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| Pregunta | Respuesta |
| Functions of genetic material (3) | replication, expression, mutation |
| Explain Levene's Tetranucleotide hypothesis | A=T=C=G, too simple to store information therefore structural role |
| discovery by Avery, MacLeod, McCarty | DNA = transforming principle, removing anything else had no effect on transformation |
| Hershey Chase Experiment | tagging protein and DNA in bacteriophages, DNA is transferred to cell |
| differences between RNA and DNA | U instead of T, single stranded, ribose vs. deoxyribose |
| basic DNA structure | nitrogenous base + sugar + phosphate |
| Chargaff's Rules | G=C and A=T, composition varies between species |
| discovery of DNA structure | Franklin and Wilkins, Watson and Crick |
| Chromosome structure in prokaryotes | 1 DNA molecule, circular chromsome, form nucleoid, supercoiled. Supercoiled and folded (loops) in bacteria |
| Levels of chromosome condensation in Eukaryotes | 1. nucleosome 2. chromatin fibre 3. metaphase chromosome |
| histones of octomer | H2a, H2b, H3, H4 |
| alpha satellite sequence | 171bp sequence repeated in human centromere |
| centromere complex | numerous proteins that contact 20-30 microtubules |
| possible models of DNA replication | conservative, semiconservative, dispersive |
| evidence from autoradiography | After meiosis 1 – both chromatids labeled, after 2 – only one labeled |
| replicon | region controlled by an origin (entire chromosome) |
| origin | site of initiation of DNA synthesis (1/chromosome) |
| Okazaki fragments | small strands synthesized in lagging strand |
| Roles of DNA polymerase 1 (3) | 5'-3' polymerization, both 3'-5' and 5'-3' exonuclease activity |
| Exonuclease | starts at either end of the DNA molecule |
| endonuclease | cleaves at internal sites |
| Activities of DNA polymerases (3) | polymerization, proofreading, primer removal |
| functions of DNA polymerase I on lagging strand | removes RNA primers, fills in gaps (ends joined by DNA ligase) |
| Proteins involved in initiation of DNA replication (3) | preprimers, DnaA, DnaB (helicase) and DnaC |
| DNA topoisomerase I | produces temporary single strand breaks |
| DNA topoisomerase II | produces temporary double strand breaks |
| DNA gyrase | cleaves both strands, passes one over the other, then reseals |
| Components of E. coli DNA polymerase III | Holoenzyme, Catalytic core (alpha, ɛ, θ), sliding clamp (2 β subunits) |
| Primosome = | DNA primase + DNA helicase, includes all steps from unwinding to ligase |
| replisome = | primosome + pol III holoenzyme |
| main differences between replication in prokaryotes and eukaryotes (4) | S phase, pairs of linear chromosomes, multiple origins, packaged in nucleosomes |
| polymerases in eukaryotic DNA replication (4) | Pol ɛ replicates leading strand, Pol ɗ extends RNA/DNA primer on lagging strand, Pol α + DNA primase prime and synthesize Okazaki fragments |
| function of ribonuclease H1 and FEN-1 | remove RNA primers |
| telomere functions (3) | prevent fusion with other ends, prevent degradation by endonucleases, facilitate end replication |
| shelterin | coats t-loop to protect from degradation |
| Reverse transcriptase | synthesizes DNA using RNA template |
| 1 gene/ 1 ribosome hypothesis | each ribosome contains RNA that directs synthesis of a unique protein (wrong) |
| Properties of mRNA | polymer of ribonucleotides, linked by phosphodiester bonds, U instead of T, unstable, transient |
| types of RNA | mRNA, tRNA, rRNA, hnRNA, snRNA, miRNA |
| RNA polymerase structure in E.Coli | Holoenzyme: α2ββ’σ, Core enzyme: α2ββ’ |
| Consensus sequences | within -35 and -10,comparison for promoter sequences to determine strength |
| 3 steps of Initation | RNAP holoenzyme binds promoter region, DNA unwinding, bond formation |
| 3 steps of termination | chain termination (RNAP encounters signal), RNA pol/DNA complex dissociates, RNA transcript released |
| Rho-independent vs dependant terminators | independant - G:C rich repeats, forms hairpin, ends with ~6A's. dependent - rho utilization (rut) |
| functions of RNAP's in eukaryotes | I - rRNA, II-mRNAs, III - tRNA, 5s rRNA, some snRNA |
| Nucleolus | site of rRNA synthesis by RNAP I and ribosome assembly |
| monogenic | each mRNA encodes only a single polypeptide |
| Three general control elements | TATA box, promoter proximal elements, enhancer elements |
| chromatin remodelling factors | methylation - nucleosome compaction, acetylation - nucleosome free regions |
| eukaryotic promoters | complex, contain multiple enhancer and repressor elements, small change = major phenotypic effects |
| modifications to eukaryotic mRNA | capping 5' end, tailing 3' end, splicing (intron removal), editing |
| functions of 5' cap | prevent degradation, recognition by ribosome |
| mRNA editing methods | insertion/deletion of nucleotides, conversion of one base to another (C-U editing) - rare in animals |
| Exons and introns | Exons: expressed sequence, Introns: intervening sequence |
| genes without introns | interferon, heat shock proteins, histones |
| functions of introns | contribute to evolution of protein families, multiple introns increase protein-coding potential |
| alternative splicing | same gene can produce different proteins |
| Splicing Mechanisms (3) | endonucleolytic cleavage and ligation, autocatalytic splicing, spliceosome-mediated |
| spliceosome components | 5 types of snRNA: U1,2,4,5,6 and ~40 different proteins forming snRNPs |
| amino acid structure | amino, carboxyl and R group, joined together by peptide bonds |
| translation machinery (5) | ribosomes, tRNA, amino acid-activiating enzymes, initiation/elongation/termination factors, mRNAs |
| steps in translation initiation | prepare 30 S subunit and initiator tRNA, formation of 30S initiation complex, formation of 70S ribosome particle |
