Exam 3 updates flash card set

"Term"

"Definition"

"Ch16: Inducible vs repressible systems"

"Inducible = OFF by default

"Ch16: Positive vs negative control"

"Negative control = regulatory protein is a repressor that inhibits transcription when active. Positive control = regulatory protein is an activator that stimulates transcription when active."

"Ch16: Default gene state in prokaryotes vs eukaryotes"

"Prokaryotes = default ON; repression is common. Eukaryotes = default OFF; induction is common."

"Ch16: Cis vs trans factors"

"Cis-acting = DNA sequence on the same DNA molecule as the gene (promoter

"Ch16: How to decide if a mutation is in a cis element or trans element"

"Use merozygotes. If a WT allele provided in trans rescues the mutant phenotype

"Ch16: Structural components of the lac operon"

"Regulatory region = promoter P and operator O. Structural genes = lacZ

"Ch16: How LacI negatively controls the lac operon"

"No lactose: LacI repressor binds operator and blocks RNA polymerase. Lactose present: allolactose binds repressor

"Ch16: Functions of lacZ

lacY

"Ch16: I- and Oc constitutive mutations"

"I- = mutant repressor cannot bind operator

"Ch16: Is mutation"

"Superrepressor. Repressor cannot bind inducer lactose

"Ch16: How CAP exerts positive control over lac operon"

"CAP binds cAMP. CAP-cAMP complex binds the CAP-binding site near the promoter and facilitates RNA polymerase binding

"Ch16: Relationship between glucose and cAMP"

"High glucose = low cAMP = CAP cannot bind = low transcription. Low glucose = high cAMP = CAP binds = high transcription."

"Ch16: Conditions for maximum lac operon transcription"

"Lactose present so repressor is inactive

"Ch16: Structure of the trp operon"

"Regulatory region = promoter trpP

"Ch16: How tryptophan represses the trp operon"

"Tryptophan acts as a corepressor. Tryptophan binds Trp repressor

"Ch16: How attenuation works in the trp operon"

"Leader region trpL contains two Trp codons. High Trp: ribosome translates quickly

"Ch16 Practice: A mutant E. coli has a nonfunctional lacI gene. Will lacZ be expressed in the absence of lactose?"

"Yes. Without functional repressor

"Ch16 Practice: In a merozygote with genotype I+ Oc Z+ / F' I- O+ Z+

will beta-galactosidase be expressed in the absence of lactose?"

"Ch16 Practice: Why does glucose repress lac operon expression even when lactose is present?"

"High glucose causes low cAMP

"Ch17: Key differences between eukaryotic and prokaryotic gene regulation"

"Eukaryotes: DNA packaged in chromatin

"Ch17: Composition of nucleosomes"

"DNA about 147 bp wrapped around a histone octamer: two copies each of H2A

"Ch17: How histone modifications affect DNA accessibility"

"Acetylation by HATs reduces positive charge on histones

"Ch17: Types of histone modifications"

"Acetylation on lysine usually activates. Methylation on lysine or arginine can activate or repress. Phosphorylation on serine or threonine has various roles. Also ubiquitination and sumoylation."

"Ch17: Core promoter vs proximal promoter"

"Core promoter surrounds the transcription start site and binds general TFs and Pol II; it determines basal transcription level. Proximal promoter elements lie about 50-200 bp upstream

"Ch17: Common core promoter elements"

"TATA box about -25 to -30

"Ch17: General vs specific transcription factors"

"General TFs such as TFIIA

"Ch17: Two functional domains on a transcription factor"

"1. DNA-binding domain recognizes specific cis-regulatory sequences. 2. Activation or repression domain interacts with cofactors and other regulatory proteins to affect transcription."

"Ch17: How enhancers regulate transcription at a distance"

"Enhancers bind activators. DNA looping brings enhancer-bound activators close to the promoter. Activators contact Mediator and general TFs to increase transcription frequency."

"Ch17: Ways activators increase transcription strength"

"Recruit chromatin remodelers such as SWI/SNF to open chromatin. Recruit HATs to acetylate histones. Contact TFIID or TFIIB directly. Recruit Mediator to stabilize Pol II initiation. Promote enhancer-promoter looping."

"Ch17: How GAL4

GAL80

"Ch17: How the GAL system is repressed by glucose"

"High glucose causes Mig1 to accumulate. Mig1 binds the Mig1 site in the GAL regulatory region and recruits Cyc8-Tup1 corepressor

"Ch17 Practice: A mutation in the TATA box of a gene would affect binding of which factor?"

"TFIID

"Ch17 Practice: If you deleted the GAL80 gene in yeast

would GAL genes be expressed in the absence of galactose?"

"Ch17 Practice: What would happen if you deleted the GAL4 gene?"

"GAL genes would never be transcribed because GAL4 is the activator required for transcription

"Ch18: Steps involved in RNA processing"

"1. 5' capping with 7-methylguanosine via a 5'-5' triphosphate linkage. 2. 3' polyadenylation: cleavage at AAUAAA signal and addition of poly(A) tail. 3. Splicing: removal of introns by the spliceosome and joining of exons."

"Ch18: Function of the 5' cap"

"Protects mRNA from 5' to 3' exonucleases such as XRN1. Recruits cap-binding proteins such as eIF4E. Required for translation initiation. Important for mRNA export and stability."

"Ch18: Function of the poly(A) tail"

"Protects mRNA from 3' to 5' degradation. Binds poly(A)-binding proteins. Promotes translation through closed-loop translation. Supports mRNA export."

