Please enable JavaScript.

Coggle requires JavaScript to display documents.

gene expression (Lac Operon (merodiploid experiments (constitutive I-…

- - - - negative control (off)
        
        prevents/lowers transcription
    - - relieves repression
        
        LacI repressor bound to allolactose cannot bind the operator (DNA sequence)
        
        transcription begins
      - produced by LacZ
    - - changes shape when bound to allolactose
  - - - promotes transcription
    - - only for low glucose levels
      - high glucose levels
        
        glucose depletes availability of adenyl cyclase and cAMP for binding to CRP
    - - changes shape when bound to cAMP so it can bind promoter
  - - - transcript might get a little off
      - rare and random "falling off" of repressor because of DNA affinity (even without lactose)
  - - - LacI not part of Lac operon
        
        I+ gene on plasmid acts in trans
        
        makes an “LacI- + Lac operon” inducible
    - - expression turned on in regulated manner
    - - expression is always on
    - - protein can bind targets sites anywhere in cell
    - - same ptype as I-: constitutive
        
        oc gene acts in cis
    - - affect only the operon to which they are connected to physically on same DNA strand
    - - allolactose can't bind it
- - - - adjacent cells pass ions, signaling molecules, and other materials between one another at cell junctions
    - - molecules bound to the cell surface provide a signal to other cells that make contact with the surface of the cell
    - - cell secretes signaling molecules that bind to receptors on its own surface and on neighboring cells of the same type to stimulate a response
      - senses cell density
        
        when cell density increases, concentration of autocrine signals increases
    - - specific cell secretes signaling molecule that does not affect itself
      - influences behavior of target cells in close proximity
      - its signal is broken down too quickly to be carried to other farther parts of the body and affect distant cells
    - - opposite of paracrine
      - occurs over relatively long distances
      - usually through hormones
        
        chemical messenger produced in gland or other structure
        
        acts on distant target cells in more than one part of an animal or plant
  - - - signaling molecule binds to the receptor in the target cell
        
        conformational change in the receptor activates the function
    - - initial signal is converted to a different signal inside the cell
        
        conducted through proteins of signal transduction pathway
      - occurs because the signaling molecule doesn't actually enter the cell
    - - alters at least one enzyme's activity
      - changes function of structural proteins in the cell
      - affects function of transcription factors
  - - - ion or molecule that nonvcovalently binds to a protein
      - conformational change
    - - cell surface receptor
        
        enables cells to respond to different kinds of signaling molecules
        
        found on plasma membrane
      - enzyme-linked receptor
        
        found in all living species
        
        protein kinase
        
        enzyme transfers phosphate groups from ATP to protein
      - G-protein coupled receptors
        
        eukaryotes
        
        interacts with G proteins to initiate cellular response
      - ligand-gated ion channels
        
        binds ligand and functions as an ion channel, either opening or closing it
        
        changes concentration of ions in the cell
        
        receptor may also respond
        
        occurs quickly
    - - dissociation contant (Kd)
        
        inverse relationship with affinity between ligand and receptor
        
        low Kd value indicates a receptor has a high affinity for a ligand
        
        small amount of ligand will result in most of the receptors having ligand bound to them
        
        response is likely to occur.
      - receptor signal leading to signal transduction (protein kinase cascade) and response
    - - no signal transduction and response
      - activated by signaling molecules that pass through plasma membrane
        
        example: steroids can enter the cell easily without assistance
        
        related to polarity
      - within the cell
    - - amplify and increase speed of signal
        
        typically for short duration
        
        when signaling molecule is no longer produced, the level falls and a larger percentage of receptors are not bound by ligands
        
        example: cAMP is small effector molecule produced from ATP that acts as 2nd messenger
      - small molecules and ions that relay signals inside cell
  - - - using signaling molecules
        
        autoinducers
        
        a sufficient concentration of these signaling molecules may elicit a response from bacteria
        
        bind transcriptional activators that induce QS genes
    - - high cell density leads to production of luciferase
        
        enzyme catalyzes a light producing biochemical reaction
      - transform E coli cells with V. fischeri DNA
        
        recombinant V. fischeri bioluminescence genes yield luminescence to E.coli
    - - when quorum met instant changes occur in their behavior, appearance and metabolism
        
        bacteria initially appear innocuous as they multiply
        
        changes lead to infection that ambushes and overwhelms immune system
      - QS proteins could be targeted by next generation of antibiotics
        
