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106 Cards in this Set
- Front
- Back
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Highly transcribed genes are ______ during interphase while silent regions are ______
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decondensed; condensed
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Describe the bacterial chromosome.
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-circular dna
-highly organized -localized in nucleoid condensation depends on supercoiling |
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What does negative supercoiling promote?
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strand separation, facilitation of DNA replication and transcription
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What is a chromatosome?
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a nucleosome which folds up to produce a fibre and loops, plus H1
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What is a histone?
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small protein rich is arginines and lysines that makes contact with phosphates of DNA; can be highly modified at N-terminus
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What is HMG?
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small non-histone protein that binds to DNA in A-T rich regions and induces DNA bending and looping; important for transcription, enhancer function, DNA replication and recombination
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Which proteins are involved in gene expression?
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TFs, chromatin modifying factors, chromatin remodelling complexes, RNA polymerases, transcription machinery
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What is the shelterin complex?
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protein in eukaryotes which caps and protects telomeres
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What does the core particle consist of?
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DNA wrapped two times around an octamer of 8 histones including two copes of H2A, H2B, H3, H4
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How is a chromatid formed?
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chromatin is further condensed to form helical fibers which form loops of DNA that are also further condensed
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What are telomeres?
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repeated sequences (cytosine nucleotides at 5' end followed by A-T rich sequences) at end of chromosomes; protects cap and stabilizes chromosome; provides means of replication for end
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What is senescence?
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irreversible growth arrest caused by telomere shortening
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Describe complimentary strand to telomeres.
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g-rich, protrudes as single stranded, invades double stranded region to form a t-loop that protects end of chromosome
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What are telomere-associated sequences?
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adjoin telomeric repeats, consist of thousands of complex, varied repeats
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What elements do artificial chromosomes require?
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origin of replication, centromere, telomeres
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What is satellite DNA?
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highly repetitive DNA sequences, migrate as a separate DNA fraction following centrifugation at high speed; T-rich and low density
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What is the structure of RNA?
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single stranded polynucleotide chain that forms an extensive secondary structure, uracil replaces thymine, sugar is ribose with 2' OH group
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How is the transcriptional unit organized?
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functionally including a promoter region which determines transcriptional initiation, RNA-coding region, terminator sequence
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What is the promoter structure in prokaryotes?
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two separate sequences, -10 consensus or Prinbnow and -35 sequence
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What is RNAP responsible for?
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Synthesis of all RNA species in the cell except for RNA primers required for DNA replication
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What is RNAP?
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multi subunit enzyme composed of a core enzyme, DNA binding unit, sigma factor, forms holoenzyme
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What are two features of Rho independent factors?
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inverted repeats forming secondary structure in RNA that induce pausing, stretch of uracils in RNA that generate an unstable DNA-RNA hybrid
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How is RNAP recruited?
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rRNA B promoter, cAMP-regulated promoter
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What is RNAP1 responsible for?
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expression of rRNA
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What is RNAP2 responsible for?
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expression of mRNA, snRNA, miRNA
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What is RNAP3 responsible for?
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expression of rRNA, tRNA, snRNA and other small RNA species
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What is transcription in eukaryotes controlled by?
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state of chromatin condensation
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Which three complexes are required for recruitment of the general transcription machinery?
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scaffold which brings TFs, chromatin modifying complexes which promote histone acetylation and makes promoter region more accesible, and chromatin remodelling complexes which have ATPase activity and are capable of moving histones or nucleosomes
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What is a transcription factor?
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factor bindig to upstream regulatory elements, including enhancers, in a sequence specific manner
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What are TAFs and what do they bind to?
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TBP-associated factors, binds to lnr and DPE
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What is the housekeeping gene devoid of?
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TATA box, DPE, BRE or lnr element
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What is the promoter of the housekeeping gene consisted of?
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multiple binding sites for ubiquitously expressed and active TFs such as Sp1 or Oct
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What is an enhancer?
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combination of distal regulatory elements, can work at a great distance, position-independent, orientation-dependant, bound by enhancesome
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What is PIC?
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complex consisting of several transcription factors including TF2B, TF2D and RNAP2; assembled sequentially leading to recruitment of RNAP2
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What is CTD? What does it do?
