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Eukaryotic Genomes and Gene Expression
Ms. Day AP Biology
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Introduction to Gene Control in Eukaryotes
hill.com/olc/dl/120080/bio31.swf
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General Characteristics
Eukaryotic genomes MUCH larger than prokaryotic genome ~22,000 genes in human genome 98% consists of non-coding regions
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Both prokaryotes and eukaryotes
Must alter their patterns of gene expression in response to changes in environmental conditions How do prokaryotes do this??? OPERONS!!! Now, let’s learn how eukaryotes do it!!!
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Prokaryotic vs. Eukaryotic Genomes
Generally are larger Have longer genes Usually NO operons Contain noncoding DNA both associated within genes Create INTRONS in mRNA!!
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Most of eukaryotic genomes have noncoding DNA sequences
Called “junk DNA” However, much evidence is shows… “junk” DNA IS important Ex: helps to creates: Telomeres Centromeres Codes for microRNA’s (miRNA)
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What is heterochromatin?
Remains HIGHLY condensed during interphase Non-coding chromatin NOT actively transcribed So why do we have it?...helps with gene expression and chromosome structure What is euchromatin? Remains LESS condensed during interphase Becomes HIGHLY condensed during mitosis Coding chromatin ACTIVELY transcribed
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Chromatin structure is based on successive levels of DNA packing
Eukaryotic DNA Combined with large amount of protein (called histones) Eukaryotic chromosomes Have A LOT of DNA relative to condensed supercoiling must occur
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(a) Nucleosomes (10-nm fiber)
In electron micrographs Unfolded chromatin has the appearance of beads on a string Each “bead” is a nucleosome Basic unit of DNA packing consists of 8 histones Allows for super coiling to occur 2 nm 10 nm DNA double helix Histone tails His- tones Linker DNA (“string”) Nucleosome (“bead”) Histone H1 (a) Nucleosomes (10-nm fiber) Figure 19.2 a
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Higher Levels of DNA Packing
The next level of packing uses the H1 histone proteins Forms the 30-nm chromatin fiber Consists of 6 nuclesomes 30 nm = diameter Nucleosome 30 nm (b) 30-nm fiber
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Forms looped domains, making up a 300-nm fiber
The 30-nm fiber, in turn Forms looped domains, making up a 300-nm fiber Protein scaffold attaches to looped domains and helps organize areas of ACTIVE transcription Protein scaffold in nuclear membrane (lamina) 300 nm (c) Looped domains (300-nm fiber) Loops Scaffold Figure 19.2 c
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(d) Metaphase chromosome
In a mitotic chromosome The looped domains themselves coil and fold forming the characteristic metaphase chromosome 700 nm 1,400 nm (d) Metaphase chromosome Figure 19.2 d
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Levels of DNA Organization
DNA wraps around histones Histones form nucleosomes Nucleosomes form 30-nm fibers 30-nm fibers attach to protein scaffolds and form 300-nm fibers Chromosome is formed
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Regulation of Gene Expression
All organisms regulate which genes are expressed During development multicellular cells undergo process of specialization called cell differentiation Most gene expression is regulated at the level of TRANSCRIPTION Each cell of a multicellular eukaryote has SAME DNA BUT…Expresses only a fraction of its genes
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PRE- TRANSCRIPTIONAL MODIFICATION
POST- TRANSCRIPTIONAL MODIFICATION
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POST- TRANSLATIONAL MODIFICATION
aa’s REVIEW: Gene Expression (animation 1-06)
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Pre Transcriptional Regulation
(BEFORE mRNA is made)
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(a) Histone tails protrude outward from a nucleosome
Histone Modification Chemical modification of histone tails affect the configuration of chromatin/ gene expression (a) Histone tails protrude outward from a nucleosome Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation DNA double helix Amino acids available for chemical modification Histone tails
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1. Histone acetylation (add –COCH3)
Acetylated histones bind DNA more loosely Enhances transcription b/c transcription proteins and enzymes can gain access to genes (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription Unacetylated histones Acetylated histones
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2. DNA Methylation Add methyl groups (-CH3) to cytosine bases after DNA synthesis reduces transcription Ex: genes not expressed are heavily methylated; DNA is more tightly coiled
