Central Dogma of molecular biology

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Central Dogma of molecular biology

• The Central Dogma of Molecular Biology
• Review of replication The Collaboration of
  Proteins During Replication
• RNA vs. DNA RNA - Ribonucleic Acid
• Video which shows the research being done with
  RNA NOVA scienceNOW RNAi PBS

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Beadle and Tatum (1940's) One Gene, One Enzyme

• Using genetic and biochemical approaches with
  bread mold (Neurospora crassa), Beadle and Tatum
  devised the first hypothesis about the functional
  nature of genes.
• Hypothesis Genes specify proteins. A defective
  protein leads to an inherited disorder DNA
  Interactive

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Beadle Tatum one gene one enzyme

• One gene makes one protein. ltscript
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• Three Types of RNA are Involved in Protein
  Synthesis
• RNA properties
• RNA nucleotide bases 5 carbon sugar (ribose
  instead of deoxyribose) phosphate
• RNA has 4 types of nucleotide bases A, C, G, U
  (U replaces T)
• RNA is usually a single strand, not a helix

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• A look at the science behind DNA
• NOVA Online Cracking the Code of Life Watch
  the Program Here

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Two steps of protein synthesis

• Transcription - in the nucleus . A copy of the
  code is made from DNA (m-RNA)m-RNA leaves the
  nucleus, goes to cytoplasm.
• Translation - In the cytoplasm, on the ribosomes,
  ribosome decodes the m-RNA and makes the correct
  protein.

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The 3 types of RNA
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Transcription

• Animation Quizzes
• An overview DNA Transcription - An Animated
  Explanation
• DNA Interactive

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Transcription

•    Genes are made from coding and noncoding
  stretches of DNA.
•       Exons  are the expressed (coding)
  regions.
•       Introns  intervening sequences are
  noncoding. .

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• Most genes also have a beginning, a promoter.  A
  promoter is a noncoding region of the gene
  (before AUG) to which regulatory proteins and the
  RNA polymerase bind.

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• Transcription is initiated by binding of the
  enzyme RNA polymerase to the promoter.
•       RNA polymerase unwinds two helical turns
  of the DNA double strand to form an open promoter
  complex and initiate a transcription bubble.

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• Polymerase works from 3' to 5' direction on the
  DNA template strand.  Therefore the 5'-end of RNA
  comes out first, exactly as in DNA replication.

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• RNA polymerase makes significantly more mistakes
  than DNA polymerase  one every 10,000 bases.
•       Recall though that the cell can afford
  sloppiness because no inheritance is at stake. 
  At worst this particular batch of protein will be
  bad.

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differences between prokaryotes and eukaryotes.

• In prokaryotes, translation is nearly
  simultaneous with transcription

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Eukaryotes

• In eukaryotes there are introns and exons, so the
  initial transcript must first be processed in the
  nucleus before ribosomes have a chance to
  synthesize protein.
• Because many enzymes (nucleases) chop RNA, hnRNA
  is protected on both ends.

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• At the 5'-end, RNA is capped by
  7-methylguanosine.  The cap also provides a
  ribosome binding site during translation.
•       At the 3' end, a poly-A tail (200-250 As)
  is attached to protect RNA from breakdown and
  serving as a signal (tag) that allows passage
  through a nuclear pore.

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• Finally, introns must be excised.  The splicing
  is done by snRPS, which are small
  ribonucleoprotein particles.  snRPS bring the
  ends of the intron together, looping it out of
  the gene, and catalyze the excision and ligation
  of the exon ends.

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• Watch
• Animations
• DNA makes RNA

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So the mRNA leaves the nucleus and translation
occurs

• Genetic Code
• How is the information stored?
•       There are 4 letters (bases), but they
  must encode 20 amino acids.
•       The solution is in the word length.
• A 3-letter code 64 combinations
• Each three is known as a codon

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Cracking the code

• http//vector.cshl.org/dnaftb/22/animation/animati
  on.html

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The amino acids

• The 20 Amino Acids
• Coding Example

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• This code is universal,  viruses to human have
  the same codons.  The only exceptions are
  mitochondria and chloroplasts.
• mitochondria use UGA to encode tryptophan (Trp)
  rather than as a chain terminator

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Special words

•   Initiation codon  The beginning of the
  sentence is denoted by an AUG triplet, which
  codes for methionine (thus, the first amino acid
  of the npolypeptide chain is always methionine).
•       Stop codons   UAG, UAA, and UGA code for
  the end of a message.

