translation, DNA mutation repair, gene regulation prokaryotes & eukaryotes
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| What is the biological polymerization of amino acids into polypeptide chains? | Translation
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| What materials are required for translation? | amino acids, mRNA, ribosomes, tRNA
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| What is one difference between eukaryotic and prokaryotic ribosomes? | Eukaryotic ribosomes are bigger and consist of more nucleotides
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| rRNA genes are____ repetitive and ___ repeated | moderately; tandemly
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| tRNAs | adapter molecules that have anticodons that base pair with mRNA codons and carry a corresponding amino acid on their 3' end
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| tRNAs contain | post-transcriptionally modified bases which enhance H-bonding efficiency during translation.(about 10% of nucleotides in tRNA are modified)
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| Aminoacyl tRNA synthetase charges (activates) | tRNAs with the appropriate amino acid
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| 20 synthetases; 1 for each type of | amino acid
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| Initiation of translation requires | the small and large ribosomal subunits
GTP
charged initiator tRNA
Mg2+
initiation factors
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| 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
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| Elongation requires both ribosomal subunits assembled with the mRNA in order to form these two sites | peptidyl and aminoacyl sites
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| GTP-dependent release factors cleave the | polypeptide chain from the tRNA and release it from the translation complex
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| termination is signaled by a | stop codon: UAG, UGA, UAA in the aminoacyl site
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| mRNAs with several ribosomes translating at once | Polysomes (or polyribosomes)
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| The eukaryotic equivalent of the Shine-Dalgarno sequence | Kozak sequence
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| Is protein folding co-translational? | yes
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| 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
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| Functional domains | impart different functional capabilities based on folding; exons are proposed to encode these domains; one or more present in proteins
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| Spontaneous mutation | happens naturally; low rates; vary from species to species and gene to gene
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| Induced mutations | result from the influence of an extraneous factor
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| somatic mutations | occur in any cell except germ cells; nontransferable
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| germ-line mutations | occur in gametes, thus making them transferable
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| autosomal mutations | occur within the genes located on autosomes
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| x-linked mutations | occur within genes located on the X chromosome
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| point mutations | one base pair is altered
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| missense mutation | change a codon;change amino acid
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| nonsense mutation | changes a codon into a stop codon causing premature termination of translation
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| silent mutation | alter a codon; no amino acid change
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| transition | pyrimidine altered to another pyrimidine or purine altered to another purine
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| transversion | pyrimidine altered to a purine or vice versa
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| frameshift mutations | insertions or deletions of a base pair
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| 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
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| "slippage" leads to | small insertions or deletions
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| tautomeric shifts(spontaneous, transient repositioning of hydrogen atom) | can result in mutations due to anomalous base pairing
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| DNA damage by ___ and __ are the most common cause of spontaneous mutation | depurination; deamination
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| depurination | loss of a purine base
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| deamination | amino group in cytosine or adenine is converted to uracil and adenine is converted to hypoxanthine
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| transposons act as | naturally occurring mutagens
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| alkylating agents donate alkyl groups to amino or keto groups resulting in | transition mutations
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| intercalating agents | cause frameshift mutations by inserting between purines and pyrimidines; causes distortions which lead to replication errors
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| UV radiation creates | pyrimidine dimers which distort the DNA conformation causing replication errors
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| ionizing radiation(gamma rays,xrays,cosmic rays) | mutagenic; transform stable molecules into free radicals
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| most human genetic diseases are | polygenic but there are some monogenic diseases
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| trinucleotide repeats | normal: <30; affected >200
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| CAG repeats | found in coding regions like the polyglutamic tract or in non coding regions like toxic RNAs that sequester regulatory proteins
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| individuals with type O blood | lack glycosyltransferase activity
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| DNA proofreading | DNA polymerase III is able to recognize and correct errors in replication; catches 99% of errors
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| Mismatch repair | corrects errors that remain after proofreading
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| post replication repair | DNA replication skips over a lesion and requires homologous recombination mediated by the RecA protein
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| SOS repair system in E.Coli | allows DNA synthesis to become error-prone
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| photoreactivation repair | in E.coli removes thymine dimers caused by UV light; depends on the activity of the photoreactivation enzyme(PRE)
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| Two types of excision repair | 1)Base excision repair(BER)
2)Nucleotide excision repair (NER)
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| Excision repair requires three steps | 1)removal of mutation(nuclease)
2)gap filling(DNA polymerase)
3)sealing of the nick (DNA ligase)
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| 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
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| Nucleotide excision repair (NER) | multienzyme complex scans the DNA for distortions
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| DNA double strand break repair in eukaryotes | activated when both strands are cleaved; nonhomologous end joining & homologous recombinational repair are the two types
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| 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
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| The Ames test | uses strains of Salmonella typhimurium with increased sensitivity to mutagens to reveal the presence of specific types of mutations
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| Inducing mutations can involve these processes | 1)ionizing radiation
2)Chemicals-ethylmethanesulfonate(EMS), nitrosoguanidine
3)Transposons
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| transposons | insert into a gene coding or regulatory region
