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From Gene to Protein (Transcription (Transcription in Prokaryotes (RNA…

- - - - Contains genes that code for proteins or RNA molecules, that have various cell functions
      - Information is stored in DNA of a cell
        
        Stored information is interpreted and transmitted for cellular processes
      - Genes
        
        Sections of DNA molecules, that contain formation that is transcribed into RNA copy
        
        Either stays as RNa, or is further translated into mRNA, and makes up amino acid sequence, to make up proteins
    - - Process of copying and interpreting genes into proteins
      - Information that is stored in DNA, specifies sequence of amino acids in protein
        
        DNA copied multiple times into mRNA
        
        mRNA translated from nucleotide to protein
        
        Gene Expression
        
        Trasncription of information encoded in DNA to RNA
  - - - Nucleotide sequence contained in gene, will determine sequence of nucleotides contained in RNA transcript
      - RNA strand is same as template strand, due to base-pairing rule; except U replaces T
    - - RNA polymerase attaches to DNA promoter regions
        
        Promoter regions show transcription starting point
        
        Transcribes in 3'-5' direction
        
        Synthesized from 5'-3' direction
        
        Terminator stops transcription
    - - Nucleotide sequence TATAAT is promoter sequence
        
        Consensus sequence
        
        Nucleotide sequence in DNA found at site
        
        Also have TTGCCA
        
        Enhance transcription rate
      - Transcription requires RNA polymerase and sigma factor proteins
        
        Bind promoter region of DNA
        
        Pair binds to create holoenzyme
        
        Binds to and unwinds double-stranded DNA helix
    - - Elongates the forming RNA transcript
      - Separates DNA double helix
        
        Ribonucleotides enter, assemble on DNA template strand
      - Passes template DNA through channel, transcribe template strand into complementary RNA
      - Restores DNA back into double helix
    - - Phosphate bond energy of incoming ribonucleoside triphosphate
        
        Drive high energy reaction process
        
        Required to create phosphodiester bond between incoming nucleotide and growing RNA transcript
      - Release and cleavage of pyrophosphate (phosphate-phosphate) group during phosphodiester bond formation, renders this polymerization reaction
        
        RNA transcript elongation irreversible
    - - Termination sequence at 3' end
      - Requires nucleotide terminator
        
        Releases RNA sequence
        
        Releases transcription complex
    - - Rho-independent terminator
        
        Inverted nucleotide repeat sequence
        
        Fold back on themselves to form G-C hairpin loop along mRNA strand
      - Rho-dependent terminator
        
        Rho factor - protein
        
        Bind to and use ATP energy to move along RNA transcript while unwinding it from DNA template
        
        Destabalize interaction between DNA and RNA template
        
        Release of transcript & transcription complex
  - - - General Transcription Factors
        
        Mediate binding of RNA polymerase to promoter
        
        Initiate transcription
      - RNA Polymerase I
        
        Transcribes genes for rRNA
        
        Termination
        
        similar to Rho-dependent factor
      - RNA Polymerase III
        
        Transcribes genes for tRNA
        
        Termination
        
        Similar to Rho-independent factors
        
        terminated after termination signal
      - RNA Polymerase II
        
        Transcribes mRNA
        
        Template for production of protein molecules
        
        Termination
        
        Poly(A)-dependent mechanisms
        
        3' end modified by polyadenylation
      - RNA polymerase produces complementary, antiparallel strand of RNA
    - - Post-transcriptional modifications
        
        Add 5' cap and 3' poly (A) tail
        
        5' end gets attachment of guanosine to mRNA through 5'-5' triphosphate linkage
        
        7-methylguanosine
        
        Adenine nucleotides added to 3' end is poly(A) tail
        
        Follows polyadenylation signal sequence (AATAAA)
    - - Amino acids that make up proteins, but do not code for anything
        
        Introns
        
        Intervening sequence
        
        Removed
        
        Exons
        
        Sequence of amino acids in protein
        
        Joined
        
        spliced
    - - Short nucleotide at each end of intron
      - Catalyzed by spliceosomes
        
        Composed of 5 nuclear ribonucleoproteins (snRNP)
      - Recognizes complimentary base pairing
        
        Finds splice site
        
        Catalyzes reaction with hydroxyl group
        
        Cut at 5' end forms a loop
        
        3' end has acceptor site
- - - - One nucleotide coded for one amino acid
        
        1-base code not enough to code all 20 amino acids
        
        4x1=4
        
        2-base code also not enough
        
        4x4=16
        
        3-base code
        
        4x4x4=64
        
        More than enough, but accommodates 20 amino acids
  - - - Same as RNA except for U replaces T in RNA
    - - Start Codon
      - Methionine
    - - Tryptophan
    - - Serine
        
        4 triplets
      - Unique condon triplets
        
        Never codes for more than one amino acid
    - - do not code
    - - Continuous sequence of a gene, begins with triplet start codon, ends with triplet stop codon
      - Coding region of a gene
  - - - When adding or subtracting nucleotide, it changes codon sequence, resulting in changes to amino acids
      - Frameshift Mutations
        
        Add or remove 2 nucleotides
    - - First/Second/Third Reading Frames
        
        mRNA can be read from 1st, 2nd, 3rd nucleotide
    - - No frameshift
      - Protein still conserved
        
        same for adding 2 nucleotides
- - - - Cellular components read genetic message in mRNA,
        
        Translate into primary amino acid
      - Initiation
      - Elongation
      - tRNA
        
        mRNA genetic message to polypeptide
        
        Cytoplasmically situated amino acids -> Transfer amino acids -> Ribosome
        
        Clover-Leaf
        
        Hydrogen bonding between complementary nucleotide bases
        
        4 double-helical segments and 3 loops
        
        L-shape
        
        Fold upon itself
        
        Anticodon
        
        Nucleotide triplet forms complementary base-pair with mRNA codon, coding for amino acid
        
