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Genetics Test 2
| Question | Answer |
|---|---|
| Non-polar amino acids | hydrophobic; Glycine Alanine Valine Leucine Isoleucine Proline Cysteine Methionine Phenylalanine Tyrosine Tryptophan |
| G | (Gly) Glycine, non-polar amino acid, simplest amino acid |
| A | (Ala) Alanine, non-polar amino acid |
| V | (Val) Valine, non-polar amino acid |
| L | (Leu) Leucine, non-polar amino acid |
| I | (Ile) Isoleucine, non-polar amino acid |
| P | (Pro) Proline, non-polar amino acid |
| C | (Cys) Cysteine, non-polar amino acid |
| M | (Met) Methionine, non-polar amino acid, 1st in translation |
| Polar Amino Acids | reactive; Serine Threonine Asparagine Glutamine |
| S | (Ser) Serine, polar amino acid, in ATP (protein Kinases) |
| T | (Thr) Threonine, polar amino acid, in ATP (protein Kinases) |
| N | (Asn) Asparagine, polar amino acid |
| Q | (Gln) Glutamine, polar amino acid |
| Acidic Amino Acids | net "-" charge; Aspartic acid Glutamic acid |
| D | (Asp) Aspartic acid, acidic amino acid |
| E | (Glu) Glutamic acid, acidic amino acid |
| Basic Amino Acid | net "+" charge, combine to "-" binding proteins; Histidine Lysine Arginine |
| H | (His) Histidine, basic amino acid |
| K | (Lys) Lysine, basic amino acid |
| R | (Arg)Arginine, basic amino acid |
| F | (Phe) Phenylalanine, non-polar amino acid |
| Y | (Tyr) Tyrosine, non-polar amino acid |
| W | (Trp) Tryptophan, non-polar amino acid |
| peptide | short group |
| 4 levels of protein structure | primary, secondary, tertiary, quarternary |
| Primary protein structure | amino acid sequence, determined by DNA |
| Secondary protein structure | repetitive folding alpha helix pleated sheet formation of hydrogen bonds for structure |
| Tertiary protein structure | 3D shape of 1 polypeptide simple protein amino acid sequence=polypeptide backbone hydrogen bonds hydrophobic interaction disulfide bonds ionic bonds |
| Quaternary protein structure | complex proteins composed of more than 1 polypeptide |
| Translation | occurs in cytoplasim amino acids tRNA adapters 100 bases in length anitcodon acceptor charged tRNA attachment of amino acid to tRNA like a battery putting energy into system to use later Ribosome mRNA gives info for tr |
| Ribosome | like a baseball glove small subunit and large subunit |
| large subunit (ribosome) | 50 proteins and rRNA A site P site |
| small subunit (ribosome) | 50 proteins and rRNA |
| A site | binding site- aminoacyl tRNA; accepts incoming (charged) tRNA |
| P site | Peptidyl-tRNA binding site; growing polypeptide |
| Phases of Translation | 1. activation 2. initiation 3. elongation 4. termination |
| activation (translation) | charging reaction attachment of amino acid to the specific tRNA requires ATP breaks down to AMP + PiPc enzyme driven by amino acid synthetase one for each amino acid requires ATP |
| initiation (translation) | -formation of initiation complex -methionine (M) is ALWAYS the 1st amino acid -mRNA binds to initiation codon binds to tRNA which binds to initiation codon which connects to large ribosomal subunit binds to tRNA in P site |
| equilibrium constant | favors dissociation |
| dissociation | ribosomes that are not translating |
| elongation (translation) | build a polymer codon recognition-aminacyl tRNA binds to codon peptide bond formation between new amindo acid and growing polypeptide translocation tRNA from p site released A tRNA moves to p site requires a lot of energy |
| termination (translation) | termination codon signal for release factor (protein) protein in A site provide H2O molecule hydrolysis: breaks bond b/w tRNA and polypeptide polypeptide released free polypeptide yields everything falls apart |
| Genetic Code | 1. 1 start codon (AUG) (M) 3 stop codon (UAA, UAG, UGA) 2. degenerate (redundant) 64 combinations - 20 amino acids 3. universally used all organisms use same combinations |
| heterochromatin | compact DNA, dark bands on chromosome |
| euchromatin | loosely packed DNA |
| DNA damage | -DNA adducts or lesions-caused by environment or spontaneous |
| environmental DNA damage | induced; eating, drinking, exposure to chemicals |
| spontaneous DNA damage | errors in: a. base pairing b. proof-reading (DNA replication) c. accessory proteins (binding proteins) d. mis-match |
| enzyme | speeds up chemical reaction and is released UNCHANGED |
