Cell Bio Ch. 11

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Cell Bio Ch. 11
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2011-11-28 02:19:33
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Cell Bio 11
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Cell bio Ch 11
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  1. Genes ____ information for producing all _______.
    store; cellular proteins
  2. Mutation in a single gene causes a single ______ in an _______ of a
    single polypeptide.
    substitution; amino acid sequence
  3. •Overview
    of Flow of Information through the Cell

    –Messenger
    RNA (mRNA): ______________

    –Transcription: __________________

    –Translation: _________________
    - intermediate between gene and polypeptide

    - process by which RNA is formed from a DNA template

    -process by which proteins are synthesized in the cytoplasm from an mRNA template
  4. Overview of flow of information in eukaryotes
    Explain.
    5 steps
    • 1.Segment of DNA transcribed to Pre-mRNA
    • 2. Pre-mRNA into mRNA
    • 3. mRNA travels outside of cytoplasm
    • 4. mRNA translated
    • 5. Protein
  5. Three classes of RNA in a cell
    • –messenger RNA (mRNA)
    • –ribosomal RNA (rRNA)
    • –transfer RNA (tRNA)
  6. •rRNA means and does what?
    ribosomal RNA recognizes other molecules, provides structural support, and catalyzes the chemical reaction in which amino acids are linked to one another
  7. •tRNAs means and does what?
    transfer RNA are required to translate information in the mRNA code into amino acids
  8. _____________ are responsible for transcription in both prokaryotes and eukaryotes.
    •DNA-dependent RNA polymerases (or RNA polymerases)
  9. •Incorporate nucleotides into a strand of RNA from a DNA template.

    –The ______ is where the enzyme
    binds prior to initiating transcription.

    –The enzyme requires the help of _____________ to
    recognize the promoter.
    • -promoter
    • -transcription factors
  10. Chain elongation during transcription.
    Explain
    Look in book.
  11. •Newly synthesized RNA chain grows in a 5’ to
    3’ direction ___________ to the DNA.
    antiparallel
  12. •Nucleotides enter the polymerization reaction as ____________ precursors.
    triphosphate
  13. •The reaction is driven forward by the _____ of
    a pyrophosphate: PPi -> 2Pi
    hydrolysis
  14. •Once polymerase has finished adding nucleotides, the DNA-RNA hybrid _________ and
    the DNA double helix ______.

    •Two enzymatic activities of RNA polymerase:
    • • dissociates; reforms
    • –digestion of incorrect nucleotides
    • –polymerization
  15. •Transcription in Bacteria

    –One type of RNA polymerase in prokaryotes: five subunits associated to form a core enzyme.

    –________-competent cells also have a ______ attached to the RNA
    polymerase before attaching to DNA.
    • - five; core enzyme
    • - Transcription; sigma factor
  16. •__________ are located upstream from the site of initiation.

    –Two conserved regions:

    –Differences in the DNA sequences at both –35 element and the Pribnow box may regulate
    _________.

    •Termination in bacteria can either require a _________ or may reach a terminator
    sequence without _____.
    • •Bacterial promoters
    • - 35element; Pribnow box
    • -gene expression

    • rho factor protein; rho
  17. Explain the promoter region in bacteria.
  18. •Transcription and Processing
    –Three types of RNA polymerases in eukaryotes:
    •Most rRNAs are transcribed by ________
    •tRNAs are transcribed by ________
    •mRNAs are transcribed by ___________
    –_______ regulate the activity of RNA
    polymerases.
    • •RNA polymerase I
    • •RNA polymerase III
    • •RNA polymerase II

