Examen final de Genética

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Examen final de Genética
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2013-05-04 12:22:53
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genetics final
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  1. A gene
    is a segment of DNA used to make a functional product– either an RNA or a polypeptide
  2. Transcription
    is the first step in gene expression, literally means the act or processof making a copy, the term refers to copying a DNA sequence into an RNA sequence
  3. The central dogma of genetics
  4. Promoter
    site for RNA polymerase binding; signals the beginning of transcription.
  5. Regulatory sequences
    site for binding of regulatory proteins that influence the rate of transcription. Regulatory sequences can be found in a variety of locations.
  6. Ribosome-binding site
    translation begins near this site in the mRNA. In eukaryotes,the ribosome scans them RNA for a start codon.
  7. The sequence of codons
    in the mRNA determines the sequence of amino acidsin a polypeptide.
  8. Bacterial mRNA may be polycistronic,
    which means it encodes two or more polypeptides
  9. The DNA strand that is transcribed
    is the template strand
  10. The RNA transcript is complementary
    to the template strand
  11. The opposite strand
    is the coding strand or the sense strand as well as the non-template strand
  12. The base sequence
    is identical to the RNA transcript except for the substitution of uracilin RNA for thymine in DNA
  13. Transcription factors
    recognize the promoter and regulatory sequences to control transcription
  14. Transcription
    occurs in three stages:Initiation Elongation Termination
  15. Initiation
    The promoter functions as a recognition site for transcription factors. The transcription factor(s) enables RNA polymerase to bind to the promoter. Following binding, theDNA is denatured into a bubble known as the open complex.
  16. Elongation/synthesis of the RNA transcript
    RNA polymerase slides along the DNA in an opencomplex to synthesize RNA.
  17. Termination
    A terminator is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA.
  18. Over 90% of all genes are structural genes
    which are transcribed into mRNA Final functional products are polypeptides
  19. The RNA transcripts from nonstructural genes
    are not translated
  20. Promoters(Bacteria)
    DNA sequences that “promote” gene expression they direct the exact location for the initiation of transcription typically located just upstream of the site where transcription of a gene actually begins bases in a promoter sequence are numbered in relation to the transcription start site
  21. System of promoters(bacteria)
  22. RNA polymerase catalyzes the synthesis of RNA(Bacteria)
    RNA polymerase holoenzyme is composed of:Core enzyme Sigma factor These subunits play distinct functional roles
  23. Initiation of Bacterial Transcription
    The RNA polymerase holoenzyme binds loosely tothe DNAIt then scans along the DNA, until it encounters apromoter regionWhen it does, the sigma factor recognizes boththe –35 and –10 regionsA region within the sigma factor that contains ahelix-turn-helix structure is involved in a tighterbinding to the DNA
  24. End of Initiation (Bacteria)
    The binding of the RNA polymerase to the promoterforms the closed complexThen, the open complex is formed when theTATAAT box in the -10 region is unwoundA short RNA strand is made within the opencomplexThe sigma factor is released at this point
  25. Transcription (Bacteria)
  26. Elongation in Bacterial Transcription
    The core enzyme slides down the DNA to synthesize an RNA strand The DNA strand used as a template for RNAsynthesis is termed the template or antisense strandThe opposite DNA strand is called the coding strand
  27. Last phase of elongation
    Behind the open complex, the DNA rewinds back into a double helix
  28. Termination of Bacterial
    • TranscriptionTermination is the end of RNA synthesisTermination occurs
    • when the short RNA-DNAhybrid of the open complex is forced toseparate
    • releasing the newly made RNA as wellas the RNA polymerase
  29. E. coli has two different mechanisms for termination
    – rho-dependent termination• Requires a protein known as r (rho)– rho-independent termination• Does not require r (rho)
  30. TRANSCRIPTION IN EUKARYOTES
    the basic features very similar to bacteria• gene transcription in eukaryotes is more complex• more complex cells (organelles)• higher cellular complexity means more genes encoding proteins are needed • Multicellularity adds another level of regulation–express genes only in the correct cells at the proper time
  31. Nuclear DNA is transcribed by three different RNA polymerases (eukaryotes)
    • RNA pol I
    • RNA pol II
    • RNA pol III
  32. RNA pol I (eukaryotes)