| DNA repair mechanisims | -not mutually exclusive-Types a. direct b. Base excision repair (BER) c. Nucleotide excision repair d. mismatched repair |
| Direct repair mechanism | -double helix and alterations (how much work needed?) a. photoreactivation b. alkyl transfer |
| photoreactivation | - direct repair mechanism-photolyase- uses light and energy to split covalent bonds(NADPH) -bacteria, yeast, goldfish |
| alkyl transfer | -direct repair mechanism-readily attach to DNA -MGMT |
| MGMT | -O6 methyl guanine DNA repair -methyl transferase-present in ALL organisms-job is to remove methyl groups |
| transferase | -protein but NOT an enzyme because it cannot be reused |
| Base excision Repair mechanism | -1 nucleotide involved-glycosylase-2 AP endonucleases - sugar and phosphates-DNA polymerase-inserts correct nucleotide-DNA ligase |
| glycosylase | -base-abasic site -removed-true enzymes-specific for bases |
| AP endonucleases | -sugar and phosphate-expose 3' hydroxyl group |
| DNA polymerase | inserts correct nucleotide |
| Nucleotide Excision Repair Mechanism | -more then 1 nucleotide-repair oligonucleotide-species specific-alteration in 3D structure of helix-excision complex-5'/3' breaks using excision complex-DNA ploymerasee recoginzes 3' hydroxyl grou-sugar/phosphate backbone is sealed w/ ligase |
| Excision complex | -used in NER-multi-subunit protein-2 incisions (1 on each side of damage) |
| Mismatched Repair Mechanism | -final check after DNA replication-2 minutes after replication new strand becomes methylated-works before methylatino -old strand is methylated; new strand is not until 2 minutes after DNA replication so mechanism can distinguish the two |
| Mismatched Repair Mechanism | -complex recognized-DNA polymerase yields a new strand-Ligase seals the backbone |
| Mutation | -change in DNA-source of genetic diversity |
| mutant | organism with a mutation |
| Types of mutations | -Spontaneous-induced-somatic-germline |
| Spontaneous mutation | -occur without explanation |
| induced mutation | -know something about parents and/or environment that caused mutation |
| somatic | cannot pass damage to the next generation (i.e. sunburn) |
| germline | -mutations in reproductive cells; can be passed to next generation-ie. teratogens |
| teratogens | target germline mutations |
| mutagenesis | process of how mutations are made-forward or backward |
| forward mutation | -normal phenotype to mutant |
| backward mutation | -mutant phenotype to normal |
| mutagens | cause mutations-chemical -alkys-physical- UV light-biological-viruses |
| Screening | isolating a mutant in a normal population via phenotypic change |
| selection | identify mutant because it grows/survives and normal population dies/fails to grow-i.e use of antibiotics |
| ampicillin | interferes with synthesis of bacteria cell walls |
| tetracycline | interfers with ribosome |
| mutation frequency | =# mutants/total population-count # of mutants |
| mutation rate | =# of mutations/base pair of DNA/cell division-look @ time mutation took place |
| mutation frequency = mutation rate...when? | if mutation occurs during last cell division |
| null loss of function mutation | recessive mutation (m)-lose 1/2 of protein then next generation loses all of the remaining protein |
| leaky loss of function mutation | -loses part of protein (m1) |
| gain of function mutation | (M) change of protein, seen in heterozygotes |
| Reading frame | nucleic acid language with out stop codons -read in triplets -altered by adding or deleting 1 base |
| Base-substitution | change 1 base pair to another base pair -simple/point mutation -transition or transversion |
| Transition | purine to purnine-GC to AT or AT ot GC |
| Transversion | purine to pyrimidine-GC to TA-AT to CG-GC to CG-AT to TA |
| EMS | -denotes a methyl group-sulfates potent-mutagen-transition mutation (GC-AT) |
| UV | -more dangerous than EMS-causes many different types of mutations-double breaks on the helix |
| AFB | -found in Peanut Butter-GC to TA (transversion) |
| Missense mutation | -1 amino acid to a 2nd amino acid |
| Effects of Missense mutation | 1. no effect2. partial loss of function3. gain of function4. alteration of function5. change in biochemical charactersitics of proteins6. complete loss of function -changing codon to stop codon |
