Test 2 Microbiology

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Test 2 Microbiology
2015-10-14 00:26:02
bacterial plasmid
test 2 material, unit 2
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  1. horizontal gene transfer
    • occurs via 3 mechanisms:
    • 1. transformation: transfer of naked DNA
    • 2. Conjugation: cell -to cell contact
    • 3. transductions: transfer by viruses (bacteria have viruses)
  2. transformation
    • recognized by surface proteins in order to be transferred, only single strand can cross porin 
    • so, get rid of 1 strand by nuclease eating it 
    • 1. transform dna -> 1 strand
    • 2. recA protein: uptake ssDNA , help get into chromosome , called "chaperones" 
    • 3. homologous recombination
    • 4. transformed cell
    • 6. force dna across membrane w/ cacl2 if necessary
    • 7. if circular, must be maintained as a plasmid (replicates free of chromosome)
    • 8. linear : must integrate into chromosome to be maintained
  3. metagenomics
    studying microbial communities base on their complete genomic content
  4. 2 types of DNA transfer
    • vertical transmission: movement from parent to child
    • horizontal transmission: movement from one cell to another cell
  5. homologous recombination
    • putting DNA that is similar onto chromosome
    • chromosome replicates and repairs dna in this stage
    • 1. endonuclease nicks donor DNA 
    • 2. ssb protein binds to this nick 
    • 3. rec a protein:recognizes both donor and recipient
    • 4. cross strand exchange so that each donor and recipient dna have each others complimentary dna
  6. plasmid
    • 1. prokaryotes: yeasts and filamentous fungi
    • 2. complete circle
    • 3. each plasmid distinct in size and copy 
    • (how many per cell)
    • a. high copy : 500-2000
    • b. medium50-100
    • c. low : 1-10
    • 4. bacteria can share plasmids
  7. resistance genes
    genes on plasmids that confer resistance to antibiotics or heavy metals
  8. genes on plasmids: virulence genes
    contirbute to ability of bacterium to cause disease
  9. metabolic genes
    • encode enzymes that degrade substances, such as pollutants, pesticides and sugars
    • gives competitive advantage
  10. transfer genes (type on plasmid)
    • enable plasmid to move from one ccell to another; about 21 genes, many of which are involved in forming a sex pilus and other transfer functions
    • not all plasmids have transfer genes
    • conjugative plasmids do though
  11. conjugative plasmid
    a plasmid that has the transfer genes and thus can move from one cell to another
  12. oriT
    origin of transfer- a DNA sequence that is at leading end of plasmid during transfer
  13. genomics
    studying organisms based on complete genetic content
  14. transformation
    • 1. transfer of naked dna
    • 2. if circular: must be maintained as a plasmid (replicates free of chromosome)
    • 3. linear: integrate into chromosome to be maintained
  15. structural gene
    string of nucleotides that can be decoded by an enzyme to produce a functional RNA molecule
  16. DNA control sequence
    • regulates expression of a structural gene
    • do not encode RNA or preotein ,
    • ex/ promoter
  17. promoter
    • not message
    • needs to begin each message
  18. transcription start site
    right after promoter and not promoter
  19. operon
    • efficient use of space
    • allows for coordinated expression of genes w/ a related function
    • allows for transfer of related genes on a cassette
  20. regulon
    regulation of multiple operons by same regulatory protein
  21. prokaryotic chromosome features
    • consolidate genomes bc have less space and less complicated
    • more effective w/ space in between : dead space
    • have far less repeating and non-coding sequences than eukaryotic sequences
  22. intron
    • only a eukaryotic cellular thing
    • space in between message
  23. exon
    • coding sequence /frame in eukaryotic cells
    • 90% of chromosomes is non-coding DNA
  24. bidirectional replication (semi -conservative replication)
    • when two original parent strands break off at origin , paired with a new complement, original never together again.