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RECALL… The Central Dogma DNA RNA PROTEIN (polypeptide formed 1st) Transcription factors are proteins that bond to specific sections of DNA, either stopping or initiating formation of RNA Proteins can also turn off some areas of DNA permanently DNA tightly coils around histones or molecules are added to DNA so RNA polymerase cannot access it This does not change the genome (DNA all still there), but does change the proteome (the proteins that can be made)
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Enhancer (aka: a switch)
Most eukaryotic genes have many control regions Segments of noncoding DNA that help regulate transcription by binding certain proteins
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Regulation of Transcription Initiation
Cluster of proteins called the transcription-initiation complex forms at eukaryotic promoter Consists of: Transcription factors that bind to promoter Transcription factor proteins that bind each other RNA polymerase
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Activators and Repressors
Transcription factors (protein) can be: Repressors Binds to DNA regions called silencers Inhibit expression of particular gene Activators Bind to DNA regions called enhancers stimulates transcription of a gene plex_and_enhancers.html
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Aka: mediators
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Eukaryotic Gene Expression
487/499125/CDA15_1/CDA15_1b/CDA15_1 b.htm hill.com/sites/ /student_view0/c hapter18/animations.html# Animation #3: Enhancers and repressors
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An activator Is a protein that binds to an enhancer and stimulates transcription of a gene
Activator protein binds to the enhancer AWAY from gene DNA bending proteins brings activators close to promoter. Mediators (coactivators) help bind activatir to RNA polymerase Activators bind to transcription factors to form initiation complex on promoter
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Coordinately Controlled Genes in Eukaryotes
NO operons in MOST Eukaryotes Most genes are: 1 promoter for 1 gene Some exceptions = round worms and fruit flies have operons BUT…eukaryotic genes have activator proteins. Different cells have different activators, so different genes are expressed in different cells!
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Many control elements for different genes are the same
It is the combination of control elements that provides specificity
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Epigenome Epigenetics
Every cell in your body contains a complete copy of your DNA (your genome) Different types of cells turn off different sections of DNA, which leads to your epigenome DNA does not change, but the amount of DNA that can be used it less than the total, so proteome smaller Epigenetics the study of changes in gene activity that do not involve changes to the genetic code but still get passed down to at least one successive generation Includes environmental factors like diet, toxins, stress and prenatal influences or histone modification (i.e.- DNA methylation)
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Post Transcriptional Regulation
(AFTER mRNA is made)
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1. Alternative RNA splicing
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Blockage of translation
2. RNA interference by single-stranded microRNAs (miRNAs) Can lead to degradation of an mRNA or block its translation 5 Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Degradation of mRNA OR Blockage of translation Target mRNA miRNA Protein complex Dicer Hydrogen bond The micro- RNA (miRNA) precursor folds back on itself, held together by hydrogen bonds. 2 An enzyme (Dicer) moves along double- stranded RNA, cutting it into segments. One strand of each short double- stranded RNA is degraded; the other strand (miRNA) then associates with a complex of proteins. 3 The bound miRNA can base-pair with any target mRNA that contains complementary sequence. The miRNA-protein complex prevents gene expression either by degrading the target mRNA or by blocking its translation.
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RNAi Video (15 min) http://www.pbs.org/wgbh/nova/body/rnai.ht ml
Other Animations hill.com/sites/ /student_view0/a nimations.html#
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Controling Translation
Translation of SOME mRNAs can be blocked by regulatory proteins that bind to specific sequences or structures of the mRNA EX: Phosphorylation olc/dl/120080/bio31.swf
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Protein Processing and Degradation
Proteasomes Are giant protein complexes that bind protein molecules and degrade them Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Ubiquitin Protein to be degraded Ubiquinated protein Proteasome and ubiquitin to be recycled Protein fragments (peptides) Protein entering a proteasome Multiple ubiquitin are attached to protein by enzymes in cytosol. 1 ubiquitin-tagged protein is recognized by proteasome, which unfolds protein and places it within a central cavity. 2 proteosome enzymes chop up the protein Figure 19.10
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Wrapping it all up… /student_view0/chapter18/animatio ns.html# 4th animation
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