     Transcribes all rRNA genes (except for the 5S rRNA)
  33. RNA pol II (eukaryotes)
    Transcribes all structural genes synthesizes all mRNAs Transcribes some snRNA genes
  34. RNA pol III (eukaryotes)
     Transcribes all tRNA genes and the 5S rRNA gene
  35. Features of most promoters (for structural genes)(eukaryotes)
    Regulatory elements  TATA box Transcriptional start siteS
  36. Core promoter (eukaryotes)
    consists of the “TATA box” and “transcriptional start site”• determining the start point for transcription– The core promoter by itself produces a low level of transcription or basal transcription
  37. Regulatory elements(eukaryotes)
    short DNA sequences that affect the binding of RNA polymerase to the promoter
  38. Transcription factors(eukaryotes)
    bind to these regulatory elements and influence the rate of transcription
  39. Three categories of proteins are required for basa ltranscription to occur at the promoter(eukaryotes)
    RNA polymerase II Five different proteins called general transcription factors (GTFs) A protein complex called mediator
  40. RNA Pol II transcriptional termination (eukaryotes)
    • Pre-mRNAs are modified by cleavage near their 3’end with subsequent attachment of a string of adenines• Transcription terminates 500 to 2000 nucleotides downstream from the polyA signal
  41. RNA MODIFICATION (eukaryotes)
    The sequence of DNA in the coding strand corresponds to the sequence of nucleotides in the mRNA• The sequence of codons in the mRNA provides the instructions for the sequence of amino acids in the polypeptide• eukaryotic structural genes reveal that they are not always colinear with their functional mRNAs
  42. Transcription produces the entire gene product(eukaryotes)
    – Introns are later removed or excised– Exons are connected together or spliced
  43. RNA transcripts can be modified in several ways (eukaryotes)
    For example• Trimming of rRNA and tRNA transcripts• 5’ Capping and 3’ polyA tailing of mRNA transcripts
  44. Exonucleases
    cleave a covalent bond between two nucleotides at one end of a strand
  45.  Endonucleases
    can cleave bonds within a strand
  46. The translation
    of the mRNA codons into amino acid sequences leads to the synthesis of proteins
  47. Genes that encode polypeptides
    are termed structural genes These are transcribed into messenger RNA (mRNA)
  48. Archibald Garrod
    First to propose (at the beginning of the 20th century) a relationship between genes and protein production Garrod studied patients who had defects in their ability to metabolize certain compounds
  49. Alkaptonuria propose
    He proposed that a relationship exists between the inheritance of the trait and the inheritance of a defective enzyme He described the disease as an inborn error of metabolism
  50. Genetic code
    Translation relies on the genetic code The genetic information is coded within mRNA in groups of three nucleotides known as codons
  51. AUG (specifies for methionine) =
    start codon
  52. UAA, UAG and UGA =
    termination, or stop, codons
  53. Overview of gene expression
  54. Polypeptide synthesis
    has a directionality that parallels the 5’ to 3’ orientation of mRNA
  55. 20 amino acids
    that may be found in polypeptides
  56. Nonpolar amino acids are
    hydrophobic
  57. Polar and charged amino acids are
    hydrophilic
  58. There are four levels of structure in proteins
    Primary  Secondary Tertiary Quaternary
  59. A protein’s primary structure
    is its amino acid sequence
  60.  The primary structure of a protein folds to form regular, repeating shapes known as
    secondary structures
  61. There are two types of secondary structures
    • α helix
    • β sheet
  62. Tertiary structure
     The short regions of secondary structure in a protein fold into a three-dimensional tertiary structure This is the final conformation of proteins that are composed of a single polypeptide Structure determined by hydrophobic and ionic interactions as well as hydrogen bonds and Van der Waals interactions
  63. Quaternary structure
     Proteins made up of two or more polypeptides have aquaternary structure This is formed when the various polypeptides associate with one another to make a functional protein
  64. Functions of proteins
    A category of proteins are enzymes Accelerate chemical reactions within a cell Can be divided into two main categories Anabolic enzymes  Synthesize molecules and macromolecules  Catabolic enzymes  Break down large molecules into small ones Important in generating cellular energy
  65. Structure and function of tRNA
     tRNAs play a direct role in the recognition of codons in the mRNA In particular, the hypothesis proposed that tRNAhas two functions 1. Recognizing a 3-base codon in mRNA 2. Carrying an amino acid that is specific for that codon
  66. During mRNA-tRNA recognition,
    the anticodonin tRNA binds to a complementary codon in mRNA
