BIOL 576: Chapter 3 - Differential Gene Expression 2024-2025. Questions & Correct Answers, Exams of Biology

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BIOL 576: Chapter 3 - Differential Gene

Expression 2024-2025. Questions and Correct

Verified Answers. Graded A

3 mechanisms of control of RNA expression by cytoplasmic location - ANS1. Diffusion and local anchoring (mRNAs can be trapped in certain locations by local proteins)

2. Localized protection (mRNAs can be degraded everyone except a specific location where a localized protein protects them from being destroyed)
3. Active transport along the cytoskeleton (3' UTR of mRNA is recognized by proteins that can bind them to motor proteins that travel along the cytoskeleton to their final destination) 3 ways transcription factors regulate gene expression - ANS1. Recruit histone- modifying enzymes
4. Stabilize RNA polymerase II
5. Coordinate the timing of RNA expression for multiple genes 3' untranslated region (3' UTR) - ANSRegion following the translation termination codon that is not transcribed into a protein; includes an AATAAA sequence needed for polyadenylation

4 levels of gene expression regulation - ANS1. Differential gene transcription

2. Selective pre-mRNA processing
3. Selective mRNA translation
4. Differential post-translational protein modification 5' methylguanosine cap - ANS5' cap on mRNA that protects the transcript from nuclease digestion and is necessary for binding of mRNA to the ribosome for translation 5' untranslated region (5' UTR) - ANSSequence of base pairs intervening between initiation points of transcription and translation; determines the rate at which translation is initiated Alternative pre-mRNA splicing - ANSA means of producing multiple proteins from the same gene by cutting, rearranging, and ligating back together different combinations of exons of pre-mRNA Basal transcription factor - ANSBinds to CpG site on the promoter to help recruit RNA polymerase II to activate transcription

Basic helix-loop-helix (bHLH) - ANSTranscription factor family that contains a DNA- binding domain of two α-helices connected by a loop (ex: MyoD, MITF, daughterless) Basic leucine zipper (bZIP) - ANSTranscription factor family that contains a DNA- binding domain of an alpha helical dimer (ex: cEBP, AP1, MITF) Central dogma - ANSThe sequence of events that enables the use and transfer of information to make the proteins of a cell (DNA → RNA → protein) Chromatin - ANSComplex of DNA and protein (histones) in which eukaryotic genes are contained Cis-regulatory element - ANSRegulatory sequence found on the same chromosome as the gene the element regulates CpG island - ANSA stretch of 1000 CG base pairs often clustered near a promoter region of a gene

Differential gene expression - ANSThe process by which cells become different from one another based upon the unique combination of genes that are expressed Differential gene transcription - ANSRegulates which of the nuclear genes are transcribed into pre-mRNA Differential post-translational protein modification - ANSRegulates which proteins are allowed to remain and function in the cell; some proteins must assemble with other proteins, bind to an ion or functional group, or travel to a specific location to be activated DNA-binding domain - ANSThe site on a transcription factor that recognizes a particular DNA sequence in the enhancer Enhancer - ANSDNA sequence that signals where and when a promoter can be used; helps recruit and stabilize RNA polymerase II to the promoter; the same genes can have more than once enhancer (ex: Pax6 gene has a different enhancer activated in the pancreas, surface ectoderm, neural tube, and retina) Epigenetics - ANSThe study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself

Euchromatin - ANSChromatin regions that are loosely packed together and therefore transcriptionally active; contains most of an organism's genes Exon - ANSRegion of DNA that codes for parts of a protein Gene regulatory network - ANSPattern generated by the interactions among transcription factors and their enhancers that help define the course that development follows Network self-assembles by:

1. The ability of maternal transcription factors to recognize elements of particular genes that encode other transcription factors
2. The ability of the new set of transcription factors to activate paracrine signaling pathways that activate/inhibit specific transcription factors in neighboring cells Genomic equivalence - ANSThe theory that every cell in an organism has the same genome

Genomic imprinting - ANSEpigenetic phenomenon in which variation in phenotype depends on whether an allele is inherited from the male or female parent Heritability of histone methylation patterns - ANSModification of histones signals the recruitment of proteins that retain the memory of the transcriptional state as cells go through mitosis (ex: Trithorax protein family keeps genes active and Polycomb protein family keeps genes repressed) Mechanism:

1. DNA methyltransferase-3 is recruited to chromatin by MeCP2, which methylates previously un-methylated cytosines in the DNA
2. DNA methyltransferase-1 recognizes cytosines on one strand of DNA and places methyl groups on the newly synthesized strand opposite it Heterochromatin - ANSChromatin regions that are tightly packed together and therefore transcriptionally inactive High CpG-content promoters (HCPs) - ANSPromoters with many CpG islands, usually found in developmental control genes; regulate synthesis of transcription factors and developmental regulatory proteins used in the construction of the organism; default state is "on"

Histone - ANSPositively charged protein molecule around which DNA is tightly coiled in chromatin Histone acetylation - ANSAddition of negatively charged acetyl groups to histones via acetyltransferase; destabilizes nucleosome packaging and makes chromatin more euchromatic Histone methylation - ANSAddition of methyl groups to histones via methyltransferase; usually results in a heterochromatic state but can also activate transcription depending on the amino acid being methylated and the presence of other acetyl/methyl groups in the vicinity Homeodomain - ANSTranscription factor family that contains a DNA-binding domain of a conserved sequence of 60 amino acids; involved in regulation of development (ex: Hox, POU, Lim, Pax) Intron - ANSNon-coding region of DNA Low CpG-content promoters (LCPs) - ANSPromoters with few CpG islands, usually found in the genes whose products characterize mature, fully differentiated cells; CpG sites are usually methylated and their default state is "off"