        Aminoacyl tRNA synthetases
        
        Activation of tRNA molecule with amino acid, carried out by enzymes
        
        Enzymes catalyze tRNA to amino acid using ATP energy
        
        Released from enzyme
        
        Grows polypeptide chain on ribosome
    - - Correct pairing of tRNA anticodon to mRNA codon
        
        Base-pairing between mRNA codon and tRNA anticodon
      - Codon-anticodon pairing interactions
        
        Wobble
        
        First base (5') of codon, bind to last base (3')
        
        Flexibility in base pairing between third nucleotide of codon, and tRNA anticodon
  - - - Eukaryotes
        
        5' cap of mRNA, scans until AUG start codon
      - Prokaryotes
        
        Shine-Dalgarno sequences
        
        Translation initiation complex assembles at 1+ ribosome binding sites
        
        Polycistronic mRNA
        
        Functionally related genes grouped together
        
        Genes transcribed as single unit
      - Assembling Initiation Complex
        
        Large & small subunits form functional ribosome when attached to mRNA molecule
        
        Initiation factors bind to 5' cap of mRNA
        
        Initiation factors bind to tRNA, charged with methionine
        
        5'-3' until AUG
    - - Methionine located in peptidyl (P) site
      - Charged tRNA enters & binds within aminoacyl (A) site
        
        Change in rRNA allowing fo peptidyl-transferase reaction
    - - Change in rRNA forms condensation reaction as peptide bond, transfers polypeptide chain into tRNA in A-site
      - Ribosome translocates along mRNA
        
        Enabled by binding of GTP-bound elongation factors
        
        Cause deacylated tRNA to move from P-site to exit (E-site)
    - - Ribosome reaches stop codon
        
        mRNA sequence, GTP-bound release factors bind to A-site
        
        Catalyze hydrolysis of terminal amino acid in polypeptide and tRNA in P-site
        
        GTP hydrolysis dissociates translation complex, ribosomal subunits, tRNA
- - - - Proteome represents full number of proteins expressed by hereditary information in DNA
        
        Genome
      - Single genes can encode multiple proteins
    - - Double membrane nucleus
      - Compartmentalization
        
        Control in regulation of cellular processes
      - Mature mRNA exported out of nucleus
        
        Cytosol
        
        Free or ER bound ribosomes facilitate translation into polypeptides
    - - Cells Detect Changes in Environment
        
        Stimuli resulting in cellular responses
        
        Sensori responses
        
        Insulin
      - Glucose Absorbed in Small Intestine
        
        Glucose absorbed into bloodstream
        
        Micovilli cells
        
        Associated with small blood vessels
      - Absorbed Glucose Transported to Target Regions
        
        Microvilli cells absorb glucose in intestinal tract
        
        Transported to blood vessles
    - - Alternative Splicing
        
        One pre-mRNA spliced at different junctions resulting in many different mature mRNA molecules
        
        Different combination of transcribed exons
        
        Exons may be excluded from splicing process
        
        Removed
        
        Produces isoforms
        
        Mature mRNA from same pre-mRNA transcript
        
        Regulate gene expression
      - Insulin
        
        mRNA isoform translated into higher affinity insulin receptor in muscle cells
        
        Lower blood glucose levels
        
        Absorb glucose to meet high energy needs
        
        Liver cells
        
        Lower affinity insulin
      - Termination
        
        High glucose stimulus detected in pancreas
        
        Insulin is effector signal
        
        Targets body's cells to absorb glucose from bloodstream
        
        Increase glucose absorption
- - - - Errors in splicing
      - Missing sequences
      - Exon skipping
      - Intron retention
      - Not producing full length protein
    - - Onset before 6mths
        
        Lifespan 2yrs
      - Affects motor movement
      - Skeletal muscles die
      - Neuron degeneration
      - Autosomal recessive disorder
        
        Chromosome 5
        
        Delta 7
        
        SMN1 Mutations
        
        8 exons (9 technically)
        
        Delta 7 has 7 exons
        
        Missing amino acid
        
        Ribosomes don't translate nucleotide
      - SMA2
        
        More = longer life expectancy
        
        Backup for SMA1
        
        Need high number
        
        Splicing
        
        Position 6, T
        
        Skipped at 7
      - Splicing
        
        Position 6, C
        
        Cut at 7
      - Gene Therapy
        
        Add SMN1
      - Molecular Therapy
        
        Stop SMN2 exton 7 skipping
- - - - Interfering with cell wall synthesis
      - Disrupting bacterial protein synthesis at ribosome
      - Inhibiting function of enzymes needed for DNA and RNA synthesis
    - - tRNA binding sites
        
        A, P, E sites
      - mRNA path
      - Large ribosomal subuit
    - - Blocking A-site
      - Interfere with tRNA delivery
    - - Disrupting tRNA transfer
        
        Prevent transfer of tRNA from A site to P site
      - Misreading
        
        Brings inappropriate codon to binding site
    - - Blocking large subunit
        
        Translation cannot start
    - - Blocking peptide bond formation
    - - Blocking peptide exit tunnel
    - - Translocation prevented
        
        Move from A-site to P-site
        
        Block P-site
    - - Inherited survival mechanism
      - Drug misuse
      - Misdiagnoses
      - Not taking full drug course
      - Chloramphenicol
        
        rRNA mutations in large ribosomal subunit
        
        Disrupts binding site
        
        Methylation of rRNA prevents binding
      - Erythromycin
        
        rRNA mutation at tunnel enterance
        
        Add methyl group, block antibiotic binding