    • product is after that will have a strand from a cell generated previously before and then the new complement
    • one of 2 ways that a plasmid can replicate
  25. rolling circle replication
    • original double stranded dna  nicked by nicking protein. nicking protein identifies a specific sequence on DNA  and makes nick at that location
    • 2. outer strand displaced, there is complement of outer strand being made simultaneously red 5' to 3'
    • 3. displaced strand is > 1 unit in length
    • 4. one of 2 ways that plasmids replicate
  26. virulence genes
    • contribute to the ability of a bacterium to cause disease
    • pre -exist
    • common on plasmids
  27. competent cells
    • cells that are able to take up DNA by transformation
    • only some bacteria are naturally competent
  28. natural transformation
  29. competency factor
    tells a bacterium is about to transform needs naked dna
  30. conjugation
    • 1. bacterial mating
    • 2. Gm + : often do this using  specialized proteins
    • 3. Gm -: dna often moves thru sex pilus (conjugation pilus)
    • 4. system steps:
    • a. rolling circle replication
    • b. single strand transfer
    • c. replicated to become double stranded
    • d. reflaxasome is disassembled (forms on membrane and regulates attraction of 2 bacteria and attracts them together, recognizes oriT site as well)
    • 1. sex pilus from F+ plasmid attached to receptors on recipient cell
    • 2. contraction of pilus draws 2 cells togetherand forms reflaxasome bridge
    • 3. F factor nicked at oriT, and 5' prime end begins to transfer original , outer strand into F- cell
    • 4. strand remaining in donor is replicated
    • 5. original strand in F- cell circulizes and replicates
    • 6. recipient now can be a donor!
  31. fertility factor
    a transferable plasmid, has ability to form pilus and export DNA for conjugation
  32. f plasmid
    integrates entire plasmid sequence into chromosome
  33. episome
    plasmid that can integrate int host chromosome (ex/plasmid) when in the chromosome, it replicates w/ host chromosome
  34. hfr strain
    • a strain w/ an integrated f plasmid (high frequency of recombination)
    • this strain exhibits higher frequency of chromosomal DNA transfer than an F+ cell
  35. F' plasmid
    a plasmid that has picked up a portion of the e. coli chromosome during excision
  36. transduction
    • 1. transfer of bacterial DNA by viruses
    • 2. only deals with bacterial virules
    • 3. only horizontal gene transfer
  37. generalized transduction
    packaging of DNA from any part of the bacterial genome into a virion and transfer to another cell
  38. generalized transduction
    • 1. p22 DNA phage infects a host cell at pac site and makes subunit components for more phage
    • 2. DNA is packaged into capsid heads. Some capsids package host DNA.
    • 3. new phage assembly is completed
    • 4. cell lyses; phage is released
    • 5. transducing phage particle injects host DNA into new cell, where it may recombine with chromosome which changes the genetic make up
  39. specialized transduction
    • 1. the packaging of DNA from only specific portions of the bacterial genome into a virion
    • and transfer to another cell
  40. specialized transduction step by step
    • 1. phage dna circularizes and detaches from host dna
    • 2. detached dna replicates
    • 3. phage synthesis is completed
    • 4. cell lyses and release normal phage
    • 1. portion of host DNA is exchanged for phage DNA both host and phage now have a little of the opposite dna as well
    • 2. detached dna replicates
    • 3. phage synthesis is completed
    • 4. cell lyses and releases defective genes that can transduce galactose genes
  41. Spontaneous mutations:
    • mutations that arise naturally in cells
    • ex/ natural uv radiation
  42. natural transformation
    • pick up a lot of resistance genes,
    • gram +, why deadly
  43. virioid
    virus particle that is non infectious
  44. induced mutations:
    • mutations that result from exposure to a mutagen (something that causes mutations)
    • ex's/ chemical mutagens, high levels of UV exposure
  45. types of mutations
    • 1. frameshift mutations
    • 2. point mutations
    • 3. deletions and insertions
  46. expression of mutations
    • silent mutations
    • nonsense mutations
    • missense mutations
  47. point mutations
    changes in a single base
  48. frameshift mutations
    • the deletion or insertion of one or more bases resulting in a shift in reading frame
    • 2. instead of 1000 , can make 1500
  49. silent mutation
    The change does not influence the protein sequence (the altered codon encodes the same amino acid)
  50. transposable genetic elements
    • pieces of DNA that move around the genome
    • 2. two major types: IS and transposons
    • 3. mobile genetic elements: move in and out of genome
    • 4. these elements can mediate recombination within the genome, causing deletions and inversions and other genomic rearrangements
  51. insertion sequence (IS)
    • 1. type of transposable genetic element
    • 2. simplest for of a transposable genetic element
    • 3. system thru non-replicative and replicative transposition
  52. transposon
    • 1. transposable genetic elements that contain genes in addition to a transposase gene
    • 2. move either replicatively or non-replicatively 
    • 3. replicative transposition results in an increase in # of transposons in genome (transposable element is copied, original remains in original dna as well as new one. this is differenct from non-replic., when only new dna has the transposable element)
  53. inactivation of a gene via transposition
    these elements may cause disruption of the gene that they insert into, or alter the expression of nearby genes
  54. processes contributing to evolution of a bacterial genome
    • 1.DNA replication errors lead to mutations.
