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    2013 10 31-From DNA To Protein

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    FaridOraha
    This document summarizes key concepts about how genetic information in DNA is expressed to produce proteins. It discusses transcription of DNA into RNA, post-transcriptional modification of RNA, translation of RNA into protein, and differences between prokaryotic and eukaryotic gene expression. The central topics covered are DNA transcription, RNA processing, protein translation, and the genetic code.

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    2013 10 31-From DNA To Protein

    Uploaded by

    FaridOraha
    32 views74 pages
    This document summarizes key concepts about how genetic information in DNA is expressed to produce proteins. It discusses transcription of DNA into RNA, post-transcriptional modification of RNA, translation of RNA into protein, and differences between prokaryotic and eukaryotic gene expression. The central topics covered are DNA transcription, RNA processing, protein translation, and the genetic code.

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    2013 10 31-From DNA to Protein

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    This document summarizes key concepts about how genetic information in DNA is expressed to produce proteins. It discusses transcription of DNA into RNA, post-transcriptional modification of RNA, translation of RNA into protein, and differences between prokaryotic and eukaryotic gene expression. The central topics covered are DNA transcription, RNA processing, protein translation, and the genetic code.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    32 views74 pages

    2013 10 31-From DNA To Protein

    Uploaded by

    FaridOraha
    This document summarizes key concepts about how genetic information in DNA is expressed to produce proteins. It discusses transcription of DNA into RNA, post-transcriptional modification of RNA, translation of RNA into protein, and differences between prokaryotic and eukaryotic gene expression. The central topics covered are DNA transcription, RNA processing, protein translation, and the genetic code.

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    © All Rights Reserved
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    of 74

    Chapter 6

    From DNA to Protein:


    How Cell Read the Genome

    Genetic information directs the synthesis of protein

    The central dogma of molecular biology

    Genes can be expressed with different efficiencies


    Untranscribed portions

    Nucleotide

    The chemical structure of RNA differs slightly


    from that of DNA

    phosphodiester
    bond

    Uracil forms a base pair with adenine

    2 hydrogen bonds

    RNA molecules can form intramolecular base pairs


    and fold into specific structures

    Base-pair with complementary sequences

    Conventional
    base-pair
    interactions

    Nonconventional
    base-pair
    interactions

    Transcription produces an RNA complementary


    to one strand of DNA
    Coding strand
    Sense strand

    Non-Coding strand
    Anti-sense strand
    Template strand

    Sense & antisense strand

    DNA duplication by DNA polymerase

    Transcription by RNA polymerase

    DNA is transcribed by the enzyme RNA polymerase

    ATP
    CTP
    UTP
    GTP

    Transcription can be visualized in the electron microscope


    rRNAs

    Gene 1

    RNA polymerase

    Gene 2

    DNA

    Ribosomal proteins

    RNA polymerase vs DNA polymerase


    RNA polymerase

    DNA polymerase

    Ribonucleotides

    Deoxyribonucleotides

    Without primer

    With primer

    1/104 error rate

    1/107 error rate

    Types of RNA produced in cells

    messenger RNA
    non-messenger RNA

    ribosomal RNA

    microRNA
    transfer RNA

    Signals in the sequence of a gene tell bacteria


    RNA polymerase where to start and stop transcription
    Bacterial RNA polymerase

    Chain elongation

    Bacterial promoters and terminators


    have specific nucleotide sequences
    that are recognized by RNA polymerase
    Bacterial RNA polymerase

    Some genes are transcribed using


    one strand DNA as a template, whereas others are
    transcribed using the other DNA strand
    The direction of transcription is determined by the orientation of the promoter at the beginning of each gene

    The three RNA polymerases in eucaryotic cells

    mRNA
    sRNAs

    sRNAs

    To begin transcription, eucaryotic RNA polymerase II


    requires a set of general transcriptional factors
    -25

    TATA-binding protein

    Dramatic local distortion in the DNA

    Phosphorylate the tail


    of RNA polymerase II
    Allow the template strand
    to be exposed by
    ATP hydrolysis

    Dephosphorylated form

    Transcription initiation complex

    TATA-binding protein (TBP) binds to TATA box sequences


    and distorts the DNA
    TBP (TATA-binding protein)

    TATA box
    DNA

    Before they can be translated, mRNA molecules made


    in the nucleus move out into the cytoplasm via pore
    in the nuclear envelope

    Pores in
    nuclear envelope

    TEM

    Phosphorylation of RNA polymerase II allows


    RNA-processing proteins to assemble on its tail

    TFIIH

    (1) Capping
    (2) Polyadenylation
    (3) Splicing

    Eucaryotic mRNA molecules are modified by


    capping and polyadenylation (1)

    Start after 25 nucleotides


    has been polymeized

    (1) To increase the stability of the eucaryotic mRNA molecule


    Functions:(2) To aid its export from the nucleus to the cytoplasm
    (3) To identify the RNA molecule as an mRNA

