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Genetics test#2
translation, DNA mutation repair, gene regulation prokaryotes & eukaryotes
| Question | Answer |
|---|---|
| What is the biological polymerization of amino acids into polypeptide chains? | Translation |
| What materials are required for translation? | amino acids, mRNA, ribosomes, tRNA |
| What is one difference between eukaryotic and prokaryotic ribosomes? | Eukaryotic ribosomes are bigger and consist of more nucleotides |
| rRNA genes are____ repetitive and ___ repeated | moderately; tandemly |
| tRNAs | adapter molecules that have anticodons that base pair with mRNA codons and carry a corresponding amino acid on their 3' end |
| tRNAs contain | post-transcriptionally modified bases which enhance H-bonding efficiency during translation.(about 10% of nucleotides in tRNA are modified) |
| Aminoacyl tRNA synthetase charges (activates) | tRNAs with the appropriate amino acid |
| 20 synthetases; 1 for each type of | amino acid |
| Initiation of translation requires | the small and large ribosomal subunits GTP charged initiator tRNA Mg2+ initiation factors |
| Initiation of translation in bacteria requires this sequence that procedes the AUG start codon. This sequence pairs with the 16S rRNA of the 30S small ribosomal subunit | Shine-Dalgarno |
| Elongation requires both ribosomal subunits assembled with the mRNA in order to form these two sites | peptidyl and aminoacyl sites |
| GTP-dependent release factors cleave the | polypeptide chain from the tRNA and release it from the translation complex |
| termination is signaled by a | stop codon: UAG, UGA, UAA in the aminoacyl site |
| mRNAs with several ribosomes translating at once | Polysomes (or polyribosomes) |
| The eukaryotic equivalent of the Shine-Dalgarno sequence | Kozak sequence |
| Is protein folding co-translational? | yes |
| post-translational modification consists of: | 1)N-terminal amino acid removed/modified 2)individul amino acid residues sometimes modified 3)carbohydrate side chains may be attached 4)polypeptide chains may be trimmed 5)signal sequences are removed 6)polypeptide chains often complexed with metals |
| Functional domains | impart different functional capabilities based on folding; exons are proposed to encode these domains; one or more present in proteins |
| Spontaneous mutation | happens naturally; low rates; vary from species to species and gene to gene |
| Induced mutations | result from the influence of an extraneous factor |
| somatic mutations | occur in any cell except germ cells; nontransferable |
| germ-line mutations | occur in gametes, thus making them transferable |
| autosomal mutations | occur within the genes located on autosomes |
| x-linked mutations | occur within genes located on the X chromosome |
| point mutations | one base pair is altered |
| missense mutation | change a codon;change amino acid |
| nonsense mutation | changes a codon into a stop codon causing premature termination of translation |
| silent mutation | alter a codon; no amino acid change |
| transition | pyrimidine altered to another pyrimidine or purine altered to another purine |
| transversion | pyrimidine altered to a purine or vice versa |
| frameshift mutations | insertions or deletions of a base pair |
| neutral mutations | (vast majority of all mutations) occur in genes or portions of the genome that don't contain genes; have no effect on gene products |
| "slippage" leads to | small insertions or deletions |
| tautomeric shifts(spontaneous, transient repositioning of hydrogen atom) | can result in mutations due to anomalous base pairing |
| DNA damage by ___ and __ are the most common cause of spontaneous mutation | depurination; deamination |
| depurination | loss of a purine base |
| deamination | amino group in cytosine or adenine is converted to uracil and adenine is converted to hypoxanthine |
| transposons act as | naturally occurring mutagens |
| alkylating agents donate alkyl groups to amino or keto groups resulting in | transition mutations |
| intercalating agents | cause frameshift mutations by inserting between purines and pyrimidines; causes distortions which lead to replication errors |
| UV radiation creates | pyrimidine dimers which distort the DNA conformation causing replication errors |
| ionizing radiation(gamma rays,xrays,cosmic rays) | mutagenic; transform stable molecules into free radicals |
| most human genetic diseases are | polygenic but there are some monogenic diseases |
| trinucleotide repeats | normal: <30; affected >200 |
| CAG repeats | found in coding regions like the polyglutamic tract or in non coding regions like toxic RNAs that sequester regulatory proteins |
| individuals with type O blood | lack glycosyltransferase activity |