    • 2. Transposable genetic elements can cause genome rearrangements due to homologous
    • recombination among elements leading to deletions and inversions.
    • 3. Horizontal gene transfer (HGT) introduces new genes. HGT can often be identified by the presence of genomic islands, (which are stretches of DNA that differ in composition (%G+C) from that of the rest of the genome.
  55. genomic islands
    • 1. Genomic islands often carry suites of genes that may provide a selective advantage. Examples include pathogenicity islands, symbiosis islands, metabolic islands, and resistance islands
    • 2. stretches of DNA that differ in composition (%G +C) from that of rest of genome
  56. virus
    • 1.a non-cellular particle that contains a genome that can replicate only inside a host cell
    • 2. impact evolution, of themselves and host
    • 3. obligate parasite
  57. virion
    • 1. individual 
    • 2. a complete viral particle; the form of a virus that occurs extracellularly (outside a host cell)
  58. virioid
    • 1.virus particle that is non-infectious 
    • 2. a lot of virus preparations are from virioid
    • 3. small, circular ssRNAs (about 250-400
    • nucleotides long)
    • 4. no capsid or envelope
    • 5. causes many plant diseases (not in animals or bacteria)
  59. enveloped virus
  60. naked virus
  61. nucleic acid (part of virus structures)
    either RNA or DNA
  62. capsid (part of virus structures)
    protein structure that packages the nucleic acid
  63. envelope
    • 1. only in enveloped viruses
    • 2. a phospholipid bilayer membrane derived from the host cell
  64. acessory proteins
    • 1.Contained within the capsid or between the envelope and the capsid, a space called
    • the tegument.
    • 2.Include enzymes important for the viral life cycle. (e.g., neuraminidase, polymerase)
    • 3. aid in transcription or replication of the viral genome EX/ RNA dependent RNA polymerase
    • 4. aid in host cell entry or release EX/ neuraminidase
  65. structure of viruses
    • 1. filamentous (helical)
    • 2. symmetrical
    • 3. complex and asymmetrical
    • 4. viruses without a capsid:
    • 1.Virions have one of the following possible nucleic acid types: ssDNA, dsDNA, ssRNA, dsRNA (ss = single-stranded, ds = double-stranded)
    • 2. Generalities:
    • a. most dna viruses have dsDNA, most RNA viruses have ssRNA
    • b. dsDNA most common among bacterial viruses
    • c. ssRNA most common among plant viruses
    • d. all types represented among animal viruses
    • 3. Genome Structure:
    • a. DNA either linear or circular
    • b. RNA always linear, may be segmented
    • 4. ssRNA viruses may be positive or negative stranded viruses:
    • a. + strand virus: messenger type RNA (mRNA) encode for proteins
    • b. - strand virus: RNA base sequence is complementary to the viral mRNA; do not code for proteins
  67. prions:
    • proteinaceous infections particles 
    • 2. naturally occurring
    • 3. transmissible spongiform encephalopathy (TSE)
    • 4.
  68. retrovirus
    • goes from RNA to ssDNA to dsDNA 
    • this is when host cell makes DNA
  69. viral life cycle (general stages)
    • 1. host recognition and attachment (adsorption)
    • 2. genome entry into host cell
    • 3. synthesis of components and assembly of virions, redirection of host resources 
    • 4. exit and transmission
  70. criteria for viral classification
    • 1. genome composition
    • a. nucleic acid type: dna or rna 
    • b. strandedness: ss or ds
    • c. structure: linear or circular, whole or segmented
    • 2. virion structure
    • a. capsid symmetry
    • b. presence or absence of envelope
    • c. size of virus particle
    • 3. host range
    • a. host range: bacteria, insects, animals, plants and species
  71. 1st step of viral life cycle: HOST RECOGNITION AND ATTACHMENT
    • 1. phage attach to specific host surface protein
    • a. pili
    • b. LPS
    • c. porin
    • 2. phage inject DNA
  72. 2nd step of viral life cycle:
    adsorption and genome entry
  73. 3rd ( 3A) step of viral life cycle: synthesis of phage components and replication of genome
    • 1.synthesis of host DNA, RNA,and protein is halted
    • 2. host dna is degraded: chopped into bits, possibly fit into?
