Term
Introduction to gene structure and expression in microbes
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Definition
oMicrobe properties (shape, metabolism, virulence) determined by genetics
oGenetic information stored in genes
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Term
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Definition
o 1 chromosome (2 rare)
o 1 or more plasmid (extrachromasomal DNA)
o Held in nucleoid in cytoplasm
o Chromosome usually circular molecule
o Associated with proteins and RNA that stabilize and regulate transcription |
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Term
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Definition
o Single thin circular molecule of DNA with 4.6 x 106 base pairs
o 1600um in length if laid straight (800x cell length)
o Packaged into 10% of cell’s volume by helicase which folds it into loops of 50k to 100k bases
o Human genome contains 3 x 109 base pairs in 46 DNA molecules
§ 1.6 meters long if stretched out, but packed into 5um in diameter nucleus |
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Term
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Definition
· Small
· Self-replicating
· Extra-chromosomal
· Circular
· DNA
· Carried in cytoplasm of come microbes
· 1% or less of chromosome
· genes for nonessential traits that confer survival in some conditions
· Types
o Fertility or F factor – contain genes for sex pili and enzymes of conjugation
o Resistance or R factor – carry genes that confer antibiotic resistance or cell toxin resistance
o Bacteriocin – contains genes for toxins that kill other bacteria
o Virulence or V factor – carry genes for virulence factors such as toxins
Dissimilation – carry genes for degradative enzymes |
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Term
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Definition
o 1 or more chromosomes in nucleus
o Extranuclear DNA in mitochondria and chloroplasts and rarely plasmids
§ Nuclear DNA contains 99.995 of information
§ Most have more than 1 chromosome
o Chromosomes of linear DNA and histones
§ DNA would in 10nm beads around histones – nucleosomes
§ Nucleosomes packed into 30nm diameter fibers called chromatin fibers
§ Euchromatin – active and loosely packed chromatin
§ Heterochromatin – tightly packed chromatin
§ Mitosis – condensing to tightly packed chromosome |
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Term
Extranuclear DNA of eukaryotes
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Definition
o Mitochondria and chloroplasts
o Circular and resembles prokaryote DNA
§ Only code for 5% of their needed proteins
§ Rest coded for by nucleus
o Plasmids found in some fungi and protozoa
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Term
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Definition
· Replication goes both directions from origin
o Prokaryotes have one origin usually
o Eukaryotes have multiple
· Methylation
o Prokaryotes methylate adenine and sometimes cytosine
o Plants and animals methylate cytosine only
o Reasons
§ Regulate gene expression
§ Mark initiation site for DNA synthesis
§ Mark their own DNA
Distinguish older from newer to help proofreading |
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Term
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Definition
Eukaryotes use RNA molecules (ribozymes) to process pre-mRNA
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Term
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Definition
· Synthesis of mRNA
· Prokaryotes – nucleoid
· Eukaryotes – nucleus but also mitochondria and chloroplasts
· Three steps
o Initiation
§ RNA polymerase binds to DNA and moves along until promotor
§ Subunit of RNA polymerase called sigma factor participates in promotor recognition
· Eukaryotes use transcription factors (separate proteins)
§ Once adhered, unwinds, and begins RNA synthesis 10 bases downstream from promoter
o Elongation
§ Sigma factor released
§ Polymerase moves 3-5 to synthesize 5-3’
§ Terminated when reaches terminator site
o Termination
Self termination mechanism or termination protein
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Term
Comparison of RNA Polymerase and DNA Polymerase |
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Definition
o RNA polymerase
§ No helicase
§ Slower
§ Uracil used
§ Lacks proofreading so it makes more errors
§ Many RNA polymerases can be on same RNA molecule |
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Term
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Definition
o Nucleotide bases dictate protein synthesis
o Requires
§ mRNA
§ Ribosomes
§ tRNA
§ GTP
§ Protein factors
o Codons – 3 bases
o 64 codons
o Genetic code is redundant
o 61 sense codons
o 3 stop codons or nonsense codons
o Start codon
§ AUG
§ Methionine in archaea and eukaryotes
§ N-formyl-methionine in bacteria, mitochondria and chloroplasts
o Same code for almost all organisms |
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Term
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Definition
o Requires no processing
o Carries more than one gene usually |
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Term
