |
| RNA | has a 2' OH on ribose sugar, replaces thymine with uracil, single stranded |
| chromatin | DNA protein complex within eukaryotic chomosomes |
| nucleosome | an octamer of 8 (4 pairs) histone proteins and 145-147 base pairs of DNA, simplest level of chromatin structure and involves DNA wrapping around histone proteins |
| euchromatin | transcriptionally active, undergoes normal process of condensation and decondensation in the cell cycle, can transition into heterochromatin |
| heterochromatin | inactive, remains in highly condensed state throughout cell cycle, can transition into euchromatin |
| 3 replication hypotheses | conservative, dispersive, semiconservative |
| requirements of replication | template strand, raw materials (dNTPs), enzymes and proteins to read template and assemble DNA |
| process of replication | H-bonds and covalent bonds must be broken, DNA needs to be unwound, DNA polymerase inserts and assembles complimentary nucleotides |
| Replication Initiation | starts at an origin (ori), which consists of A-T rich consensus sequences, and proceeds bidirectionally |
| helicase | binds to lagging strand template at each replication fork, moving in a 5' to 3' direction, breaking H bonds and moving the replication fork |
| DNA gyrase/topoisomerase | uncoils DNA ahead of replication fork, prevents supercoiling |
| multiple origins of replication | eukaryotes synthesize DNA too slow, therefore multiple ori are necessary to fully copy a human genome |
| replication Elongation | DNA polymerase adds new nucleotides to 3'-OH of polymer |
| okazaki fragments | short fragments of DNA produced by discontinuous synthesis |
| leading strand | continuous synthesis in 5' -> 3' direction to towards replication fork |
| lagging strand | synthesis begins at the replication fork but goes opposite way of unwinding, soon running out of template and leaving Okazaki fragments |
| primer | only one required on leading strand, new primer must be generated at beginning of each Okazaki fragment |
| exonuclease | DNA polymerase I replaces RNA nucleotides of primer with DNA nucleotides via this |
| nick in sugar phosphate backbone | DNA ligase seals the nick left behind by replacing the primers via phosphodiester bond between 5' phosphate groups of the nucleotide |
| DNA polymerase III | built in proofreading function, can detect mismatched bases by deflection of daughter strand at 3' end, redirecting the incorrect base to 3' exonuclease site |
| Bacteria vs eukaryotic replication | replication initiated at multiple origin and is coordinated with the cell cycle, eukaryotes have linear chromosomes |
| telomeres | ends of eukaryotic chromosomes, at the end of lagging strands DNA polymerase I removes the last RNA primer but cannot synthesize new DNA, resulting in shortening of telomere in somatic cells |
| telomerase | enzyme that extends telomeric sequences in germline cells, elongating them by creating many repeats at the ends of chromosomes, protecting against chromosomal degradation |
| gene | a sequence of DNA with a transcription start site that encodes an RNA |
| transcription | information transfer of DNA to RNA |
| product of transcription | single stranded RNA molecule encoded on one DNA strand |
| template strand | where transcription occurs, RNA synthesis is complementary and antiparallel to template, new nucleotides added to 3'-OH of growing RNA in the 5' -> 3' direction |
| transcription requirements | DNA template, rNTPs, transcription apparatus proteins |
| makeup of transcription unit | promoter, RNA coding region, terminator |
| promoter region | where transcription apparatus binds |
| RNA coding region | where DNA sequences transcribed to RNA |
| terminator region | where transcription ends |
| upstream vs downstream | upstream by promoter are -, downstream of transcription start is + |
| transcription apparatus | bacterial RNA polymerase, large multimeric enzyme, catalyzes synthesis of mRNA, tRNA and rRNA, core enzyme made of 5 subunits |
| sigma factor | requirement for binding of RNA polymerase to promoter, + = holoenzyme, specific required for binding to particular set of promoters |
| transcription initiation | promoter recognition, formation of transcription bubble, rNTP bond formation, transcription apparatus leaves promoter |
| consensus sequence | compromises the most commonly encountered nucleotides at each site, RNA polymerase binds to -35 and -10 consensus sequences to initiate unwinding |
| transcription elongation | slower than replication, RNA polymerase released from promoter and moves downstream, unwinding DNA at leading edge and joins nucleotides to growing RNA, rewinds DNA at trailing edge |
| rho-dependent terminators | rho binds to RNA and moves to 3' end, following RNA polymerase |
| terminator site | DNA sequence that causes RNA polymerase to pause |
| rut site | C-rich sequence upstream of terminator where rho binds |
| rho-independent terminators | DNA contains GC-rich inverted repeats followed by 7-9 As, when Us try to bind to As, RNA polymerase pauses forming a hairpin loop and destabilizes RNA from DNA |