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The carboxyl terminal domain of largest subunit of RNAP2, governs promoter clearance and beginning of elongation, composed of tandom repeats, recognition platform for: capping enzymes, splicing factors, cleavage and polyadenylation factors
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What do all three RNAPs depend on for termination?
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A-U rich sequences
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What are the functions of coactivators?
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-chromatin modification
-recruitment of GTM -regulation of activator activity -integration of gene expression |
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What is HAT?
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Histone acetyl transferase, activity of coactivators targets N-terminus of histones, promotes chromatin decondensation and gene activation
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Which proteins are involved in capping?
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RNA triphosphatase, guanylyl transferase, methyl transferase, cap binding complex
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What is the function of capping?
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mRNA stability, coupling to splicing, mRNA export, mRNA translation
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What is the function of poly(a) tail?
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protection, translatability
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Describe group 1 splicing introns
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found in rRNAs in protists, some mitochondrial genes in fungi and bacteriophage
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Describe group 2 splicing introns
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found in some mitochondrial genes, splicing involves formation of lariat intermediate, suggests nuclear pre-mRNA origin
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What is alternative splicing?
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mechanism that generates functionally different gene products through interaction of a splicing junction with accessory factors
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What is involved in RNA editing?
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-generation of mature RNA sequences
-observed in mRNA, tRNA and rRNA -base conversion by deaminases -nucleotide insertion by gRNA -cleavage by endonucleases uridylate added by TUTase -mature generated by RNA ligases |
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What is the structure and function of tRNA?
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-small
-transport amino acids to ribosome -interact with codons in mRNA to govern insertion of amino acids -have rare modified bases generated post-transcriptionally -often trimmed |
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Significance of snoRNAs?
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small nucleolar RNAs involved in base pairing with rRNA precurser guiding rRNA processing events
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List some features of lncRNAs
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-lack of ORF
-expressed at low levels -enriched in polyA -spliced -less conserved -nuclear |
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What is HOTTAIR's role in gene repression?
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lincRNA involved in recruitment of PcB
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What is HOTTIP's role in gene activation?
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lincRNA involved in recruitment of trithorax/ML11
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What is heterochromatin?
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condensed chromatin found at highly repetitive dna
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What is the role of PcG complex?
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-highly regulated silent chromatin
-maintains cell-lineage identity -important for developmental processes |
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How is transcription controlled?
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acetylation-deacetylation, methylation
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How can spurious transcription occur?
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H3K36 is not recruited
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What is H3K4me3 associated with?
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H3/H4 acetylation, chromatin decondensation, gene activation
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What is H3K36me3 associated with?
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H3/H4 deacetylation, chromatin condensation, gene repression
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What is DNA methylation a mark of?
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Silencing
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How does DNA methylation promote silencing?
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-interferes with binding of transcription initiation complexes to promoter
-inhibits RNAP2 -recruits factors acting as repressors |
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Explain progeria.
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Disease caused by defects in the nuclear lamina (point mutation in A) in which chromatin modification is severely disturbed.
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What are microRNAs?
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-small regulatory, noncoding RNAs
-target mRNAs and cause translational repression or degredation |
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How does translation in prokaryotes begin?
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shine-dalgamo sequence
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What are the steps of translation in prokaryotes?
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1) tRNA charging
2) Initiation 3) Elogation 4) Termination and peptide release |
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What are the beginning steps of translation in eukaryotes?
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1) initiation codon is found within kozak sequence
2) RNA helicase unwinds secondary structure of mRNA 3) assembly of ribosome occurs after AUG |
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What are two components of the translational apparatus?
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1) eIF4E: cap binding protein
2) eEF1A2: elongation factor *both oncogenic when overexpressed |
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What are oncomirs?
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miRNAs acting as dominant oncogenes, promote formation of cancer cells
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What are transposable elements?
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DNA sequences that can move from one location to another in the genome
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What is different between class 1 and 2 transposable elements?
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class 1 replicates through an RNA intermediate and function by retrotransposition while class 2 uses a cut and paste mechanism
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What does expression of inverted repeats trigger?
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RNA interference, transcript degradation and chromatin silencing
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What are retrotransposons?
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mutagenic DNA transposons which can create deletions, promote chromosomal rearrangements and lead to gene duplication
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What does RISC initiate?