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Definition
o Noncoding introns between coding exons
o mRNA first called pre-messenger RNA
o Has to be processed to remove introns
o Ribozymes
§ RNA molecules that have enzymatic activity
§ Remove introns and splice exons back together
o Contains only one gene
o mRNA transported out nuclear pores |
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Term
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Definition
o RNA molecules with anticodon and amino acid attached
o About 75 ribonucleotides
o Highly folded with loops and turns, and a 3’ amino acid acceptor site
o Anticodon complementary with amino acid codon
o 3’ end carries amino acid
o Each tRNA has own loading enzyme that loads with ATP and attaches amino acids covalently
o Some bind only to 2 nucleotides often and allow the third one to wobble |
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Term
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Definition
· rRNA and proteins
· Carry out protein synthesis
· Prokaryotes
o 70 S
o 50 S and 30 S subunits
§ 50 S comprised of 2 single stranded rRNA molecules (23S and 5 S) and 33 structurally different proteins
§ 30 S subunit comprised of 1 single stranded rRNA molecule (16S size) and 21 structurally different proteins
· Eukaryotes
o 80 S
o 60 S and 40 S subunits
§ 60 S comprised of 2 single stranded rRNA molecules (25S and 5 S) and 34 structurally different proteins
§ 40 S subunit comprised of 1 single stranded rRNA molecule (18S size) and 21 structurally different proteins
· Prokaryotic 30 S subunit can bind 3 mRNA codons at a time
· Large 50 S subunit holds 2 tRNAs in E, P, and A site
· A site accepts charged tRNAs
· P site holds tRNA with polypeptide chain attached
· E is exit site for dischared tRNAs
· Difference in ribosomes allow some antibiotics to be specific
Erythromycin binds to 23 S rRNA
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Term
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Definition
o Initiation
o Elongation
o Termination
o All stages require protein factors
o Initiation and elongation requires energy supplied by GTP |
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Term
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Definition
o 30S subunit binds to mRNA at AUG start site in P site
o tRNA-fmet binds to AUG using GTP
o 50S subunit binds to complex forming ribosome-mRNA initiation complex
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Term
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Definition
· Cyclic process
o Charged tRNA binds to A site
o Ribozyme in 50S subunit transfers P amino acid to A amino acid
o Shifts down one spot with GTP
o E site releases old P site amino acid
o A site accepts next charged tRNA
· Requires elongation factors and energy from GTP
· Enormous energy cost
o GTP for each tRNA in A site
o GTP for each move
o ATP to charge tRNA
o GTP to initiate
o GTP to terminate
Multiple ribosomes can work same mRNA |
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Term
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Definition
o Ribosome reaches stop codon
o Release factors cause dissociation of complex |
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Term
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Definition
o 75% of genes constituitive – not regulated (essential)
o 25% regulated to be expressed only when needed
§ Regulation happens at transcription of genes to mRNA usually
§ Regulation conserved energy by preventing synthesis of unneeded proteins |
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Term
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Definition
· Explains how prokaryotic cells regulate genes
· Operon is a segment of DNA that contains
o Promoter site where RNA polymerase binds
o Operator – adjacent regulatory site
o One or more structural genes that code for one or more enzymes or proteins
· Separate regulatory gene coding for repressor protein that turns operon off when it binds to operator or on when it doesn’t bind
· Inducible operons
o Not transcribed unless activated by inducer
o See figure 7a-61
o When no inducer (lactose) repressor binds to operator and blocks transcription
o When inducer present, it binds to repressor and inactivates it
o Operon transcription occurs
· Repressible operons
o Transcribed continually until deactivated by repressor
§ Repressor binds to corepressor before activated
§ Tryptophan model in Figure 7a-63
§ When corepressor (tryptophan) absent, repressor is inactive and operon is transcribed
When corepressor accumulates, binds to and activates repressor and blocks transcription |
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Term
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Definition
o Inducible operons typically are catabolic pathways
§ Substrate is the inducer
o Repressible operons typically are anabolic pathways
§ End product corepressor
o Other mechanisms
§ Catabolic enzyme genes also controlled by glucose dependent catabolic repression involving cAMP
· Cells metabolize glucose first
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