    • 3. host cell machinery is redirected to synthesize viral constituents
    • tricks host cell to make only phage cell
  74. 3rd (3B) step of viral life cycle: assembly
    genome + coat proteins SELF ASSEMBLE into capsids (package DNA into pahge head)
  75. 4th step of viral life cycle
    lysis of host cell (assisted by encoding lysozome)
  76. lytic lifecycle of bacteriophage
    • bacteriophage infect and quickly replicate, lysing and killing the host cell . the released virions continue the cycle
    • virions quickly attach themselves on neighboring cells
  77. lytic phage = virulent phage
    a phage that experience only a lytic lifecycle, such as the E.coli T4 phage; it doesn't integrate into the host genome
  78. lysogenic life cycle
    bacteriophage infect and the genome integrates into the host’s genome
  79. lysogenic phage = temperate phage
    a phage that experiences lytic and lysogenic cycles, such as the E. coli lambda phage
  80. prophage
    - a phage that is integrated into the host’s genome
  81. lysogeny
    • a state in which a phage remains within the bacterial host cell after infection and
    • reproduces as the bacterial host cell reproduces
  82. lysogen
    • – a bacterium that carries a viral prophage and has the potential to produce bacteriophage
    • under the proper conditions
  83. induction
    the process in which phage reproduction is initiated in a lysogen
  84. slow-release phage
    • 1.a phage such as some filamentous phage, that can extrude through cell envelope one at a time without lysing the host cell
    • 2. excruciating slow
    • 3. only w/ filamentous phage
  85. slow release phage general steps
    • 1. the coat proteins insert into the cytoplasmic membrane
    • 2. the capsid assembles around the phage DNA as it is
    • secreted
    • 3.new phage are continually released during the life of the
    • cell
  86. slow release lifecycle bacteriophage
    • 1. phage inserts ssDNA
    • 2. phage dna forms double stranded circle
    • 3. cell replicates, ssDNA
    • 4. phages assemble and exit w/out lysis 
    • 5. while phages reproduces and exit cell, cell reproduces slowly
  87. animal virus lifecycles
    • 1.virus binds specific receptor proteins on host cells, usually cell surface glycoproteins
    • 2. receptors determine viral tropism
    • 3.host specificity is determined by the
    • presence or absence of these receptors. Similarly, specificity for distinct tissues, called tissue tropism,
    • is due to the presence or absence of receptors in those tissues.
  88. tropism
    ability of virus to infect a certain type of tissue
  89. adsorption and genome entry of animal viruses
    • 1.Most animal viruses enter host as virions and then uncoat the nucleic acid through dissassembly of the capsid.
    • 2. Entry and uncoating take place in different ways, depending on the virus:
  90. basic steps of virus lifecycle
    • 1. host recognition and attachment,
    • 2. genome entry into host cell,
    • 3. synthesis of components,
    • 4. assembly of virions,
    • 5. and exit and transmission.
  91. Bacteriophage T4 and lambda
    highlight both lytic and lysogenic life cycles of bacteriophage
  92. reproduction of lytic bacteriophage such as T4
    • 1. adsorption and attachment
    • 2. penetration or injection of the phage genome into the host cell
    • 3. redirection of host cell biosynthetic
    • machinery towards synthesis of phage nucleic acid and capsid proteins
    • 4. assembly of complete virions,  
    • 5. release of phage particles from the host via host cell lysis.
  93. animal viruses
    1. enter the cell as virions and then uncoat the nucleic acid. This can be done in a variety of ways.
  94. bacterial virus cultivation
    • 1.cultivated on an agar plate, with individual viral particles developing into a zone of clearing called a plaque
    • 2.batch culture (a flask of liquid medium), where their growth follows a characteristic pattern designated a one-step growth curve.
