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71 Cards in this Set
- Front
- Back
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lac operon experiment basic principle |
proteins (tran-acting factors) bind to specific DNA sequences in genes to regulate transcription initiation |
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Factors that influence binding of proteins to specific DNA sequences |
small molecules within cells or that enter cells from external environment |
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what points that bacteria regulates gene expression |
at point of transcriptional initiation and also transcriptional elongation |
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function of trp attenuator |
reflects the concentrations of small molecules allows cells to respond to environmental conditions |
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trp attenuator structure |
sequence of RNA
can assume alternative configurations |
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cis acting RNA leader sequences
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regulates transcription elongation and initiation of translation
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small trans actin RNAs
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also regulate translation initiation
are encoded in bacterial genomes |
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antisense RNAs
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can influence transcription of a gene
or stability or translation of the gene's RNA |
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operons
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unit made of cluster of genes that make the same product
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how genes in operon are expressed...
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into a single, multicistronic RNA
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if you can control the transcription of the operon, you can regulate...
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the genes comprising the operon
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gene expression
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genetic info is converted into RNA (transcription) and then into a polypeptide (translation)
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RNA polymerase
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enzyme that transcribes DNA sequence into RNA transcript
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promoter
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DNA sequences near to (usually upstream) of gene's transcription start site
RNA polymerase binds to it to initiate transcription |
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ribsome binding site
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on prokaryotic mRNA
contains both initiation codon and Shine-Dalgarno box ribosomes bind to it to start translation of protein coding sequences on the mRNAs |
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catabolic pathway
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metabolic pathway
breaks down complex molecules to make smaller ones (and usually energy) |
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anabolic pathway
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metabolic pathway
makes complex molecule from simpler ones |
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transcription factor
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protein
binds to specific DNA sequence and regulates transcription |
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positive vs negative regulators
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positive - activate transcription
negative- inhibit transcription (repressors) |
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inducible regulation
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transcription occurs only in presence of inducer
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inducer
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small molecule
binds to positive regulator alters the pos regs conformation so that it can bind to DNA (important in catabolic path) |
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repressible regulation
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transcription occurs only in absence of corepressor
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corepressor
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binds to repressor
alters repressors conformation so that it can bind to DNA (important in anabolic path) |
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induction
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when an inducers causes transcription of a gene
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operon
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DNA composed of structural genes (encode functional products)
+ promoter + operator work together to express the structural genes to environmental changes |
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allosteric protein
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changes conformation reversibly when bound to specific effector molecule
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constitutive mutants
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cause gene transcription to occur all the time
regardless of environmental conditions |
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effector
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binds to allosteric protein or RNA to cause conformational change
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in trans
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describes action of protein or RNA
can bind to target sites on any DNA or RNA in cel diffuse through cell to find target |
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in cis
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describes action of DNA site of region in RNA that acts only on DNA/RNA to which it is physically connected
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domain
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region of protein with particular function
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catabolite expression
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inhibition of expression of genes or operons
when glucose or preferred catabolite is present lac-operon is example |
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RNA leader sequence
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5 prime UTR in mRNA
in prokaryotes: act in cis to regulate transcription elongation or transcript's translation |
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hairpin loops
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occurs when single strand of RNA folds back on itself due to complementary base pairing between different regions in same molecule
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attenuation
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type of gene regulation
responds to translation of ORF in RNA leader when ORF is translated efficiently, transcription terminates in RNA leader sequence before complete mRNA transcript is made |
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attenuator
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RNA lead
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terminator
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in prokaryotes: stem loop structures, cause RNA polymerase to stop downstream transcription
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antiterminator
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can prevent formation of terminator
is a competing stem loop structrue |
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riboswitch
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allosteric RNA leader
binds effector - controls gene expression |
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RNA thermometer
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allosteric RNA leader
regulates translation in response to temperature stability of stem loop in this case is temp dependent |
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sRNAs
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small RNAs
regulate transcription in trans base pair with sites on mRNAs can hide or expose ribosome bining site on mRNA |
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antisense RNAs
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regulatory mRNAs
complementary to mRNAs they regulate can block transcription or translation of their target mRNA |
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fusion gene
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made of recombinant DNA technology
parts of 2 or more different genes |
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reporter gene
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fusion gene
ORF encodes easy to detect protein expression of this gene reports activity of fusion gene's promoter |
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RNA seq (cDNA deep sequencing)
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all transcripts of organism
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quorum sensing
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regulation of transcription of particular genes
in response to sensing of population density |
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gene regulation involves what DNA elements and what factors that bind them
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cis acting DNA elements
trans acting factors that bind them |
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do transcription factors bind to double or single stranded DNA?
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double
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do DNA strands denature in order to bind transcription factors?
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no, do not denature
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what forms bonds with amino acid R groups within DNA binding domain of the transcription factor? and what type of bond is formed?
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atoms at the edges of the base pairs (not involved in forming H bonds between complementary base pairs)
form noncovalent bonds |
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what makes a transcription factor have more affinity for the binding site?
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the particular sequence of amino acids in DNA binding domain and particular base pair sequence of the binding site
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transcription factor equilibrium between...
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bound and unbound states
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factors that determine how frequently a transcription factor is bound to particular site on DNA...
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affinity of DNA binding domain of protein for that base pair sequence
concentrations of protein and DNA in nucleus |
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When does the regulation of prokaryotic gene expression in response to the environment occur?
And what 3 components does it require? |
during initiation of transcription
1. functional structural gene (lac Z+) 2. intact cis acting DNA sites (promoter P and operator o) 3. functional trans acting factor gene (lacI+) |
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cis acting sites examples
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promoter and operator (at 5 prime end of every operon) - function only with that operon
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trans acting proteins example
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transcription factors - can work on any operon in the cell (diffuses in the cytoplasm to find its binding site on any DNA molecule present in there)
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prokaryotic promoters
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specific base pair sequence that attracts RNA polymerase to initiate transcription of a gene or operon
amino acids in DNA binding domain of RNA polymerase have higher affinity for promoter's base pair sequence |
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positive regulator
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increase affinity of RNA polymerase for the promoter
bind DNA sites near the promoter, where the factors make contact with RNA polymerase |
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promoter with bond positive regulator...
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has higher affinity for RNA polymerase than when unbound
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negative regulators
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bind to DNA sites (operators) that overlap with the promoter
prevents RNA polymerase from binding there (prevents initiation of transcription) |
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induction
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stimulation of protein synthesis by specific molecule
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repressor
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negative regulator
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operator
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site to which repressor binds
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allostery
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protein or RNA undergoes reversible conformational change
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operon
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group of genes transcribed into one RNA
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catabolite repression
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glucose prevents expression of catabolic operons
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reporter gene
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often fused to regulatory regions of genes whose expression is being monitored
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attenuation
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termination of transcription elongation in response to translation
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sRNA
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regulates translation of mRNAs in trans
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riboswitch
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RNA leader that regulates gene expression in response to small molecule or ion
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