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RNA degradation and chromatin silencing at transposable elements
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What does transposon silencing depend on?
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RISC, H3K9 methylation, HP1, DNA methylation
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What acts as the master regulators of silencing in X-inactivation?
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lncRNAs
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Why does X-inactivation occur?
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Females have two copies of each gene and cell must compensate
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What are ways cell can compensate for extra genes?
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-increasing expression of single X in males
-decreasing expression from two X in females -turning off expression of one X in females |
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What is an epigenetic phenomenon?
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a heritable change in gene expression that does not involve a change in DNA sequence
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Is Xic sufficient and necessary for X-inactivation?
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Yes
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What is Xic's role in X-inactivation?
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-determines all steps in silencing process including X chromosome counting, selecting, and silencing
-encodes several lncRNAs including Xist |
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What is Xist's role in X-inactivation?
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RNA expression on X-chromosome is selected for in-activation, coating the chromosome, initiates silencing by recruiting chromatin modifying and remodelling complexes
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What is the effect of imprinting?
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expression of gene is determined by whether the gene is inherited from the mother or father
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What do imprinting regions depend on?
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imprinting control region (ICR)
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What is the difference between paternal and maternal imprinting?
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Paternally expressed genes promote embryonic growth for competition while maternally expressed genes inhibit growth to conserve resources
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What are the two modes of imprinting?
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-control of insulator function by DNA methylation
-control of Igf2 receptor by lncRNA |
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LncRNA involved in imprinting work in _____
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cis
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What is prader-willi syndrome?
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-disease where infants are small, weak and have poor feeding for first 6 m of age and then after 12 m eating increases uncontrollably
-from deletion that is paternally inherited -symptoms due to lack of function SNRPN |
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What is angelman syndrome?
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-disease causing motor and mental retardation, hyperactivity
-from deletion that is maternally inherited -symptoms due to lack of function of gene involved in ubiquitination pathways known as UBE3A |
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What are the major classes of cancer?
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-carcinomas: arising from epithelium
-sarcomas: arising from cells supporting tissue -leukemias and lymphomas: arising from cells of the hematopoietic system |
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What are some properties of transformed cancer cells?
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-altered morphology
-proliferation without constraints -immortalization -block to differentiation -escape from apoptosis -tumorigenic -capacity to invade |
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What are oncogenes?
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behave as gain of function mutations, wildtype has positive effect on cell proliferation
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What are tumor suppressors?
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mutations are lack of function, wildtype is required to prevent cell proliferation
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What are mutator genes?
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required to maintain genomic stability
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What are oncoproteins? Examples?
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-function in controlling cell proliferation
-ex. growth factors, receptors, TFs, cell cycle regulators |
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How can over-expression be obtained?
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-transduction in a retrovirus
-promoter insertions -gene amplification -chromosomal rearrangement |
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Why are mutations in tumor supressor genes recessive?
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Both alleles need to be knocked out
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What is retinoblastoma?
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rare tumor of the retina, familial or sporadic form, deletion in the Rb locus
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What is the multi-hit model?
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When one mutant allele is inherited from parent and second allele is lost, giving rise to cancer, loss of heterozygosity
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What is the function of Rb?
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It interacts with a number of cellular proteins forming a transcriptional repressor complex that recruits chromatin modifying complexes
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How are TSGs silenced?
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DNA methylation or hypermethylation
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RF of unlinked genes
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50%
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RF of linked genes
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<50%
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What is a testcross?
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cross between two individuals that are homozygous at each gene loci with respect to one parent and complimentary at each gene loci with respect to the other parent
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What is inference?
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When the crossover in one interval reduced the probability that additional crossovers will occur nearby
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When is recombination frequency actually representative of map distance?
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When distance is short (7mu) because it is likely there will only be one crossover
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What is a DNA marker?
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a locus with known location that come in identifiable variations/alleles in population
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Describe RFLP
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-Technique where DNA is cut with restriction enzymes which recognize specific DNA sequences
- Fragments are places in agarose gel wells and ran through electric current -fragments move according to size -radiolabelled probe is added |
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How can microsatellites be identified?
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PCR amplification or gel electrophoresis
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What is huntingtons disease?
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-dominant degenerative disorder with allele on short arm of chromosome 4
-causes cel death of medium sized spiny neurons in striatum |