  95. growing animal viruses
    must be grown in host cells, but can be grown in cultured host cells, in whole animals, or in eggs
  96. 3 ways for entry and uncoating of animal viruses
    • 1. taking coat off at door, or uncoat nucleic acid  (envelope fuses with host membrane)
    • 2. uncoating w/in endosomes:  (a. lysosome fuses w/ and acidifies endosome
    • b.viral envelope fuses with endosome membrane
    • c.uncoating of RNA genome)
    • 3. uncoating at nuclear membrane: creates endosome, then inside opens up, attaches to nucleus, and releases DsDNA genome
  97. Replication of genome
    • depends on type of genome of the virus:
    • 1.DNA viruses: use host replication machinery
    • 2. RNA viruses: use an RNA-dependent RNA polymerase to transcribe their mRNA 
    • need for replication
    • 3. retroviruses: use a reverse transcriptase to copy their genomic sequence into DNA for insertion into the host chromosome
  98. synthesis of viral components for animal viruses
    all animal viruses make proteins w/ host ribosomes and translation occurs in the cytoplasm
  99. assembly of virions for animal viruses
    this may occur in the cytoplasm or nucleus
  100. release (exit) of virions of animal viruses
    • 1. release may occur by cell lysis or by "budding" 
    • 2. spike proteins are inserted into the membrane during budding
    • 3. membrane can be the cell membrane or an organelle membrane
  101. acute infection
    • infection with a rapid
    • onset that lasts for a short time
  102. plasmodesmata
    the channel bewteen plant cells , allows virions to travel easily from cell to cell
  103. plant cell virus and plant cell characteristic
    • need to rupture cell wall , so waits for something else to cause cell wall injury mechanically
    • so contact w/ damaged tissues, transmission by an insect vector, transmission through seed
  104. growth of bacteriophage in batch culture
    • 1. eclipse period: 1st stage, quiet,
    • similar to lag phase
    • attachment
    • genome insertion
    • no physical effects 
    • 2. Rise period
    • a. lysis
    • b. viral component synthesis
    • c. assembly  
  105. cultivation of animal viruses
    • animal viruses van be cultured in 
    • 1.cultured animal cells,
    • 2.by serial passage in animals, or
    • 3.in eggs.
  106. in natural ecosystems, viruses
    • 1. limit host population density
    • 2. select for host diversity
    • 3. viruses are the most numerous and genetically diverse microbes in the ocean.  They are a major driver of the turnover of microbes, including phytoplankton, killing >20% each day
  107. animal virus lifecycles
    • 1. host cell recognition and attachment site
    • 2. adsorption and genome entry
    • a. entry of naked genome 
    • OR uncoating of capsid
    • b. cell membrane (membrane fusion)
    • c. within endosomes, or 
    • d. at nuclear membrane
    • 3. replication of genome
    • 4. synthesis of viral components
    • 5. assembly of virions
    • 6. release (exit) of virions
  108. herpes
    to creep
  109. transcription
    • the synthesis of RNA based on a
    • DNA template; it requires RNA polymerase
  110. translation
    • the synthesis of a polypeptide/protein
    • based on an mRNA template; it requires ribosomes
  111. major groove
    occurs where the backbones are far apart,
  112. minor groove
    backbones closely together of dna
  113. Bacterial RNA polymerase
    • an enzyme that produces an RNA that is complementary to a DNA template; this RNA is
    • called a transcript
  114. protein-dna interactions
    recognition and binding depends on fit and chemical bonding between the bases and the protein
  115. bacterial RNA polymerase
    • composition:
    • 1. core polymerase
    • 2. sigma factor
    • 3. holenzyme
  116. core polymerase
    which itself is composed of four polypeptides: two alpha subunits, a beta subunit, and a b’ subunit; this synthesizes the RNA polymer that is complementary to a DNA template
  117. sigma factor
    a protein that is required to initiate RNA synthesis; it recognizes the sequences w/in the promoters of genes
  118. haloenzyme
    • sigma factor + core polymerase 
    • (of bacterial RNA polymerase)
  119. initiation of transcription
    • RNA polymerase haloenzyme binds at promoter
    • promoter recognized by sigma factor
  120. bacterial sigma factors
    • each bacterial species makes multiple sigma factors
    • ex/ e. coli makes 7 sig. factors
    • Each sigma factor recognizes a different consensus sequence (an approximate sequence that reflects the most likely base at each position).
