Block One Text 9

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Block One Text 9
2014-09-28 12:47:47
Test One
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  1. a.       A cell’s genome includes __ and __
    b.      Genotype: __/ Phenotype: __
    c.       The entire genome does not consist of back-to-back genes
                                                                              i.      __ occur in most genomes
    • chromosomes and plasmids
    • collection of genes
    • collection of proteins
    • Noncoding regions called short tandem repeats (STRs)
  2. a.       Replication requires enzymes
                                                                              i.      __: relaxes supercoiling
                                                                            ii.      __: unwinds and separates two strands
                                                                          iii.      __: newly added nucleotides are joined by this enzyme; adds only onto the 3’ end
                                                                           iv.      Point at which replication occurs is the __
    • Topoisomerase or gyrase
    • Helicase
    • DNA Polymerase
    • replication fork
  3. a.       Semiconservative model: __ 

    b.      Directionality
                                                                              i.      Paired bases are __ relative to each
                                                                            ii.      The two strands fit together in the __direction of one strand, which runs counter to the __ of the other strand
    c.       Energy is supplied by the __
                                                                              i.      __ are removed to add the nucleotide
    • new strand contains one parent strand and one new srand
    • upside down
    • five to three 
    • five to three direction
    • nucleotides
    • Two phosphate groups
  4. a.       DNA replication in bacteria is __, meaning what?
    • bidirectional
    • i. Two replication forks move in opposite directions away from the origin of replication and meet when replication is finished
    • 1. The two loops must be separated by a topoisomerease
  5. a.       RNA and Protein Synthesis
                                                                              i.      Transcription: __
    1.       __ and __ play a part
    2.       genetic info stored in the __ is rewritten so that the same info appears in the base sequence of mRNA
    3.       requires __, which binds to __; synthesizes in the __ until reaching the __
    • DNA--> RNA
    • rRNA and tRNA
    • sequence of nitrogenous bases of DNA
    • RNA polymerase,
    • DNA promoter site
    • five-->three direcition
    • terminator
  6.                                                                           i.      Translation: __

    1.       mRNA is in __, which determine the sequence o famino acids (__)
    a.       most amino acids have several __, called __
    • RNAà Protein
    • codons
    • 64 codons
    • alternative codons
    • degeneracy of the code
  7.    i.      61 are __; 3 are __
    1.       Sense code for __
    2.       Nonsence are stop condos:__, __, __
    3.       Start is __, which codes for __ rather than __ 
    • sense codons
    • nonsense codons
    • amino acids
    • UAA, UGA, UAG
    • AUG
    • formylmethionine rather than methionine
  8. 1.       Each tRNA has an __so that it can base pair with its associated codon
    2.       Process: ___

    • 1) Components come together
    • 2) on ribosome, a tRNA carrying the first amino acid is paired with the start codon on mRNA at the P site
    • 3) the second codon of the mRNA pairs with a tRNA carrying the second amino acid at the A site
    • 4) the ribosome moves along the mRNA until the second tRNA is in the P site; the next codon to be translated is brought into the A site, while the first exits the E site
    • 5) the second amino acid joins the third by a peptide bond and the first tRNA is release
    • 6) the ribosome continues to move along the mRNA, and new amino acids are added
    • 7) stop codon releasesthe polypeptide
    • 8) the last tRNA is released and the ribosomes comes apart
  9. a.       The common feature of all metabolic reactions is that they are __
    b.      __ stops enzymes that have already been synthesized
    c.       Many genes are not regulated but are instead __, meaning that __

                                                                              i.      These genes, which are turned on all the time, code for __
    • catalyzed by enzymes
    • Feedback inhibition
    • constitutive
    • their products are constantly produced at a fixed rate
    • enzymes that the cell needs in large amounts for its major life processes
  10. a.       Pre-Transcriptional control: control __ and __ in cell, not __
                                                                              i.      Repression: __
    1.       Mediated by __, which do what?
    • formation and amounts of enzymes
    • activities

    inhibits gene expression and decreases the synthesis of enzymes; response to overabundance of end-product of metabolic pathway, causing decrease in rate of synthesis of enzymes leading to formation of product