    -transcription factors
  19. •Newly transcribed RNAs are processed.
    –A transcription unit is the DNA segment corresponding to a _______ transcript.
    –A primary transcript (or pre-RNA) is _________
    •A variety of small RNAs are required for RNA processing.
    • -primary
    • -the initial RNA molecule synthesized.
  20. •A eukaryotic cell may contain millions of_______.
    •The DNA sequence encoding rRNA is called____
    and is usually clustered in the genome.
    •In nondividing cells, rDNA are _____ in the
    _______, where_____ are produced.
    • •ribosomes
    • •rDNA
    • •clustered; nucleoli, ribosomes
  21. •Synthesizing the rRNA Precursor
    –rRNA genes are arranged in _____.
    –rRNA transcription has a “_________” pattern.
    –Proteins that convert rRNA precursors into mature rRNA become associated with pre-rRNA during
    ______.
    –The _______ separates transcription units in a ribosomal gene cluster.
    • -tandem
    • -"christmas tree"
    • -transcription
    • -nonstranscribed spacer
  22. •Processing the rRNA Precursor
    –A single primary transcript (pre-rRNA) can be spliced into three rRNAs: __________
    –Pre-rRNA contains large numbers of ______ and ___________.
    –Unaltered sections of the pre-rRNA are _____.
    • -28S, 18S, 5.8S
    • -methylated nucleotides; pseudouridine residues
    • -discarded
  23. •The Role of snoRNAs:
    - Processing of________
    •packaged with proteins into ________
    •modify bases in _______
    • –Processing of pre-rRNA is helped by small, nucleolar RNAs (snoRNAs).
    • •snoRNPs (small, nucleolar ribonucleoproteins)
    • •pre-RNAs
  24. •Synthesis and Processing of the 5S rRNA