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Degeneracy

• Because there are more words than amino acids,
  there is a built in tolerance to mutations.  We
  can afford a few mistakes.
•       We can also afford to mumble the third
  base is less important, as long as the first two
  bases are recognized correctly.  This phenomenon
  is called tRNA wobble.

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Translation

• The process of forming peptide bonds between
  amino acids in a sequence defined by mRNA is
  called translation.
• Involves
• (i)  charging of the tRNA with the specific
  amino acids and
• (ii)  synthesis of polypeptide chain by the
  ribosomes.

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Transfer RNA

• tRNA is a single-stranded molecule that folds on
  itself like a hairpin.  The straightened-out
  structure has a clover-leaf shape  three loops
  joined by short stems consisting of the paired
  nitrogenous bases.

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tRNA
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• The exact 3D conformations are different for
  tRNAs specific for given amino acids. 
•       The functions of tRNA are to read the
  codon of the mRNA and to fetch correct amino
  acid.  Not surprisingly, the two sites are at
  opposite ends of the molecule. 

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Anticodon

•    The middle loop that sticks out from the
  opposite end of the tRNA contains a triplet of
  bases complementary to the bases of the mRNA. 
  This triplet is referred to as an anticodon. 

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• The reading of the codon on mRNA is really
  formation of hydrogen bonds between codon and
  anticodon on tRNA. 
•       Often, only the first two bases of the
  codon are important and the third position is
  ignored by the tRNA.  This phenomenon results in
  a wobble of the genetic code.

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Ribosomes

• Ribosomes are huge nucleic acid-protein
  complexes, each made of two subunits (small and
  large) that come together only during protein
  synthesis.  Otherwise they float separately in
  the cytoplasm.

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An overview of the subject

• Transcription and Translation
• Translation the Sequence
• http//carbon.cudenver.edu/bstith/transla.MOV

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Polysomes multiple copies of gene
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review

• DNA Structure and Replication Introduction

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control

• eLearning ( this will go through everything we
  know and need to know. Go to all of the links
  for a great review. )
• Animation Quizzes lac and tryp
• The lac Operon in E. coli Introduction
• PHSchool - The Biology Place

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Mutations

• In the living cell, DNA undergoes frequent
  chemical change, especially when it is being
  replicated (in S phase of the eukaryotic cell
  cycle). Most of these changes are quickly
  repaired. Those that are not result in a
  mutation. Thus, mutation is a failure of DNA
  repair.

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Single-base substitutions

• A single base, say an A, becomes replaced by
  another. Single base substitutions are also
  called point mutations.
• Sickle cell anemia is a point mutation

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• Missense mutations (point mutation)-With a
  missense mutation, the new nucleotide alters the
  codon so as to produce an altered amino acid in
  the protein product

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Sickle cell anemia

• The replacement of A by T at the 17th nucleotide
  of the gene for the beta chain of hemoglobin
  changes the codon GAG (for glutamic acid) to GTG
  (which encodes valine). Teachers' Domain A
  Mutation Story

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Nonsense mutations(point mutation)

• With a nonsense mutation, the new nucleotide
  changes a codon that specified an amino acid to
  one of the STOP codons (TAA, TAG, or TGA).
  Therefore, translation of the messenger RNA
  transcribed from this mutant gene will stop
  prematurely. The earlier in the gene that this
  occurs, the more truncated the protein product
  and the more likely that it will be unable to
  function.

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Cystic fibrosis is an example

• cystic fibrosis the substitution of a T for a C
  at nucleotide 1609 converted a glutamine codon
  (CAG) to a STOP codon (TAG). The protein produced
  by this patient had only the first 493 amino
  acids of the normal chain of 1480 and could not
  function.

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Silent mutations

• Most amino acids are encoded by several different
  codons. For example, if the third base in the TCT
  codon for serine is changed to any one of the
  other three bases, serine will still be encoded.
  Such mutations are said to be silent because they
  cause no change in their product and cannot be
  detected without sequencing the gene (or its
  mRNA).