    • repressors
    • block the ability or RNA pol to initiate transcription from the repressed gene
  11. Induction : __
    Inducer: __
    2.       Enzymes that are synthesized in the presence of inducers: __
    • turns on transcription of genes
    • induces transcription
    • inducible enzymes
  12.                                                                           i.      The Operon Model of Gene Expression
    1.       Genes that are regulated together are __
    2.       In the control region of the lac operon are two relatively short segments of DNA
    a.       Promoter: __
    b.      Operator: is a __
    3.       The promoter and operator sights, as well as structural genes: __
    4.       A regulatory gene can __ that does what?
    • structural genes
    • region where RNA Pol initiates transcription
    • traffic light that acts as a go or stop signal for transcription of the structural genes
    • operon
    • encode a repressor protein that switches inducible and repressible operons on or off
  13. 1.       In inducible operons:what happens? 
    • a. In the absence of lactose, for example, the repressor binds to the operator site, thus preventing transcription
    • b. If present, the repressor binds elsewhere
  14. 1.       In repressible operons, what happens?
    • a. Structural genes are transcribed until they are turned off, or repressed
    • b. When excess of something is present, the excess object acts as a corepressor binding to the repressor protein i. The repressor protein can now bind to the operator, stopping further tryptophan synthesis
  15.                                                                           i.      Positive Regulation
    1.       cAMP: derived from __that serves as a __
    a.       when glucose is not available, cAMP __, which binds to the __, initiating transcription by doing what?
    b.      it is an __, a chemical alarm signal that promotes a cell’s response to environmental or nutritional stress
    c.       inhibition of the metabolism of alternative carbon sources b glucose is __
                                                                                                                                                      i.      when glucose is available, the level of cAMP in the cell is __, and consequently __
    • ATP 
    • cellular alarm signal
    • accumulates and binds to the allosteric site of catabolic activator protein (CAP)
    • promoter
    • making it easier for RNA polymerase to bind to the promoter
    • alarmone
    • catabolite repression
    • low
    • CAP is not bound
  16.                                                                           i.      epigenetic control
    1.       eukaryotic and bacterial cells can turn genes off by __, which are passed to offspring cells-> epigenetic inheritance
    methylating certain nucleotides
  17. a.       Posttranslational Control
                                                                              i.      Single-stranded RNA molecules of approximately 22 nucleotides, called __inhibit protein production in eukaryotic cells; allow different cells to produce different proteins
                                                                            ii.      An miRNA binds with  complementary mRNA, forming a __, which is __ so that the __ is not made
    • microRNAs 
    • double-standard RNA
    • enzymatically destroyed
    • mRNA-encoded protein is not made
  18.                                                                           i.      __: single base is replaced; in translation, it may cause another amino acid, which is a __--> bad (sickle cell)
                                                                            ii.      __: creating a stop codon in the middle of an mRNA molecule
                                                                          iii.      __: one or a few nucleotide pairs are deleted or inserted in the DNA, changing the codons
                                                                           iv.      What are spontaneous mutations? 
    • Base substitution
    • missense mutation
    • Nonsense mutation
    • Frameshift mutation

    Spontaneous mutations occur in absence of mutation causing agents, which are called mutagens
  19. I.                    Mutagens
    a.       Chemical: 

    1) Nitrous acid
    2) Nucleoside analog
    3) Other
    •                                                                           i.      Nitrous acid: A pairs with Cà two different strands (one with AT and another with CG)
    •                                                                         ii.      Nucleoside analog: slightly altered base-pairing properties; the analogs are randomly incorporated into cellular DNA in place of normal basesà mistakes in base pairing
    •                                                                       iii.      Other chemical mutagens cause small deletions or insertions, which can result in frameshifts (they are often potent carcinogens)
  20. Mutagens: Radiaiton

    X and Gamma rays
    •                                                                           i.      can ionize atoms and molecules, causing electrons to pop out of their usual shells, which then cause more damage to other molecules
    • 1.       Can oxidize bases in DNA, resulting in errors in DNA replication
  21. Mutagens: Radiaiton

    UV rays
    •                                                                           i.      form covalent bonds between certain bases, creating dimers
    • 1.       Enzymes can repair UV induced damage, like photolases (separate the dimer)
  22.                                                                           i.      __: repair mutations by cutting out and filling in the gap with correct bases
    1.       __add a __ to selected bases soon after a DNA strand is made to allow them to be recognzed
    • Nucleotide excision repair
    • Methylases 
    • methyl group
  23. c. The frequency of mutation

    - Mutation rate?

    - How specific

    - Mutations can be __ and __

    - mutagen
    •                                                                           i.      Mutation rate: probability that a gene will mutate when a cell divides
    •                                                                         ii.      Occur randomly along a chromosome
    •                                                                       iii.      Mutations can be adaptive and beneficial
    •                                                                        iv.      A mutagen increases the spontaneous rate of mutation 
  24. Identifying mutants

    - positive

    - negative
    •                                                                           i.      Positive (direct) selection: detection of mutant cells by rejection of the unmutated parent cells
    •                                                                         ii.      Negative (indirect) selection: selects a cell that cannot perform a certain function, using replica plating
  25. How to test via negative indirect selection
    • 1.       Grow all on one plat with nutrients, histidines, etc., then transfer them, via a velvet paper, to other plates that lack what is trying to be tested for.
    • a.       Any mutant microorganism having a nutritional requirement that is absent in the parent is an auxotroph
  26. Identifying Chemical Carcinogens
    •                                                                           i.      Ames test: uses bacteria as carcinogen indicators
    • 1.       Based on observation that exposure of mutant bacteria to mutagenic substances may cause new mutations that reverse the effect of the original mutation: reversions