    Eucaryotic mRNA molecules are modified by


    capping and polyadenylation (2)
    CH3
    2
    1

    3
    4
    5

    Eucaryotic and bacterial genes are organized differently

    Promoter

    Intron is longer than exon

    Most human genes are broken into exons and introns

    3 exons

    26 exons

    Special nucleotide sequences signal


    the beginning and the end of an intron
    Branch point of the lariat

    long

    intron-exon
    boundary (border)

    short

    R: A or G
    Y: C or U
    N: A or C or G or U

    RNA splicing might occurred before or after polyadenylation

    RNA splicing

    An introns forms a branched structure during splicing

    Branch point of the lariat


    3

    Spliceosome

    Small nuclear RNAs (snRNAs) + Proteins


    = Small nuclear ribonucleoprotein particles
    (snRNPs)

    The -tropomyosin gene can be spliced in different ways

    (1) Many different protein to be produced from the same gene by alternative splicing
    (2) 60% of human genes probably undergo alternative splicing

    A specialized set of RNA-binding proteins signal that


    a mature mRNA is ready for export to the cytoplasm
    Recognizes and exports
    only completed mRNAs

    Exon junction complex (EJC)


    Mark completed RNA splices
    Life times depends on
    (1) Nucleotide sequence (3 untranslated sequence)
    (2) The type of cell

    3 untranslated region

    Procaryote and eucaryotes handle


    their RNA transcripts differently

    Transcription in procaryotic or eucaryotic cells (1)

    Transcription in procaryotic or eucaryotic cells (2)


    Bacteria

    Eucaryotic cells

    RNA polymerase

    Single type

    Three types (I, II, III)

    Accessory proteins

    General transcription factors

    Nontranscribed DNA between genes Short

    Long

    Small RNAs
    (1) siRNA (small interfering RNA)
    (2) miRNA (microRNA)
    (3) piRNA (piwi-interacting RNA)

    miRNA

    siRNA

    Amino Three-nucleotide
    codons
    acids

    The nucleotide sequence of an mRNA is translated into


    the amino acid sequence of a protein
    via the genetic code

    Start
    codon

    Stop
    codons

    UUU codes for phenylalanine

    Marshall Nirenberg

    Heinrich Matthaei

    Messages of mixed repeating sequences further


    narrowed the coding possibilities

    Gobind Khorana

    The Nobel Prize in Physiology or Medicine 1968

    Interpretation of the genetic code and its function in protein synthesis

    An RNA molecule can be translated


    in three possible reading frames

    Reading frame

    Frame shift

    tRNA molecules are molecular adaptors,


    linking amino acids to codons

    L-shape molecule

    dihydrouridine

    pseudouridine

    Wobble base-pairing

    61 codons
    31 anticodons

    20 amino acids

    The genetic code is translated by means of two adaptors


    that act one after another

    Charging

    1
    Aminoacyl-tRNA synthase

    2
    Charged tRNA

    Anticodon

    Ribosomes are found in the cytoplasm of a eucaryotic cell

    Attached to the ER

    Ribosome

    Free in the
    cytosol

    TEM

    A ribosome is a large complex of four RNAs and


    more than 80 proteins

    (rRNA)
    (rRNA)

    Catalyzes the formation


    of polypeptide chain

    Matches the tRNA to


    the codon of the mRNA

    1/3

    2/3

    Each ribosome has a binding site for mRNA


    and three binding sites for tRNA
    Large subunit

    peptidyl-tRNA
    Large subunit

    Small subunit

    Exit

    aminoacyl-tRNA

    Small subunit

    Translation takes place in a four-step cycle

    Catalyzed by an enzymatic site


    in the large subunit

    Large subunit

    Ribosomal RNAs give the ribosome its overall shape


    Rate of sedimentation in an ultracentrifuge

    Protein

    Catalytic site for peptide bond formation

    Large subunit of a bacterial ribosome

    Initiation of protein synthesis in eucaryotes requires


    initiation factors and a special initiator tRNA
    or formylmethionine in bacteria

    only this charged RNA


    can binds to the P-site
    E

    P A

    A
    Start codon

    In the final phase of protein synthesis, the binding of


    release factor to an A-site bearing a stop codon
    terminates translation
    Stop codons
    UAG
    UGA
    UAA

    A single procaryotic mRNA molecule can encode


    several different proteins

    Operons

    Polycistronic

    Procaryote

    Proteins are translated by polyribosomes

    Polyribosomes (Polysomes)

    Inhibitors of procaryotic protein synthesis


    are used as antibiotics

    The proteosome degrades short-lived and


    misfolded proteins

    Active site of
    the proteases

    Ubiquination for protein degradation

    Ubiquitin

    Protein production in a eucaryotic cell


    requires many steps

    Many proteins require additional modification


    to become fully functional

    Glycosylation (> 100 kinds)

    An RNA world may have existed


    before modern cells arose

    An RNA molecule can in principle guide


    the formation of an exact copy of itself

    Ribozyme
    Ribozyme RNA molecules that possess catalytic activity

    A ribozyme is an RNA molecule that possesses


    catalytic activity

    Biochemical reactions that can be catalyzed by ribozymes

    Could an RNA molecule catalyze its own synthesis?

    RNA may have preceded DNA and proteins in evolution

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