The Structure and Function of DNA

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Chapter 10

• The Structure and Function of DNA

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DNA Structure and Replication

• Knew there was DNA in cells but not its role in
  heredity until much later
• Knew that chromosomes were made of DNA and
  protein
• Figured out the structure of DNA after knowing
  the atoms that it was made of

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Remember the DNA/RNA

• DNA has deoxyribose
• RNA has ribose
• Both are nucleic acid and made of nucleotides
• Many combinations of 4 nucleotides
• Joined between sugar of 1st nucleotide and
  phosphate of 2nd nucleotide by phosodiester bond
• Bases hang off like ribs on spine

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Nucleotides

• Made up of sugar, phosphate and nitrogenous base
• Can function as an acid (phosphate) or as a base
  (nitrogen base)
• C and T are single ring structure, as is U in RNA
• A and G are double ringed structure

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Discoverers of DNA Structure

• Watson and Crick used the information from the
  X-ray crystallography of Franklin and wire models
  to figure out structure
• Needed to keep the sugar phosphate backbone
  parallel so had to have A pair with T and G with C

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DNA
See the DNA in several different types of
models Ribbon model shows the anti-parallel
nature of DNA
No restriction in order of nucleotides
countless sequences
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DNA Replication

• Uses existing DNA as a template using
  complementary base pairing
• Parent strand separates and then makes the copy
  that stays linked to parent strand

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DNA Polymerase

• DNA polymerase is an enzyme that links the
  nucleotides together
• Concept is simple but process is actually very
  complex
• requires dozen enzymes and other proteins
• Polymerase adds nucleotides very rapidly and very
  accurately 50 nt/sec with 1 in 1 billion
  mistakenly added nucleotide
• most mistakes get corrected before process is done

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DNA Damage

• DNA polymerase and other proteins can correct
  damage done to DNA before starting replication
• UV light and X-ray can cause damage to DNA

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Origin of Replication

• DNA replication machinery opens the DNA and
  starts to add nucleotides at places called the
  origin of replication
• form bubbles in the DNA
• Have many origins in each chromosome to speed the
  replication
• Eventually has 2 new strands that are joined at
  the centromere
• Now cell can undergo mitosis or meiosis

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Flow of Genetic Information

• Moves from DNA which is the directions to RNA
  which carries out the mission and then to protein
  which carries out the wishes of DNA
• Genotype produces phenotype
• genotype is the nucleotides that are in the
  allele that is the gene
• phenotype is the specific trait that is caused by
  the proteins

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DNA Directs Proteins

• Not a direct relationship must go thru a RNA
  intermediate
• DNA to RNA is transcription
• RNA to protein is translation

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DNA History

• Early 1900s a doctor hypothesized that inherited
  diseases were caused by defective enzymes
  wasnt proved correct until years later
• all metabolism is dictated by enzymes miss one
  enzyme and you wont be able to complete the
  pathway
• 1940 found bread mold that couldnt grow on
  usual media that they were missing a gene that
  made a specific enyme
• hypothesized that 1 gene makes 1 enzyme
• now know that the gene encodes 1polypeptide as
  many enzymes have multiple subunits

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Nucleotides to Amino Acids

• Nucleic acids can be thought of as a 4 letter
  language
• DNA A G C T
• RNA A G C U
• Proteins are a 20 alphabet language
• amino acids must be able to be made from the
  nucleic acid alphabet

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Translation

• Genes consists of 1000 of nucleotides
• Many genes per DNA molecule
• Transcribe DNA to RNA
• transcribe because same language (nucleic acid)
• Translate from RNA to protein
• translate because going between 2 languages)

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RNA is a Messenger

• DNA dictates the polypeptide sequence but uses
  RNA as a messenger between the 2
• Use 3 RNA nucleotides to write 1 amino acid
• 64 different combinations of 3 nucleotides to
  make all 20 amino acids
• 3 nucleotides per amino acid alphabet is a codon
• word for amino acid

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Genetic Code

• Nucleotides to amino acid code
• Codon dictionary to make translation between
  nucleic acid and amino acids
• 4 special codons
• start codon AUG, all proteins start with Met
• 3 STOP codons UAA, UAG and UGA tells the
  ribosome that the protein is done
• Code is redundant all amino acids but Met and
  Trp have more than 1 codon but not 1 codon
  defines 2 different amino acids