        immunity would provide no selective advantage to cells
        
        antibiotic resistant strains can be targeted successfully
- - - - frameshifts
        
        add or subtract a base and shift ORF
        
        insertion
        
        deletion
      - substitutions
        
        missense
        
        new nucleotide alters the codon and produces altered amino acid in the protein product
        
        nonsense
        
        new nucleotide changes a codon that specified an amino acid to one of the STOP codons and prematurely end translation
        
        the earlier in the gene that this occurs, the more truncated the protein product and the more likely that it will be unable to function
        
        silent
        
        cause no change in their product and cannot be detected without sequencing the gene
  - - - sometimes incompletely dominant
      - rare mutation because usually dominant mutant alleles are lethal when homozygous
    - - receptor protein is always active
        
        produce excessively active normal protein
        
        produce excess normal protein
      - caused by missense mutation
      - example: achondroplasia (dwarfism)
    - - express a normal protein in the wrong place or at the wrong time
        
        produce protein with new function
        
        due to ectopic expression
      - example: antennapedia
    - - produce proteins that interfere with the wild-type version of the protein
        
        block activity of wt alleles of same gene
      - "dominant negative"
      - usually seen in genes that encode multimeric proteins
  - - - haploinsufficiency
        
        caused by nonsense mutation
        
        example: polydactyly
        
        needs two wt copies
        
        heterozygous for wt and LOF express mutant ptype
        
        level of gene activity not enough to produce normal ptype
      - hypomorphic (incomplete)
        
        "leaky"
        
        produces less of wt protein
        
        produces mutant protein with weak, but detectable function
    - - amorphic
        
        "null"
        
        abolish function of a gene
        
        prevent synthesis of both protein and RNA
        
        promote synthesis of protein or RNA incapable of carrying out any function
  - - - step 1: nonsense mutation in a protein-coding gene creates a truncated, nonfunctional protein
      - step 2: second, nonsense suppressing (intragenic) mutation in the anticodon of a tRNA gene allows production of a (mutant) full-length polypeptide
      - restores wt ptype (intragenic suppression)
- - - - manipulate plasmids to carry genes of interest that can be introduced into bacteria
    - - resistance to antibiotics,
  - - - operon promotes co-expression of related genes
    - - repression, activation, attenuation
      - most common target of gene regulation
    - - affected by translation and the 3’ stem-loops, have “degradosome"
    - - repression, activation and autoregulation
    - - least common target because cell has already expended energy and resources to form protein
  - - - genes code for proteins that break down complex molecules
      - off by default
      - inducible regulation
        
        only turned on if substrate is present
    - - genes code for proteins that build molecules
      - on by default
      - repressible regulation
        
        only turned off if cell has enough product
- - - - used as vectors for transgenes
    - - also cuts genomic DNA to insert transposon into new site in chromosome
      - transgene markers usually dominant
  - - - target mammary gland enhancer and insert blood clotting factor gene so it is expressed through milk
    - - bacteria
      - carrot cells
      - in suspension
- - - - promoters are hidden when wrapped in nucleosomes
    - - affect chromatin modeling (open or closed)
  - - - located near transcription start
      - in cis
    - - flexible location and direction
      - single gene may have multiple enhancers
      - more than one tf can bind to single enhancer
      - in cis
    - - ensure that enhancers only have access to certain promoters
      - CTCD proteins bind, forming loops in the DNA
        
        if insulator between them, promoter and enhancer will be on separate loops
  - - - sequence specific
    - - activators
        
        recruit RNAP to
        promoter
        
        recruit co-activators
        
        make DNA accessible to RNAP
        
        chromatin remodeling proteins
        
        histone acetyl transferases (HATs)
      - repressors
        
        recruit co-repressors to directly prevent RNAP from binding promoter
        
        recruit co-repressors
        
        prevent basal transcription factors from binding DNA
        
        histone deacetylases (HDACs)
        
        histone methyl transferases (HMTs)
        
        modify histones to make DNA inaccessible
      - bind enhancers
    - - basal level
      - bind promoter
- - - - enhancers
      - activators
- - - - FruM transcription factor helps with expression of fruitless
        
        made depending on absence of the female-specific RNA binding protein called transformer (TRA)
        
        action of single gene sufficient enough to generate complex innate behavior
        
        FruM and FruF are transcription factors with opposite effects
      - two X’s (female) required to make SXL early
        
        when SXL turned on later in life for males and females, SXL modifies its own splicing
        
        females that do not express SXL later will undergo the "default" male alternative splicing, binding FruM (instead of FruF) and expressing the ptype of courting femaies
- - - - transcriptional control of targets, GFP localization of specific sequences, etc.