    –The 5S rRNA genes are located outside the nucleolus.
    –It is transcribed by __________, which uses an
    internal ______.
    • -nucleolus
    • -RNA polymerase III; promoter
  25. •Transfer RNAs
    –Genes are located in small clusters scattered around the
    __________.
    –tRNAs have_____ within the coding region of the gene.
    –During processing, the tRNA precursor is ____and numerous bases must be modified.
    • -genome
    • -promoter sequences
    • -trimmed
  26. •The precursors of mRNAs are represented by diverse RNAs called _________.
    –Found only in the _______.
    –Have large molecular weights.
    –Degraded after a very short time.
    • •heterogeneous nuclear RNAs (hnRNAs)
    • -nucleus
  27. •The Machinery for mRNA Transcription
    –RNA polymerase II is assisted by general transcription
    factors (GTFs) to form the _________.
    –The critical portion of the promoter lies ________ from the initiation site and contains the TATA box.
    –The preinitiation complex of GTFs and polymerase assemble at the ____ box.
    • -preinitiation complex (PIC)
    • -24-32 bases upstream
    • -TATA
  28. •The preinitiation complex assembly
    starts with the ________________
    –TBP is a subunit of the _________
    –Binding to the promoter causes a _______
    in DNA
    • •binding of the TATA-binding protein (TBP) to the promoter.
    • -TFIID
    • -conformational change
  29. •Binding of TFIID sets the stage for the assembly of the complete PIC.
    •The three GTFs bound to the promoter allow the binding of RNA polymerase with its TFIIF.
    -As long as TFIID
    remains bound to the promoter, additional _____________
    for additional rounds of transcription.
    • •TFIID; PIC
    • •three GTFs; the binding; TFIIF
    • -RNA polymerases may be able to attach
  30. •RNA polymerase is heavily phosphorylated at the
    _____________.
    –(answer from above) phosphorylation can be catalyzed by different _______.
    –TFIIH acts as the ____________.
    •Termination of transcription is not well understood.
    • •carboxyl-terminal domain (CTD)
    • -protein kinases
    • -protein kinase
  31. •Messenger RNAs share certain structural properties
    –Each code for a specific ______.
    –Are found in the _______.
    –Are attached to ______ when translated.
    –Most have a noncoding segment.
    Eukaryotic mRNAs
    modifications at their 5’ (guanosone cap) and 3’ poly(A) tail.
    • -polypeptide
    • -cytoplasm
    • -ribosomes
  32. •Split Genes: An Unexpected Finding
    –The difference between heterogenous nuclear RNA (hnRNA) and mRNA provided early clues about RNA processing.
    –Eukaryotic genes contain intervening sequences which are missing from mature mRNAs.
    –The presence of genes with intervening sequences are
    called ______.
    –The parts of the split gene that contribute to the
    mature mRNA are called _____.
    –The intervening sequences are called _____.
    • -split genes
    • -exons
    • -introns
  33. •Hybridization experiments supported the concept of mRNA precursors (pre-mRNAs).
    •Loops in the DNA-RNA complex were the introns.
    –Resulted from introns that were not __________ to any part of the gene.
    complementary
  34. •RNA transcripts become associated with _______ as they are synthesized.
    •During processing, a 5’ methylguanosine cap and a 3’
    poly(A) tail are added.
    •Intervening sequences are ______ and exons are connected by ________.
    • •ribonucleoproteins
    • •removed; RNA splicing
  35. •RNA Splicing: _______ of _____ from a Pre-mRNA
    –Breaks are introduced at the 5’ and 3’ ends of the
    splice sites.
    –Sequences between exon-intron boundaries are highly _________.
    –Sequence most commonly found at the boundary is g/GU at the 5’ end and AG/G at the 3’ end.
    • •Removal; Introns
    • -introduced; splice sites
    • -conserved
  36. •Studying RNA splicing has led to the study of RNA enzymes, or __________.
    –RNA splicing is thought to have evolved from
    ___________.
    –An example of a self-splicing intron is the _________, discovered in various organisms.
    • •ribozymes
    • -self-splicing RNAs
    • -group II intron
  37. •The pre-mRNA is not capable of self-splicing
    –requires small nuclear RNAs (snRNAs)
    •As each hnRNA is transcribed, it
    becomes associated with a_________.
    •Processing occurs as each intron becomes associated
    with a complex called ______.
    •The spliceosome consists of ____________.
    •Removal of an intron requires
    –Several snRNP particles.
    Each snRNP contains a dozen or
    more proteins, such as the Sm protein family.
    • -small nuclear RNA's (snRNAs)
    • • hnRNP (heterogeneous nuclear ribonucleoprotein)
    • •spliceosome
    • •small nuclear ribonucleoproteins (snRNPs)
  38. Assembly of the Splicing machinery. Explain.
    Explain
  39. •Evolutionary Implications of Split Genes and RNA Splicing
    –The idea of an “RNA world” suggests that RNA was the earliest molecule to both store information and catalyze reactions.
    –RNA splicing via spliceosomes could have evolved from _________.
    –Exon shuffling could have played a role in the evolution of many genes.
    -self-splicing RNAs
  40. •________ results in the
    destruction of some mRNAs.
    •RNAi is produced when a double-stranded RNA shares the __________ as the target ____.
    •RNAi is part of a broader phenomenon of RNA silencing, in which small RNAs
    inhibit gene expression in various ways.
    •3 Types:
    • •RNA interference (RNAi)
    • •same sequence; mRNA
    • types:
    • -small interfering RNAs (siRNAs)
    • -micro RNA (miRNAs)
    • -piwi-interacting RNAs (piRNAs)
  41. •The steps involved in RNAi include:
    –dsRNA is cleaved into small interfering RNAs (siRNAs) by an enzyme called ____.
    -The small dsRNAs are loaded into a complex named _____ that bind ____ to a target RNA.
    • -Dicer
    • -RISC; siRNA
  42. •Micro RNAs (miRNAs)
    –Are derived from a single-stranded precursor RNA that
    contain ________ that allow them to fold back to form _____.
    –The pseudo dsRNA is cleaved to generate a ________.
    –The single-stranded miRNA binds to a complementary region on an ______ and inhibits
    translation of the message. Are thought to play a regulatory role in development.
    • -complementary sequences; dsRNA
    • - pre-miRNA
    • -mRNA; translation
  43. Know and Explain
    Look at book
  44. •_____________ are
    small RNAs that suppress the movement of transposable elements in the __________.
    •piwi-interacting RNAs (piRNAS); germline
  45. •Strategies for using RNAi to combat cancer,
    viruses, and some genetic disorders.
    •Some obstacles:
    –Delivering genes for siRNAs can lead to complications.
    –Viral genes mutate rapidly, making some siRNAs ___________.
    -ineffective for treatment against viral diseases
  46. •Information stored in a gene is present in the form of a _______.