"Ch18: Types of introns and their splicing mechanisms"

"Spliceosomal introns are removed by the spliceosome and form a lariat; most common in eukaryotic mRNA. Group I introns self-splice with a free guanosine and release linear intron. Group II introns self-splice with internal adenosine and form a lariat intermediate. tRNA introns are removed by protein enzymes."

"Ch18: Steps of spliceosome-mediated splicing"

"U1 binds 5' splice site and U2 binds branch point A. U4/U6-U5 complex joins. U1 and U4 leave; U2 and U6 form catalytic core. Branch-point A 2'-OH attacks 5' splice site

"Ch18: Alternative splicing"

"Different combinations of exons are joined to produce multiple mRNA isoforms from a single pre-mRNA. About 90 percent of human genes undergo alternative splicing. Types include cassette exons

"Ch18: How alternative splicing controls Drosophila sex determination"

"XX female: Sxl protein directs female-specific splicing of tra

"Ch18: Nonsense-mediated decay (NMD)"

"mRNA surveillance pathway that degrades mRNAs with premature termination codons. Splicing deposits exon junction complexes. Normal mRNA: ribosome removes EJCs. PTC mRNA: ribosome stops early

"Ch18: Difference between siRNA and miRNA"

"siRNA is derived from long dsRNA such as viral RNA and guides cleavage of target mRNA with exact complementarity. miRNA is derived from hairpin precursors and guides translational repression and mRNA decay

"Ch18: How miRNA silencing works"

"Pri-miRNA is transcribed in nucleus and processed by Drosha to pre-miRNA. Exported to cytoplasm and processed by Dicer to miRNA duplex. One strand loads into RISC with Argonaute. miRNA guides RISC to target mRNA 3' UTR. Partial complementarity causes translational repression and mRNA decay."

"Ch18: Cytoplasmic polyadenylation"

"Regulation of translation by controlling poly(A) tail length in cytoplasm. Dormant state: CPEB binds CPE

"Ch18 Practice: A mutation that destroys the 5' cap of an mRNA would affect what?"

"The mRNA would be rapidly degraded by XRN1 5' to 3' exonuclease

"Ch18 Practice: In SMA

why does SMN2 not fully compensate for loss of SMN1?"

"Ch18 Practice: How does the drug Spinraza treat SMA?"

"Spinraza is an antisense oligonucleotide that binds intron 7 of SMN2 pre-mRNA

"Ch19: Epigenetic trait"

"A stable

"Ch19: Three major mechanisms of epigenetic changes"

"1. DNA methylation

"Ch19: Biochemical basis of DNA methylation"

"A methyl group is added to the 5-carbon of cytosine to make 5-methylcytosine. Catalyzed by DNA methyltransferases. Occurs mainly at CpG dinucleotides

"Ch19: CpG islands"

"Regions of high CpG density often located in or near promoter sequences. About 70 percent of gene promoters are associated with CpG islands. Usually unmethylated in active genes; methylated CpG islands cause gene silencing."

"Ch19: How DNA methylation is maintained during DNA replication"

"DNMT1 is the maintenance methyltransferase and recognizes hemimethylated DNA. It is recruited to the replication fork by UHRF1

"Ch19: How DNA methylation causes transcriptional silencing"

"Methyl groups occupy the major groove and block transcription factor binding. They recruit methyl-CpG-binding proteins such as MBD2

"Ch19: How histone modification is maintained during DNA replication"

"Parental histones with their modifications are segregated onto both daughter strands. Reader-writer complexes recognize existing marks on parental histones and recruit writer enzymes to place the same marks on new histones. This creates a self-propagating epigenetic feedback loop."

"Ch19: Types of monoallelic expression"

"1. Parent-of-origin imprinting: only maternal or paternal allele expressed. 2. Random X-chromosome inactivation: one X randomly silenced in female cells. 3. Random autosomal inactivation: random choice of one allele

"Ch19: How imprinting leads to parent-specific allele expression"

"Differential methylation of CpG-rich imprinting control regions during gametogenesis. Imprints are erased in primordial germ cells and reset according to the sex of the individual. Example IGF2/H19: paternal ICR methylated so CTCF cannot bind and enhancer activates IGF2; maternal ICR unmethylated so CTCF binds and blocks enhancer

"Ch19: Beckwith-Wiedemann Syndrome (BWS)"

"Imprinting disorder caused by abnormal methylation. Maternal chromosome gains methylation at the ICR and resembles the paternal pattern. Maternal IGF2 is activated and maternal H19 is silenced. IGF2 is expressed from both alleles

"Ch19: How X chromosome inactivation works"

"Occurs in female mammals; about half of cells inactivate maternal X and half paternal X. Xic contains XIST and TSIX. XIST is a long noncoding RNA that coats the X in cis and recruits silencing complexes such as PRC2

"Ch19: Relationship between maternal nurturing and GR expression in rats"

"High maternal nurturing: increased serotonin

"Ch19: How epigenetic changes contribute to cancer"

"Global hypomethylation is common in cancers and causes genomic instability. Focal hypermethylation silences tumor suppressor promoters at CpG islands. Hypermethylated genes include DNA repair

"Ch19 Practice: If a gene's promoter CpG island becomes hypermethylated

what happens to its expression?"

"Ch19 Practice: A female cat has tortoiseshell fur with patches of orange and black. What explains this pattern?"

"Random X-chromosome inactivation. Different cells randomly inactivate either the maternal or paternal X chromosome. The X chromosome carries the orange/black fur color gene

"Ch19 Practice: Why are imprinted genes important for prenatal growth?"

"Most imprinted genes regulate growth. Proper imprinting ensures balanced expression

"Summary: Prokaryote vs eukaryote regulation comparison"

"Prokaryotes: default ON

"Summary: lac vs trp vs GAL systems"

"lac operon: allolactose inducer