Maternal contributions - ANSThe stored mRNAs and proteins within the cytoplasm of the egg, produced from the maternal genome during the primary oocyte stage; messages stay dormant until activated during fertilization Mechanism of how DNA methylation blocks transcription - ANSMethylation blocks binding of transcription factors as transcription factors cannot bind to DNA if one of its cytosines is methylated; a methylated cytosine can recruit the binding of proteins (ex: MeCP2) that facilitate methylation or de-acetylation of histones microRNA (miRNA) - ANSA small RNA molecule (22 nucleotides) complementary to a portion of a particular mRNA that regulates translation of a specific message; usually bind to the 3' UTR of mRNA to inhibit translation mRNA - ANSprocessed transcript; contains 5' cap, exons spliced together, and 3' polyA tail for stabilization Neural restrictive silencer element (NRSE) - ANSDNA sequence that prevents a promoter's activation in any tissue except neurons Neural restrictive silencer factor (NRSF) - ANSProtein that binds NRSE; expressed in every cell except for mature neurons

Nucleosome - ANSBasic unit of chromatin structure; composed of an octamer of histone proteins (2 copies of H2A, H2B, H3, and H4) wrapped with two loops containing 147bp of DNA with more than a dozen contacts between the DNA and histones Pioneer transcription factor - ANSTranscription factor that can penetrate repressed chromatin and bind to enhancer DNA sequences; begin the process of making a region available for transcription and are critical for specifying certain cell lineages (ex: Sox2, Oct3/4, c-Myc, and Klf-4 bind to closed chromatin to enable cell fate programming and reprogramming in iPSCs) PolyA tail - ANSConfers stability on the mRNA, allows the mRNA to exit the nucleus, and permits the mRNA to be translated into protein pre-mRNA - ANSSingle-stranded polymer of similar molecules; contains cap sequence, 5' UTR, introns, exons, and 3' UTR Promoter - ANSRegion of a gene containing the DNA sequence to which RNA polymerase II binds to initiate transcription; found upstream of the transcription initiation site and typically contain a CpG island

Protein-protein interaction domain - ANSAllows transcription factor activity to be modulated by transcriptional co-regulators or other transcription factors Reporter gene - ANSA gene that encodes a visible marker; can be fused to regulator elements, inserted into embryos, and monitored for reporter gene expression RNA interference (RNAi) - ANSthe process by which miRNA molecules inhibit expression of specific genes by degrading their mRNAs RNA polymerase II - ANSAn enzyme that binds to a promoter on DNA to catalyze transcription of an RNA template from the DNA RNA-induced silencing complex (RISC) - ANSA complex containing several proteins and a miRNA which can bind to the 3' UTR of mRNA and inhibit translation; binding can recruit endonucleases or block binding of initiation factors/ribosomes Selective mRNA translation - ANSRegulates which of the mRNAs in the cytoplasm are translated into proteins; mRNAs can be selectively stabilized at specific times in specific cells (ex: Hu proteins can stabilize groups of mRNA that would otherwise degrade quickly)

Selective pre-mRNA processing - ANSRegulates which parts of the transcribed RNAs can enter the cytoplasm and become mRNAs; pre-mRNA can be spliced into messages that specify different proteins by using different combinations of exons Silencer - ANSDNA sequence that prevents promoter use and inhibits transcription Solenoid - ANSStructure, created from tightly wound nucleosomes stabilized by histone H1, that inhibits transcription of genes by preventing transcription factors and RNA polymerases from gaining access to genes Splicing factor - ANSA protein that regulates the choice of splice sites in the process of RNA splicing; cells can differ in their ability to recognize a sequence as an intron or exon by producing different splicing factors (ex: Dscam gene in Drosophila has 38,016 isoforms) Trans-activating domain - ANSActivates or suppresses the transcription of the gene whose promoter or enhancer it binds to; usually enables the transcription factor to interact with the proteins involved in binding RNA polymerase II or with enzymes involved in histone modification Transcription - ANSThe process of a DNA sequence in a gene being copied into pre-mRNA

Transcription factor - ANSa protein that binds to DNA with precise sequence recognition for specific promoters, enhancers, or silencers; recruit nucleosome- modifying proteins to that region of the genome and make chromatin more accessible for RNA polymerase II and recruit transcriptional co-regulators to form bridges by linking transcription factors that are bound to the promoter and enhancer togetherr Transcription initiation site (cap sequence) - ANSDNA sequence that codes for the addition of modified nucleotide cap at the 5' end of the RNA after it is transcribed Transcription termination sequence - ANSSequence where transcription is terminated; transcription continues for 1000 nucleotides beyond the AATAAA site of the 3' UTR Translation - ANSProcess by which each codon of the mRNA is decoded to produce a chain of covalently attached amino acids Translation initiation site - ANSThe ATG codon that signals the beginning of the first exon of a gene

Translation termination codon - ANSThe TAA, TAG, or TGA codon that causes the ribosome to dissociate and the protein to be released Zinc finger - ANSTranscription factor family that contains a DNA-binding domain of a stretch of amino acids surrounding a zinc molecule (ex: WT1, Kruppel, Engrailed, and many hormone receptors)