| DNA proofreading | DNA polymerase III is able to recognize and correct errors in replication; catches 99% of errors |
| Mismatch repair | corrects errors that remain after proofreading |
| post replication repair | DNA replication skips over a lesion and requires homologous recombination mediated by the RecA protein |
| SOS repair system in E.Coli | allows DNA synthesis to become error-prone |
| photoreactivation repair | in E.coli removes thymine dimers caused by UV light; depends on the activity of the photoreactivation enzyme(PRE) |
| Two types of excision repair | 1)Base excision repair(BER) 2)Nucleotide excision repair (NER) |
| Excision repair requires three steps | 1)removal of mutation(nuclease) 2)gap filling(DNA polymerase) 3)sealing of the nick (DNA ligase) |
| Base excision repair (BER) | DNA glysolyase enzymes recognize specific bases; enzyme cleaves the glycosyl bond that connects a particular recognized base to the back bone sugar, removing it from the DNA |
| Nucleotide excision repair (NER) | multienzyme complex scans the DNA for distortions |
| DNA double strand break repair in eukaryotes | activated when both strands are cleaved; nonhomologous end joining & homologous recombinational repair are the two types |
| Homologous recombinational repair | digest back the 5' ends of the broken helix; 3' ends interact with a region of undamaged sister chromatid; DNA polymerase copies the undamaged DNA sequence into the damaged strand |
| The Ames test | uses strains of Salmonella typhimurium with increased sensitivity to mutagens to reveal the presence of specific types of mutations |
| Inducing mutations can involve these processes | 1)ionizing radiation 2)Chemicals-ethylmethanesulfonate(EMS), nitrosoguanidine 3)Transposons |
| transposons | insert into a gene coding or regulatory region |
| Chemicals - ethyl methane sulfonate (EMS), nitrosoguanidine | single base pair changes, deletions, insertions |
| ionizing radiation | chromosomal breaks, deletions, translocations |
| genetic screen | visual or biochemical examination of large numbers of mutagenized organisms |
| Bacteria often respond to environmental change by | regulating transcription |
| Jacob and Monod's operon model | a group of genes is regulated and expressed together as a unit |
| The structural genes of the lac operon are transcribed as a | polycistronic mRNA |
| operon | a cluster of functionally related genes undeer coordinated control by a single on-off "switch" |
| Three parts of the operon | 1)operator: stretch of DNA that acts as a regulatory "switch"-usually within the promoter 2)promoter 3)genes that they control |
| lactose metabolism in E.coli is regulated by an ___ _____ | inducible system |
| lac Z gene | encodes for beta galactosidase which converts lactose into glucose and galactose |
| lac Y gene | encodes for permease which transports lactose into the bacterial cell |
| lac A gene | encodes for transacetylase which may be involved in the removal of toxic by-products of lactose digestion from the cell |
| in the absence of lactose, the lac operon | is bound by the lac repressor molecule at the operator, which blocks transcription of the lac genes |
| lac I | regulates transcription of the structural genes by producing a repressor molecule |
| regulatory elements are almost always located____ | upstream of the gene cluster they control; cis-acting |
| molecules that bind cis-acting sites are ______ ____ | trans-acting elements |
| analysis of lac expression in the absence or presence of lactose in ____ ___ ___ was used to prove the operon model for the lac operon | partial diploid merozygotes |
| if glucose and lactose are both present which does the cell prefer to use? | glucose, because it requires one less step of metabolism |
| maximal expression requires | no repressor bound at the operator and CAP must be bound at the CAP-binding site |
| catabolite-activating protein(CAP) | exerts positive control of lac operon; binds the CAP-binding site and facilitates the binding of RNA polymerase at the promoter |
| Can glucose inhibit CAP? if so how? | yes. cAMP is required for CAP binding. glucose represses the expression of adenylyl cyclase, which catalyzes the production of cAMP |
| ___ ___ analysis of repressor complexes has confirmed the operon model | crystal structure analysis |
| binding of repressor to operators O1 and O3 creates ___ __ which prevents access of RNA polymerase to promoter | repression loop |
| binding of the ___ ___ ___ at a cis-acting site can regulate the gene cluster both positively and negatively | trans-acting element |
| positive regulation | turns on transcription |
| negative regulation | turns off transcription |
| Trp operon operator is bound by the repressor in the _______ of tryptophan | presence; the trp operon is a catabolic pathway |