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| Chemicals - ethyl methane sulfonate (EMS), nitrosoguanidine | single base pair changes, deletions, insertions
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| ionizing radiation | chromosomal breaks, deletions, translocations
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| genetic screen | visual or biochemical examination of large numbers of mutagenized organisms
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| Bacteria often respond to environmental change by | regulating transcription
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| Jacob and Monod's operon model | a group of genes is regulated and expressed together as a unit
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| The structural genes of the lac operon are transcribed as a | polycistronic mRNA
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| operon | a cluster of functionally related genes undeer coordinated control by a single on-off "switch"
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| 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
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| lactose metabolism in E.coli is regulated by an ___ _____ | inducible system
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| lac Z gene | encodes for beta galactosidase which converts lactose into glucose and galactose
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| lac Y gene | encodes for permease which transports lactose into the bacterial cell
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| lac A gene | encodes for transacetylase which may be involved in the removal of toxic by-products of lactose digestion from the cell
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| 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
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| lac I | regulates transcription of the structural genes by producing a repressor molecule
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| regulatory elements are almost always located____ | upstream of the gene cluster they control; cis-acting
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| molecules that bind cis-acting sites are ______ ____ | trans-acting elements
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| 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
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| if glucose and lactose are both present which does the cell prefer to use? | glucose, because it requires one less step of metabolism
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| maximal expression requires | no repressor bound at the operator and CAP must be bound at the CAP-binding site
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| 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
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| 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
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| ___ ___ analysis of repressor complexes has confirmed the operon model | crystal structure analysis
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| binding of repressor to operators O1 and O3 creates ___ __ which prevents access of RNA polymerase to promoter | repression loop
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| binding of the ___ ___ ___ at a cis-acting site can regulate the gene cluster both positively and negatively | trans-acting element
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| positive regulation | turns on transcription
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| negative regulation | turns off transcription
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| Trp operon operator is bound by the repressor in the _______ of tryptophan | presence; the trp operon is a catabolic pathway
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| 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
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| attenuator | a regulatory sequence on a leader sequence that precedes trp structural genes
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| 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
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| 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
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| trp present: _____ structures formed act as a transcriptional terminator | hairpin
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| trp absent: a different hairpin forms and act as as an ____ and transcription proceeds | antiterminator
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| other operons that utilize attenuation include | threonine, histidine, leucine, and phenylalanine
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| B. subtilis utilizes _____ instead of the ribosome stalling mechanism of attenuation | TRAP (trp RNA-binding attenuation protein)
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| a fully saturated TRAP can bind to 5' leader sequence to form ___ ____ and prevemt the formation of the ___ ____ | terminator hairpin; antiterminator hairpin
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| uncharged tRNAtrp induces expression of the _____ gene, which sends the signal that trp is scarce | anti-TRAP (AT)
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| The AT protein | associates with TRAP in the tryptophan activated state and inhibits binding to the target leader RNA sequence
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| trypanosome vsg genes are ___ regulated | temporally. in multicellular eukaryotes these genes are also spatially regulated
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| prokaryotes ____ and ___; eukaryotes ____ and ____ | grow; divide; develop; differentiate;
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| 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
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| 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
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| ___ __ in B-cells contribute to antibody diversity | DNA rearrangement
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| random recombination: how many different LV and J regions? | 30-50 different functional LV regions/ 5 different J regions
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| 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)
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| chromatin modification can | regulate gene expression
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| changes to nucleosomes: | 1)histone variants
2)Histone modification
3)chromatin remodeling
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| histone modification | chemical modification of histone tails alters the structure of chromatin, making genes accessible or inaccessible for transcription
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| 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
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| histone code | sum of complex patterns and interactions of histone modifications that change chromatin organization and gene expression
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| chromatin remodeling | repositioning of nucleosomes lets different chromosomal region become accessible to transcription proteins. an example is SWI/SNF
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| 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
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| 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
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| CpG islands | located in and near promoter sequences and adjacent to genes
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| epigenetic trait | a stable, mitotically and meotically heritable phenotype that results from changes in gene expression without alterations in the DNA sequence
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| three major epigenetic mechanisms | 1)DNA methylation
2)histone modification
3)RNA interference
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| whether methylation is beneficial or detrimental depends on | the particular gene and on the environment
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| transcriptionally inert regions are often found to be | hypermethylated
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| methylation patterns are ____ and ___ | tissue-specific; heritable
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| 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
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| 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
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