  121. transcription
    • 1) Initiation: RNA polymerase holoenzyme binds to the promoter, directed by the sigma factor
    • 2) Elongation: The RNA chain is extended
    • 3) Termination: RNA polymerase detaches from the DNA, and the transcript is released
  122. transcription process steps
    • 1. sigma recognizes promoter and initiation site
    • 2. transcription begins, sigma is released, RNA chain growth continues until termination site
    • 3. termination site reached; chain growth stops
    • 4. release of polymerase and RNA (to make protein)
  123. transcription elongation
    • 1. 1st base of transcript usually purine (A or G) designated as position +1 on DNA template and indicates start of transcript
    • 2.The energy released by cleaving a ribonucleoside
    • triphosphate (e.g., ATP) to release a
    • pyrophosphate is used to form a phosphodiester
    • bond
    • 3. original RNA polymerase moves along template, synthesizing RNA at 45 bases/sec
  124. transcription termination
    • 1. Rho-dependent:Requires a protein called
    • Rho and a strong pause site at the 3´end of the gene
    • 2. Rho-independent: - Requires GC-rich inverted
    • repeats in the RNA that form a stem-loop, or
    • hairpin structure, followed by 4–8 consecutive U
    • residues. The hairpin causes the RNA polymerase
    • to pause. The remaining U-A base pairing is weak and thus allows the RNA to pull away from the DNA, ending transcription.
    • RNA -> U-weak base pairing
    • start codon that is recognized by AUG
  125. mRNA
    • carries message directing protein synthesis
    • these are rapidly degraded to allow cells to respond rapidly to changing conditions by quickly halting the synthesis of many proteins
    • will self-destruct
    • can focus attention on new messages
  126. 6 major types of RNA
    • 1. mRNA
    • 2. rRNA (ribosomal rna): small snippett of RNA needed for other functions
    • 3. tRNA: tag single acids onto something
    • lots of 2ndary structure
    • 4. sRNA (small RNA): new wave of killing bacteria
    • 5. tmRNA
    • 6. catalytic RNA
  127. sRNA
    can help regulate gene expression by base pairing to short regions of an mRNA and thus obstructing ribosome access
  128. differences between euk. and prok. transcription
    • 1.Eukaryotic mRNA is usually monogenic (=monocistronic); prokaryotic mRNA is often polygenic (= polycistronic)
    • 2.The number of RNA polymerases differs.
    • Prokaryotes have one RNA polymerase; it synthesizes all RNAs
    • Eukaryotes have three RNA polymerases:
    • RNA polymerase I – synthesizes rRNA
    • RNA polymerase II – synthesizes mRNA
    • RNA polymerase III – synthesizes tRNA
    • (above listed are 3 dif. RNA dependent RNA polymerases , dont need to know specifics)
    • 3. The number of subunits in the polymerase for mRNA differs.
