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Gene Expression. Gene expression?. Biological processes, such as transcription, and in case of proteins, also translation, that yield a gene product. A gene is expressed when its biological product is present and active. Gene expression is regulated at multiple levels. Methods of regulation.
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Gene expression? • Biological processes, such as transcription, and in case of proteins, also translation, that yield a gene product. • A gene is expressed when its biological product is present and active. • Gene expression is regulated at multiple levels.
Methods of regulation • Normally slow relative to metabolic control • Allows metabolism to be changed in response to environmental factors • Transcriptional control most common • Sometimes variation in transcription rate not reflected in enzyme amount • Translational control also found • No change in mRNA levels but changes in protein amounts
Expression of Genetic Information • Production of proteins requires two steps: • Transcription involves an enzyme (RNA polymerase) making an RNA copy of part of one DNA strand. There are four main classes of RNA: i. Messenger RNAs (mRNA), which specify the amino acid sequence of a protein by using codons of the genetic code. ii. Transfer RNAs (tRNA). iii. Ribosomal RNAs (rRNA). iv. Small nuclear RNAs (snRNA), found only in eukaryotes. • Translation converts the information in mRNA into the amino acid sequence of a protein using ribosomes, large complexes of rRNAs and proteins.
RNA Synthesis • DNA template: 3’-to-5’ • RNA synthesis: 5’-3’; no primer needed
Protein Coding Genes • ORF • long (usually >100 aa) • “known” proteins likely • Basal signals • Transcription, translation • Regulatory signals • Depend on organism • Prokaryotes vs Eukaryotes
Eukaryotic gene organization 1. Transcripts begin and end beyond the coding region (5’UTR and 3’UTR) 2. The primary transcript is processed by: 5’ capping 3’ formation / polyA splicing 3. Mature transcripts are transported to the cytoplasm for translation
Regulation of gene expression Promoter Gene (red) with an intron (green) Plasmid single copy vs. multicopy plasmids 1. DNA replication 2.Transcription Primary transcript mRNA degradation 3. Posttranscriptional processing Mature mRNA 4. Translation inactive protein Protein degradation 5. Posttranslational processing active protein
Proposed Model rRNA, tRNA etc. Proteins DNA Pre-RNA mRNA
Post-Transcriptional Modification in Eukaryotes • primary transcriptformed first • then processed (3 steps) to form mature mRNA • then transported to cytoplasm Step 1: 7- methyl-guanosine “5’-cap” added to 5’ end Step 2: introns spliced out; exons link up Step 3: Poly-A tail added to 3’ end mature mRNA 5’-cap- exons -3’ PolyA tail
Intron Splicing in Eukaryotes • Exons: coding regions • Introns:noncoding regions • Introns are removed by “splicing” GU at 5’ end of intron AG at 3’ end of intron
Splicesomes Roles in Spicing out Intron RNA splicing occurs in small nuclear ribonucleoprotein particles (snRNPS) in spliceosomes Spliceosomes: protein + small RNAs (U1-8) complementary to the splice junctions
Splicesomes Roles in Spicing out Intron • 5’ exon then moves to the 3’ splice acceptor site where a second cut is made by the spliceosome • Exon termini are joined and sealed 1 2 U1, U2 & U 5 recognize donor and acceptor sites for splicing specificity 2 1 1 2
Mode of gene regulations • Constitutively expressed genes: Genes that are actively transcribed (and translated) under all experimental conditions, at essentially all developmental stages, or in virtually all cells. • Inducible genes: Genes that are transcribed and translated at higher levels in response to an inducing factor • Repressible genes: Genes whose transcription and translation decreases in response to a repressing signal
Definitions • Housekeeping genes: • genes for enzymes of central metabolic pathways (e.g. TCA cycle) • these genes are constitutively expressed • the level of gene expression may vary
Condition 2 “turned off” “turned on” 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 25 26 19 20 21 22 23 24 induced gene repressed gene constitutively expressed gene inducible/ repressible genes Gene regulation (1) Condition 1 “turned off” “turned on” Chr. I Chr. II Chr. III
Condition 4 upregulated gene expression down regulated gene expression Gene regulation (2) Condition 3 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 25 26 19 20 21 22 23 24 constitutively expressed gene
Modulators of transcription • Modulators: (1) specificity factors, (2) repressors, (3) activators • Specificity factors: Alter the specificity of RNA polymerase Examples: s-factors (s70, s32 ) s70 s32 Standard promoter Heat shock promoter Housekeeping gene Heat shock gene
Modulators of transcription 2. Repressors: • mediate negative gene regulation • may impede access of RNA polymerase to the promoter • actively block transcription • bind to specific “operator” sequences (repressor binding sites) • Repressor binding is modulated by specific effectors Effector (e.g. endproduct) Repressor Operator Coding sequence Promoter
Negative regulation (1) Repressor Effector Example: lac operon RESULT: Transcription occurs when the gene is derepressed
Negative regulation (2) Repressor Effector (= co-repressor) Example: pur-repressor in E. coli; regulates transcription of genes involved in nucleotide metabolism
Modulators of transcription 3.Activators: • mediate positive gene regulation • bind to specific regulatory DNA sequences (e.g. enhancers) • enhance the RNA polymerase -promoter interaction and actively stimulate transcription • common in eukaryotes RNA pol. Activator promoter Coding sequence
Positive regulation (1) Activator
Positive regulation (2) Activator Effector RNA polymerase
Operons • a promoter plus a set of adjacent genes whose gene products function together. • usually contain 2 –6 genes, (up to 20 genes) • these genes are transcribed as a polycistronic transcript. • relatively common in prokaryotes • rare in eukaryotes
Pi I P Q1 Z Y A Q3 Q2 The lactose (lac) operon • Contains several elements • lacZ gene = b-galactosidase • lacY gene = galactosidase permease • lacA gene = thiogalactoside transacetylase • lacI gene = lac repressor • Pi = promoter for the lacI gene • P = promoter for lac-operon • O1 = main operator • O2 and O3 = secondary operator sites (pseudo-operators)
LacZ LacY LacA Inducer molecules: Allolactose: - natural inducer, degradable IPTG (Isopropylthiogalactoside) - synthetic inducer, not metabolized, lac repressor Pi Pi I I P P Q1 Q1 Z Z Y Y A A Q3 Q3 Q2 Q2 Regulation of the lac operon