| Change in biochemical characteristics of proteis | -change in protein stability -temperature effect -pH effect |
| toxic compounds | -100,000 reduced down to 1 that makes it to humans (pharmaceuticals)-ideal test will reduce toxic compounds by 1/2-mutations/lethalities removed |
| Ames test | -detects mutatgenic compounds quickly and cheaply -bacterial assay -Salmunella -reverse mutation -amino acid histodine (his) -biosynthetic pathway -his (minus) need aa to grow |
| auxotroph | mutant bacterial strain that need nutrional (His (minus)) |
| prototroph | does not need his nutrients (His (plus)) |
| liver | -p450 system -Base pair to base pair dial |
| p450 system | -in liver-oxygenases add hydroxyl groups |
| BP-BP | -in liver-mutagenic-activated form of Base pair is mutagenic |
| Clincal Trials | Phase I = 10 pplPhase II = 100 pplPhase III= 1000 ppltakes about 15 years to get to phase III |
| Mutants (Miller 1932) | 1.amorph2.hypomorph3.hypermorph4.antimorph5.neomorph |
| amorph | comlete loss of functionrecessive mutation |
| hypomorph | less than normal functionrecessive mutation |
| hypermorph | more than normal functionrecessive and dominant mutation |
| antimorph | antagonistic to normal function (loss of function)dominant mutation |
| neomorph | new functiongain of functiondominant mutation |
| Prokaryotic vs. Eukaryotic genome | -much smaller-1 circular chromosome-most DNA = coding sequences-operons are a common occurance-introns are rare-plasmids common |
| Prokaryotic circular chromosome | only 1 linkage group vs 23 linear groups in humans (23 linkage groups) |
| Prokaryotic coding sequences | -exons-no extensive splicing mechanisms -very few to no introns-no interrupted genes-plasmids are common -confer antibacterial resistance |
| operon | cluster of functionally related genes which are under regulatory control |
| operon | 1. transcribed by a sinlge mRNA: polycistronic message2. cistron DNA is transcribed then translated to multiple polypeptides -segment of DNA that thru transcription gives rise to a polypeptide3. controlled by a promoter |
| Promoter sequence in a Prokaryote | -10= Pribnow Box-35 |
| Pribnow Box and -35 | set basal rate of transcription |
| repressors | reduce the rate of transcription |
| enhancers | elevate the rate of transcription |
| Lactose operon (structure) | -lac Z - Beta Galatosidase-lac Y - Permease (transport)-lac A - Transacetylase (yields multiple polypeptides)-mRNA is a polycistronic message that has multiple functions-1 unit of DNA yields 3 polypeptide functions |
| lac I | -repressor gene -upstream sequence -operator sequence -favors binding-if repressor is bound to operator there is no expression-no lactose means lac I and thus no expression b/c it prevents transcription of lac operon |
| allosteric site | -binding site for sugar-if lactose is present it binds to allosteric site which changes the confirmation of binding site which leads to transcription and expression of the operon |
| Jacob/Monod (1960's) | -constitutive mutant -lactose operon is always on -even if no lactose strain is present it still expresses the lactose operon-conjugation |
| conjugation | -F+ (male) F Factor (episome) integrated into the chromosome, extra DNA -F- (female)-HFR (aggressive) |
| plasmid | extra DNA |
| episome | piece of DNA that can exist in 2 different states |
| sexual conjugation | partial diploid (merodiploid) to diploid-monitor conjugation by changes in phenotype-E. Coli genome is in minutes (0-100) NOT map units |
| merodiploid | partial diploid thru sexual conjugation |
| lac I-/lac I+ (diploid) | lac I+ = repressor-cannot distinguish between the 2 operators-transdominance-wild type allele produces a difusable product that can move thru space-+lacI phenotype b/c lacI+ is dominant |
| lacI+/lacIs | -repressor S is a protein that lost binding site for lactose-LacI+ is a repressor that can bind to lactose-no expression of lactose operon-also transdominance-lacIs is the dominant allele |
| Oc/Oc | -wild type operator and constitutive operator (lost binding site)-no lactose-operator mutation only affects expression downstream-cis mutation |
| complementation | -phenomenom (observation)-isolate purple eyed mutant-get another purpe eyed mutat-cross both mutants-F1 is either normal or mutant |
| polytene chromosomes | dna replicates but cel does not divide |
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