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Transcription DNA to RNA

• DNA separates near place where gene is located
• Use only one strand as template for RNA
• Nucleotides add 1 at a time complementary to the
  DNA sequence
• H-bonds as in DNA
• RNA polymerase is the enzyme that adds the
  nucleotides

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3 Step Process

• Initiation use special sequence in DNA to know
  where to start promoter attach RNA polymerase
  and start synthesis
• RNA elongation RNA grows and separates from the
  DNA and DNA recoils
• Termination polymerase reaches another special
  signal in DNA template called the terminator
  end of gene, complex falls apart and releases RNA

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RNA Processing

• In prokaryotic cells the RNA can act as the
  message for translation without processing
• In eukaryotic cells the RNA must be modified
  before leaving the safety of the nucleus to the
  harsh environment of the cytoplasm
• add a cap and a tail to prevent the message from
  being destroyed in cytoplasm
• must remove non-coding sequence to actually make
  the message (mRNA)
• non-coding are called introns and coding are
  called exons

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mRNA

• Once remove introns in a process called RNA
  splicing, the RNA is now a message and ready to
  move out of the nucleus and into cytoplasm

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Translation

• Translation requires additional machinery because
  we are going from 1 language to another language
• Need 3 things to do the conversion
• mRNA made during transcription and RNA
  processing
• tRNA transfer RNA the link between nucleic
  acid language to amino acid language
• ribosomes the organelle for protein synthesis

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tRNA

• Job is to recognize the codons in the mRNA and
  brings in the right amino acid
• 2 functions of tRNA
• pick up appropriate amino acids available in the
  cytoplasm
• recognize the codon by the anti-codon in the tRNA
  which is complementary to mRNA codon

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Ribosome

• Combines mRNA and tRNA together to make the
  protein with all additional molecules necessary
• Ribosome is made of 2 subunits made up of
  proteins and rRNA (ribosomal RNA)
• large subunit is where the peptide is formed
• 2 sites A site is where incoming amino acid
  comes in and the P site where the growing protein
  chain is held
• small subunit is where the mRNA is held

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Translation

• 3 phases like in transcription
• Initiation brings in the mRNA and 1st tRNA into
  the small subunit and then the large subunit
• Remember, the mRNA is longer than needed for
  protein contains the sequences that alert the
  ribosome that this message must be translated

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Elongation

• Adding 1 amino acid at a time
• 3 steps involved in elongation
• codon recognition by incoming tRNA
• peptide bond formation by adding the peptide from
  the tRNA in P site to the amino acid in the A
  site bond made by the large subunit
• translocation tRNA in P site leaves and the
  ribosome moves done the mRNA to expose the next
  codon and A site
• repeat

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Termination

• Elongation continues until a STOP codon ends up
  in the A site
• Once the STOP codon is recognized, the ribosome
  releases the message, the protein and the tRNAs
• ribosome dissociates until it finds another mRNA

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Summary

• Starts in nucleus with transcription and
  processing of RNA
• Moves to cytoplasm to make protein that then will
  fold into its 3-D structure
• Each step has control mechanisms to make sure
  that we really want the protein made

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Mutations

• Describe heritable differences in molecular terms
  
• say in sickle cell disease traced back to 1
  nucleotide changed that resulted in altered amino
  acid that makes the protein not function normally
• Other diseases also have this type of underlying
  issue change in the DNA sequence mutation

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2 Types of Mutations

• Base substitution replace 1 base with another
  base
• Base insertion or deletion have a nucleotide
  removed or inserted by some mechanism

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Base Substitution

• 3 possible outcomes
• no change to the protein redundant code may
  allow for a nucleotide change that doesnt cause
  an amino acid change
• change may be insignificant
• may be crucial to the function of protein
• 2 and 3 are called missense mutations
• Nonsense mutations nucleotide change introduces
  a STOP codon and protein is prematurely terminated

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Base Insertion/Deletions

• Often have more disastrous effects
• Changes the codon sequence and after the
  insertion or deletion the amino acids will be
  different disrupts proteins function
• AAG UUU GGC GCA AAG UUG GCG CA
• lys phe gly ala lys leu ala
  -

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Mutagens

• Mutations arising during DNA synthesis or
  recombination are called spontaneous mutations
• Others come from physical/chemical agents called
  mutagens
• physical UV light or X-rays
• chemical many different ones
• Scientists use mutations to study the function of
  proteins and other molecules in the cell