| the binding of tryptophan to its repressor causes | a conformation change in the repressor allowing it to bind to the operator of the trp operon |
| attenuator | a regulatory sequence on a leader sequence that precedes trp structural genes |
| Attenuation | 1)when tryptophan is present: transciption of leader regions still occurs but is abruptly halted before the operon genes are transcribed 2)when tryptophan is absent: transciption proceeds through the entire operon |
| leader sequence can form two conformations depending on the presence or absence of tryptophan | 1) 1&2 + 3&4: transcription termination conformation 2) 2&3: non terminating conformation |
| trp present: _____ structures formed act as a transcriptional terminator | hairpin |
| trp absent: a different hairpin forms and act as as an ____ and transcription proceeds | antiterminator |
| other operons that utilize attenuation include | threonine, histidine, leucine, and phenylalanine |
| B. subtilis utilizes _____ instead of the ribosome stalling mechanism of attenuation | TRAP (trp RNA-binding attenuation protein) |
| a fully saturated TRAP can bind to 5' leader sequence to form ___ ____ and prevemt the formation of the ___ ____ | terminator hairpin; antiterminator hairpin |
| uncharged tRNAtrp induces expression of the _____ gene, which sends the signal that trp is scarce | anti-TRAP (AT) |
| The AT protein | associates with TRAP in the tryptophan activated state and inhibits binding to the target leader RNA sequence |
| trypanosome vsg genes are ___ regulated | temporally. in multicellular eukaryotes these genes are also spatially regulated |
| prokaryotes ____ and ___; eukaryotes ____ and ____ | grow; divide; develop; differentiate; |
| Gene regulation in eukaryotes is ___ ___ than it is in prokaryotes | more complex. regulation can occur at any one of the steps leading from DNA to protein product |
| humoral immunity | B-cells produce immunoglobins that bind antigens; each B-cell produces only one type of immunoglobulin; variable regions allow recognition of a specific antigen |
| ___ __ in B-cells contribute to antibody diversity | DNA rearrangement |
| random recombination: how many different LV and J regions? | 30-50 different functional LV regions/ 5 different J regions |
| two other mechanisms that increase antibody diversity are: | 1) imprecise recombination between any pair of LV and J regions 2) high hypermutation(random somatic mutation) |
| chromatin modification can | regulate gene expression |
| changes to nucleosomes: | 1)histone variants 2)Histone modification 3)chromatin remodeling |
| histone modification | chemical modification of histone tails alters the structure of chromatin, making genes accessible or inaccessible for transcription |
| types of histone modification: | 1) acetylation by histone acetyltransferase(HAT) opens up chromatin 2)removal of acetyl groups by histone deacetylase(HDAC) closes the configuration 3)phosphorylation 4)methylation |
| histone code | sum of complex patterns and interactions of histone modifications that change chromatin organization and gene expression |
| chromatin remodeling | repositioning of nucleosomes lets different chromosomal region become accessible to transcription proteins. an example is SWI/SNF |
| chromatin remodeling complexes may alter nucleosome structure in several ways including | 1)altering contacts between DNA and histones 2)altering the path of the DNA around the nucleosome 3)altering the structure of the nucleosome core itself |
| DNA methylation | is associated with decreased gene expression. the addtion of methyl groups catalyzed by methyltransferase. occurs most often on the cytosine of CpG dinucleotides; clustered regions called CpG islands |
| CpG islands | located in and near promoter sequences and adjacent to genes |
| epigenetic trait | a stable, mitotically and meotically heritable phenotype that results from changes in gene expression without alterations in the DNA sequence |
| three major epigenetic mechanisms | 1)DNA methylation 2)histone modification 3)RNA interference |
| whether methylation is beneficial or detrimental depends on | the particular gene and on the environment |
| transcriptionally inert regions are often found to be | hypermethylated |
| methylation patterns are ____ and ___ | tissue-specific; heritable |
| the incorporation of base analog that cannot be methylated causes what? | a change in the pattern of gene expression by inducing the expression of normally silent genes |
| histone modification and DNA methylation interact to determine availability for transcription | 1)ope n config.=DNA is unmethylated and histones are acetylated, allowing genes to be transcribed 2)closed config.=DNA methylatted at CpG islands and histones are deacetylated. genes can't be transcribed |
Created by:
ESPOLADE
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