    •Properties of the Genetic Code
    –The _______ for amino acids are
    non-overlapping triplets of nucleotides.
    –It is _________, some of the amino
    acids are specified by more than one codon.
    • •genetic code
    • - codon
    • -degenerate
  47. •Identifying the Codons

    –Codon assignment was determined by transcription of
    ________.
    –The first two codon bases for a particular amino acid are ______, whereas the third base may vary.
    • -artificial mRNAs
    • -invariant (never changing)
  48. •Structure of tRNAs

    •The secondary structure resembles a _______, while
    the tertiary structure is an _____.
    –The amino acid is attached to the 3’ end of tRNA.
    –The anticodon on tRNA complements the codon of the ______.
    –The wobble hypothesis suggests that a ____ can recognize codons with variable third bases.
    • •cloverleaf; L shape
    • -mRNA
    • -tRNA
  49. •Amino Acid Activation
    –Specific _______ link amino acids with their respective tRNAs.
    –Energy from ATP is used to activate the amino acid,
    which is then transferred to the tRNA molecule.
    –Codons of the mRNA are interpreted according to the
    recognition abilities of the ______.
    • -aminoacyl-tRNA synthetases (aaRS)
    • -ATP; tRNA
    • -aaRS
  50. •________ is the most complex
    activity of the cell.
    •Translation is divided into: (3 parts)
    • •Protein synthesis (translation)
    • •3 parts:
    • –Initiation
    • –Elongation
    • –Termination
  51. •Initiation
    –Translation begins at the ________, which then puts the ribosome in the proper ________.
    –The small ribosomal subunit identifies the correct AUG codon.
    –Initiation requires proteins called________
    –In bacterial cells, the ________ sequence guides the small ribosomal subunit to the correct initiation codon.
    –In eukaryotes, the smallest ribosomal subunit recognizes
    the 5’ end of the message and finds the first _______ by scanning.
    • - AUG initiation codon; reading frame
    • - initiation factors or IFs (eIFs in eukaryotes)
    • -Shine-Dalgarno
    • -AUG triplet
  52. •Bringing the First aa-tRNA Into the Ribosome
    –AUG codes for ______ so it is always the first amino acid to be incorporated into the polypeptide chain.
    –There are two differenet methionyl-tRNAs: one for ______ and one for the____________.
    -After the initiation tRNA is _____, the large
    subunit of the ribosome _____ the complex.
    • -methionine
    • -initiation; residues in the polypeptide
    • -bound, joins
  53. •The Role of the Ribosome
    –Ribosomes have three sites for tRNAs: ____
    –Ribosomes receive each tRNA in successive steps of the ________.
    • -A(aminoacyl) site
    • -P (peptidyl) site
    • -E(exit) site.

    • - elongation cycle
  54. •Elongation
    –The process of ______ each subsequent amino acid to the ___________.
    •With the charged amino acid in the P site, the next aminoacyl-tRNA binds to the _______.
    •Several elongation factors are required.
    -Peptidyl trasnferase catalyzes the peptide bond formation between ______.
    • - adding; growing polypeptide chain
    • • vacant P site
    • - amino acids
  55. •Elongation
    –The ribosome moves three nucleotides (one codon) along the mRNA in the 5’ -> 3’ direction during translocation.
    –Translocation is driven by conformational changes in an
    elongation factor (EF-G or eEF2).
    –Mutations that add or delete nucleotides that affect
    translocation are called frameshift mutations, and produce an abnormal sequence of amino acids.
    • - translocation
    • - elongation factor
    • -

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