| steps in translation elongation | specific aminoacyl-tRNA binds to A site, formation of peptide bond (join aa), ribosome moves to next codon towards 3' end of mRNA, repeat steps to 1-3 |
| stop codons (3) | UAA, UAG, UGA |
| steps of translation Termination | release factors bind when stop codon in A site, peptidyl transferase adds H2O to C-terminus of peptide, mRNA released and subunits dissociate |
| main differences in eukaryote translation initiation | more initiation factors, tRNAimet not , initiation complex forms at 5' end of mRNA and scans until 1st AUG |
| steps in Eukaryote initiation | preinitiation complex forms, scans until 1st AUG, elf-2 released and 60S binds, aminoacyl-tRNA binds A site |
| differences in eukaryote translation elongation | proteins have different names, single release factor (eRF1) recognizes all stop codons |
| Kozak Sequence | optimal sequence surrounding start codon (GCC(G/A)CCAUGG) |
| Codon | triplet of nucleotides that specifies an amino acid |
| suppressor mutations | cancel effects of original mutations |
| reading frame | linear sequence of codons in mRNA determined by positioning on ribosome |
| Partial vs complete degeneracy | swapping just among purines/pyrimidines vs swapping any nucleotide |
| wobble hypothesis | 3rd position less stringent, tRNAs capable of binding more than 1 codon |
| conservative substitution | similar amino acids differ by only 1 base, mutations will substitute similar aa that may not change functional properties |
| characteristics of genetic code | triplet, nonoverlapping, comma-free, degenerate, ordered degeneracy, start and stops (punctuated), universal |
| induced mutation | result from influence of artificial factors |
| somatic mutations | affect descendants of that cell, not progeny (impact greater in embryonic development) |
| chromosomal aberration | changes in chromosome number or arrangement (ex. Down syndrome, cancer) |
| gene mutation | changes in DNA sequence, source of most new alleles |
| effects of mutation at amino acid level | silent (no change), neutral (similar), missense (effects), non-sense (stop), frameshift |
| suppressor mutation | second, DIFFERENT mutation that suppresses effect of 1st |
| conditional mutation | lethal/inactive in restrictive environment, viable/active in permissive |
| auxotroph | unable to synthesize essential metabolite |
| suppressor sensitive | viable in presence of suppressor |
| tautomeric shift | movement of hydrogen atoms between common and rare positions on a base (exist briefly) |
| 4 mutations induced by chemicals | alkylating agents, base analogs, oxidative deamination, intercalating agents |
| mutagenic potential | # test colonies - # control colonies (related to tumor forming potential) |
| DNA Repair mechanisms | photo-reactivation, excision, mismatch, post-replication, double-strand break |
| Xeroderma Pigmentosum | recessive disorder in repair enzymes - hyper-sensitive to UV light, risk of skin cancer |
| DNA recombination | Genetic exchange at equivalent positions along two chromosomes with extensive DNA sequence homology |
| size of Bacteriophage T4 dsDNA genome | 168000bp, 150 genes |
| bacteriophage T4 life cycle | 2min - mRNA synthesis, 6min -DNA replication, 14min – assembly begins, 17 min- assembled phage, 25 min – host cell lysis/progeny released |
| size of bacteriophage lambda genome | 48,502 bp, 50 genes |
| prophage | integrated state of the ג chromosome |
| lysogenic state | phage proteins not expressed |
| size of single bacterial chromosome (Escherichia coli) | 4.64 Million nucleotides, 4,377 genes |
| plasmid | replicate independently of bacterial chromosome, can transfer between bacteria, present in single or multiple copies |
| mechanisms of gene transfer in bacteria (3) | transformation, conjugation, transduction |
| test for gene transfer mechanism | with barrier (cannot be conjugation), DNase addition (must be transduction) |
| heteroduplex DNA | each strand contains different alleles |
| contransformation frequencies | measured to calculate map distances |
| sexduction | F1 x F- mating |
| generalized transduction | random fragment of bacterial DNA is packaged in phage head in place of phage chromosome and recombines with recipient chromosome |
| specialized transduction | phage chromosome packaged in phage head contains some bacterial DNA arising from a recombination event between phage and bacterial DNA (more common) |
| Resistance transfer factor (RTF) | encodes genes required for conjugation |
| R-Determinant | encodes genes providing antiobiotic resistance |
| composite transposons | two insertion sequences insert next to each other |
| tnpA, tnpR, bla, res | transposase: catalyzes insertion, resolvase/repressor: involved in recombination, β-lactamase: breaks down ampicillin, resolution site: recombination separation site |
| Transposons and Genome Organization | Telomere maintenance, recombination resulting in deletions and duplications |
| non-replicative transposable elements | IS, composite, Ac/Ds, P |
| Replicative transposable elements (DNA and RNA intermediate) | DNA - noncomposite (Tn3), RNA - retrovirus-like and Retroposons |
| operon | coordinately regulated units of genes with related functions (promoter, operator and structural genes) |
| patterns of gene expression (3) | constitutive (always ON), inducible (default OFF), repressible (default ON) |
| lac operon constitutive mutants | lac enzyme produced in presence or absence of lactose (lacI- or lacOc) |
| cis vs. trans acting factors | cis - physically linked, trans - separate entities |
| levels of trp operon control | repression (negative mechanism), attenuation |
| attenuation | termination of mRNA synthesis (transcription), after initiation |
| post-transcriptional control of gene expression in bacteria (3) | translation initiation efficiency, ribosome movement efficiency, mRNA processing and degradation |
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