    • Bacterial RNA polymerase 4 subunits + a sigma factor
    • Eukaryotic RNA polymerase II has ≥ 10 subunits
    • Archaea have one RNA polymerase, but it resembles the RNA polymerase II of eukaryotes (has ≥8 subunits)
  129. bacterial rna composed of
    core polymerase + sigma factor
  130. transcription and translation in prokaryotes
    transcript is bound to ribosomes and translated into a polypeptide (coupled transcription/translation)
  131. codon
    • 3 bases that contain
    • information for recognizing a specific
    • amino acid
    • 64 codons, 3 are stop codons
  132. degenerate/redundant codon
    when multiple codons can encode same amino acid
  133. wobble theory
    since 3rd base vaires but offers same amino acid, helps guarantee correct amino acid will be generated even though there was mutation "silent mutation"
  134. trna
    • 1.translates the nucleic acid sequence into a protein (the translator)
    • 2.73-93 nucleotides that are folded into a clover leaf shape (in 2-D) and a boomerang (in 3-D)
    • 3. acceptor stem: region that binds an amino acid (has amino acid attached to it)
    • 4. anitcodon: region that forms Hydrogen bonding w/ the mRNA codon , 3 bases that are complementary to the codon
    • resistant to RNAses bc are highly folded and have unusual bases
  135. charging of tRNA
    • 1. process of adding correct amino acid onto correct tRNA
    • 2. carried out by amino-acyl tRNA synthetases
    • only fxn is to make charges tRNA's
  136. aminoacyl-tRNA synthetase
    enzymes that carry out the process of adding correct amino acid onto correct tRNA (the process is called charging the tRNA)
  137. ribosome binding site
    • where ribosome binds 
    • ribosome recognizes series of G's and A's 
    • short purine rich region that is just upstream of start codon
  138. site on ribosome harbors 3 binding sites for tRNA:
    • A (acceptor) site: Binds incoming aminoacyl-tRNA
    • P (peptidyl-tRNA) site: Harbors the tRNA with the growing polypeptide chain
    • E (exit) site: Binds a tRNA recently stripped of its polypeptide (ejector site)
  139. orf
    • open reading frame
    • coding region
  140. gene regulation
    • transcriptional regulation mediated by a regulatory protein
    • can regulate gene by promoters
    • must be upstream of start in the promoter
    • regulatory protein binds to specific sequence of DNA
  141. activator protein
    • 1.type of regulator protein
    • 2.a protein that binds to specific DNA sequences and increases transcription
    • 3. activator binds ligand; complex binds the regulatory sequence and activates target gene; removing ligand stops transcription
  142. activator binding site
    DNA region that is bound by an activator protein; usually upstream of the promoter; activator binding helps recruit RNA polymerase
  143. repressor protein
    • a protein that binds to specific DNA regions and prevents transcription. binding to a ligand causes some repressors to bind DNA , and causes others to release from the DNA
    • prevents translation and transcription of gene!
  144. e. coli lactose operon
    • encodes a permease for lactose uptake 
    • encodes an enzyme, B-galactosidase, for lactose utilization
  145. how lactose repressor works, when ABSENCE OF LACTOSE
    • 1. repressor lacl binds to lacO.
    • 2. bound protein overlaps lacZYA promoter (lacP) and prevents transcription.
  146. presence of lactose
    • a. lactose is INDUCER
    • b. allolactase (inducer) binds to lacl repressor. 
    • c. reduced lacl affinity for lacO, and transcription  of the operon occurs
  147. sensor kinase
    • 1. in cell membrane
    • 2. detects an environmental signal and in response activates itself by autophosphorylation
    • 3. transfers phosphate to response regulator
    • 4. receptor outside recognizes ligand or protein
  148. response regulator
    • binds DNA regulatory sequences and activates or represses the expression of genes and operons
    • special signal involved called phospho relay
  149. chaperones
    • bind peptide sequence and help protein into its quaternary structure
    • Ex/ GroEL-ATP and GroEL - GroES
  150. degrons
    • recognized by proteasomes 
    • degrade mal-shaped and truncated proteins
  151. enzyme peptidase
    chaperones guides protein to proteosome
  152. activator
    binds DNA to activate transcription
  153. repressor
    • binds DNA to prevent transcription
    • may bind ligand
    • bind specific sequence 
    • typically in pairs
  154. operator
    dna region bound by a repressor. is usually DOWNSTREAM of promoter and thus prevents RNA polymerase from binding or proceeding
  155. derepression
    results in transcription
  156. two component signal transduction systems
    • 1. sensor kinase in cell membrane "detects" an environmental signal
    • 2. autophosphorylation
    • 3. transfers phosphate to a response regulator
    • 4. response regulator regulates gene expression (phosphorelay)
  157. regulon
    • coordinately regulating gens around the chromosome in response to same stimuli
    • can be same regulatory
  158. sRNAs
    • 1.small, unstranslated RNAs involved in regulation
    • 2. often act at post-transcriptional level by binding to a mRNA and blocking translation
    • form a double-stranded RNA molecule, 
    • 3.acts as anti-sense
  159. Fur Repressor
    protein that represses the expression of many genes scattered around the chromosome when it is bound to iron
  160. fur regulon
    all of genes regulated by fur protein
  161. quorum sensing
    • global regulatory control system in which genes and operons respond to population density (party)
    • AHLacotne
    • low molecular weight
    • soluble 
    • freely diffuse thru membrane