  67. The secondary structure of tRNAs exhibits
    a cloverleaf pattern It contains Three stem-loop structures A few variable sites An acceptor stem with a 3’ single strand region
  68. The enzymes that attach amino acids to tRNAsare known as
    aminoacyl-tRNA synthetases
  69. Aminoacyl-tRNA synthetases catalyze a two-step reaction involving three different molecules
    Amino acid, tRNA and ATP (for energy)
  70. The aminoacyl-tRNA synthetases are responsible for the
    “second genetic code”
  71. Translation occurs on the surface of a large macromolecular complex termed
    the ribosome
  72. Bacterial cells have one type of ribosome
    Found in their cytoplasm
  73.  Eukaryotic cells have two types of ribosomes
    One type is found in the cytoplasm The other is found in organelles Mitochondria ; Chloroplasts
  74. A ribosome is composed of structures called
    the large and small subunits
  75.  Ribosomes contain three discrete sites
    Peptidyl site (P site) Aminoacyl site (A site) Exit site (E site)
  76. Translation initiaton
    The mRNA, initiator tRNA, and ribosomal subunits associate to form an initiation complex  This process requires three Initiation Factors The initiator tRNA recognizes the start codon in mRNA In bacteria, this tRNA is designated tRNAfmet It carries a methionine that has been covalently modified to N-formylmethionine The start codon is AUG
  77. The binding of mRNA to the 30S subunit is facilitated by
    a ribosomal-binding site or Shine-Dalgarno sequence This is complementary to a sequence in the 16S rRNA
  78. Translation elongation
    During this stage, amino acids are added to the polypeptide chain, one at a time
  79. Translation termination
    The final stage occurs when a stop codon is reached in the mRNA In most species there are three stop or nonsense codons UAG UAA  UGA These codons are not recognized by tRNAs, but by proteins called release factors Indeed, the 3-D structure of release factors mimicsthat of tRNAs
  80. Bacteria have
    three release factors
  81.  Eukaryotes only have one
    release factor eRF, which recognizes all three stop codons
  82. Bacterial Translation Can Begin Before Transcription Is Completed
    Bacteria lack a nucleus Therefore, both transcription and translation occur in the cytoplasm
  83. Transcription + translation
  84. Gene regulation
    refers to the ability of cells to control their level of gene expression
  85. Constitutive genes
    are unregulated and have constant levels of expression
  86. Benefits of gene regulation
    Conserves energyproteins produced only when neededAccurate gene expressionEnsures genes expressed in appropriate cell type and at the correct stage in development
  87. Gene regulation in prokaryotes
    used to respond to changes in the environment
  88. Gene regulation in eukaryotes
    All of the organism’s cells contain the same genome but express different proteomes
  89.  Bacterial gene regulation
    Most commonly occurs at the level of transcription Or control rate mRNA translated Or regulated at protein or post-translation level
  90. Eukaryotic gene regulation
    Transcriptional regulation commonRNA processingTranslationPost-translation
  91.  Bacterial gene regulation
  92. Eukaryotic gene regulation
  93. Transcriptional regulation in bacteria
    Involves regulatory transcription factors Bind to DNA near a promoter and affect transcription of one or more nearby genes Repressors inhibit transcriptionNegative control Activators increase the rate of transcriptionPositive control
  94. Operon
    in bacteria is a cluster of genes under transcriptional control of one promoterRegulatory region called operator
  95. lac operon
    In E. coli contains several genes for lactose metabolism lacP - promoter 3 structural geneslacZ – β-galactosidase Allolactose important in lac operon regulationlacY – lactose permeaselacA – galactosidase transacetylase
  96. When lactose is absent
    Lac repressor binds to nucleotides of lacoperator site preventing RNA polymerase from transcribing lacZ, lacY and lacARNA polymerase can not move forward
  97. When lactose is present
    Allolactose is a small effector moleculeallolactose molecules binding to lacrepressor prevents repressor from bindingProcess called induction and lac operon is inducible
  98.  Operon is turned off
    when CAP is not bound
  99. CAP binding to DNA
    enhances RNA polymerase binding which increases transcription
  100. trp operon
    In E. coli, encodes enzymes required to make amino acid tryptophan Regulated by a repressor protein encoded by trpR gene Binding of repressor to trp operator site inhibits transcription
  101. DNA methylation
    DNA methylase attaches methyl groups Common in some eukaryotes but not all In mammals, 5% of DNA is methylated Usually inhibits transcription Unmethylated areas are correlated with active genes

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