| polycistronic mRNA | group of genes with one terminator |
| eukaryotic transcription | different types of promoters in classes of RNAs recognized by different RNA polymers, promoter region and initiation uses more accessory proteins, chromatin structure must be modified before, |
| transcription factors | general transcription factors or others |
| core promoter | immediately upstream, basal transcription apparatus binds, continued by TATA box and other consensus sequences |
| TATA box | -25 is most strongly conserved promoter element in eukaryotes, binding site where core transcription factors bind as part of promoter sequence |
| activators | bind enhancers |
| repressors | bind silencers |
| polyadenylation signal sequence | transcription downstream of stop codon, attracting enzyme complex that binds to signal sequence and cuts transcript at cleavage site |
| transcription termination | RNA polymerase II doesn't occur at a specific sequence, RNA synthesis continues past coding sequence, pre mRNA cleaved into 2 pieces, RAT I degrades trailing RNA and is terminated when it reached RNA polymerase |
| RNA processing in bacteria | in bacteria, transcription and translation are coupled |
| RNA processing in eukaryotes | in eukaryotes, processing occurs in the nucleus before it is transported to the cytoplasm for translation |
| eukaryotic genes | not co-linear, meaning the size of the DNA is not equal to the size of the mRNA due to intron splicing |
| exons | only coding part of DNA |
| polyadenylation site | AAUAAA, polyadenylation proteins cut transcript ~20 nucleotides downstream of stop and adds poly-A tail / UTR |
| 5' cap | helps with translation by binding initiation factors and helps remove first introns in splicing, added while RNA is being synthesized |
| poly-A tail | helps make sure mRNA is stable and secure during transport from nucleus to cytoplasm |
| neurospora | fungus used to study relationship of genes to proteins, main vegetative state is haploid so effects for mutations can easily be seen |
| auxotrophs | cannot grow on minimal media; grow on media with substance they can no longer synthesize |
| translation | mRNA transcript with triplet codons bind with tRNA anticodons in ribosome, adding amino acids to make a polypeptide |
| genetic code is degenerate | amino acids can be specified by more than one codon |
| ribosomes | large and small subunits made of rRNA and proteins |
| peptidyl (P) site | where a growing peptide is centered in ribosome |
| aminoacyl (A) site | where the new charged tRNA enters and works with P site to create new aminoacyl bond |
| exit (E) site | where uncharges tRNA exits the ribosome |
| tRNA charging | adding amino acids to tRNAs; specificity between an amino acid and its tRNA is determined by each individual aminoacyl-tRNA synthetase |
| tRNA structure | enzymes add same 3 nucleotides (5'-CCA-3') to the 3' end of tRNA, designating 3' amino acid acceptor stem |
| synonymous mutations | substitutions change the codon but not amino acid, therefore silent |
| nonsynonymous mutations | substitutions change both codon and amino acid |
| nonsense mutation | changes codon to STOP codon |
| missense mutation | changes codon and amino acid |
| Shine-Dalgarno sequence | only in bacteria translation initiation, located in 5' UTR of mRNA transcript before start codon, positions start codon (AUG) with P site |
| eukaryotic initiation facotr (eIF) | keeps large ribosomal subunit from binding while small subunit binds 5' cap of mRNA and scans toward 3' end until locating AUG |
| Kozak consensus sequence | rRNA sequence in ribosomes complementary to AUG codon within seq, binding to rRNA |
| translation elongation | energy release (GTP->GDP) helps rRNA ribozyme in large subunit catalyze new peptide bond between peptide chain in P site and new charged tRNA in A site |
| elongation factor (EF-G) | along with GTP, shifts ribosomes 1 codon in 3' direction, moving uncharged tRNA from P to E sites, new tRNA recruited to A site and adds a new amino acid to the growing peptide |
| translation similarities in prokaryotes and eukaryotes | GTP hydrolysis provides energy, charged tRNAs with elongation factor proteins are recruited to A site, rRNA in large subunit catalyzes peptide bond formation between polypeptide chain in P site and new in A site, EFs translocate ribosomes by moving it 3' |
| release factor proteins | translation termination triggered by presence of stop codon in mRNA at A site |
| genetic code is redundant and universal | contains 64 different codons and translates to 20 amino acids, 61 AA and 3 stop codons |
| reading frames | specify codon order in which gene is read, AUG identifies 1st base pair position |
| codon bias | traditional view of synonymous substitutions, preferrential use of specific codons over others that code for same amino acid |
Created by:
sadiejude
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