Nucleic Acids

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Nucleic Acids
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2 Classes of Nucleic Acids

• DNA and RNA
• Store our genetic in formation and help to make
  proteins essential for life
• Every cell in an organism contains a complete set
  of DNA
• Determine all factors about an organism (eg.
  Color, height, etc.)

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Basic Definitions

• Nucleic Acids
• Organic macromolecule (polymer) made of chains of
  Nucleotides
• Nucleotide
• Chemical unit consisting of a phosphate, a sugar,
  and a nitrogen base

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Nitrogen Bases

• Purine these are made up of a double ring
  structure consisting of a six and five sided ring
  
• A Adenine
• G Guanine
• Pyrimidine six sided ring structures
• C Cytosine
• T Thymine
• U Uracil (RNA)

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Base Pairing

• Known as Chargaffs Rule (Erwin Chargaff,
  biochemist, 1949)
• If a purine was to pair with another purine they
  would be too wide for the DNAs 2nm diameter
• If a pyramdine was to pair with a pyrimidine the
  result would be too wide

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Nucleotide Base Pairing (bp)
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Phosphate

• The phosphate and sugar make up the backbone of
  the nucleic acids.
• The phosphate compound always stays the same and
  looks like
• _

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Deoxyribose

• The sugar in DNA looks like

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Ribose

• The sugar in RNA looks like

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DNA

• Deoxyribonucleic Acid
• Linear or circular (bacteria and viruses)
• Found only in the nucleus all living organisms
• Double stranded molecule unless it is being
  replicated
• Utilizes Adenine, Guanine, Cytosine, and Thymine
• No two organisms can have the same genetic makeup
  unless they are twins or have been cloned

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DNA Double Helix Dimensions

• Width 2nm
• Complete twist 3.4nm
• Space between nucleotides .34nm

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DNA Replication

• Helicase is the enzyme that does the unwinding
• Unwinding occurs at various sites simultaneously
  at places called replication forks
• The gyrase enzyme helps to keep the strands from
  forming together again
• Binding proteins help to stabilize the strands as
  they are apart from one another

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Leading DNA Strand

• One the leading strand replication is continuous
  from the 5 end to the 3 end
• Occurs this way because it leaves one of the OH
  groups of the growing sugar-phosphate exposed and
  this is the only site where nucleotides can be
  joined
• As the DNA polymerase adds nucleotides the
  binding proteins leave from the outside of the
  strand

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Lagging DNA Strand

• At the forks binding proteins are displaced when
  primers are added
• Primers are like start tags as to where
  replication will start
• Composed discontinuously in Okazaki (Reiji
  Okazaki) fragments of 1000 2000 strands
• DNA polymerases and DNA ligases fill in and seal
  the nucleotides

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Replication Results

• Each of the new strands is identical to one
  another and to the old one

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DNA Packing
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RNA

• Ribonucleic Acid
• Transcribed from DNA
• Appears in three forms (Messenger RNA mRNA,
  Transfer RNA tRNA, and Ribosomal RNA rRNA)
• Found in the nucleus or cytoplasm of all living
  organisms
• Single stranded molecule
• Utilizes Adenine, Guanine, Cytosine, and Uracil

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RNA Transcription

• Similar to DNA replication
• Only part of a DNA molecule
• RNA polymerase is used and attaches to the
  promoter on the DNA molecule
• As the RNA polymerase moves along the DNA, RNA
  nucleotides are added
• The terminator determines the end of
  transcription

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Transcription Results

• Average length of transcribed RNA is 8000
  nucleotides
• Takes close to 1200 nucleotides to code for a
  protein of 400 amino acids

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Pre-mRNA

• Pre-Messenger RNA
• Has a cap at the 5 end and a Ploy (A) tail at 3
• Cap Guanosine triphosphate
• Poly (A) Tail 30 to 200 adenine nucleotides
• A lot of the pre-mRNA are introns - nucleotide
  sequences that dont code for anything
• The part that actually codes for amino acids are
  called exons

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Pre-mRNA continued

• Pre-mRNA stays in the nucleus
• Small nuclear ribonucleoproteins snRNPs
  (snurps) are composed of snRNA and they join with
  other proteins to make a spliceosome that
  identifies the ends of introns and splices them
  out and immediately joins the exons
• Result is m-RNA that leaves the nucleus to the
  cytoplasm

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t-RNA

• Transcribed from DNA templates
• About 80 nucleotides long
• Used repeatedly
• Takes on the shape of a t
• Hydrogen bonds are created between the fold
• 3 end is where the amino acid attaches

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r-RNA

• Ribosomal RNA
• Transcribed from DNA, in the nucleus
• Composed by the help of proteins imported from
  the cytoplasm
• Ribosomal subunits then leave the nucleus and
  assemble in the cytoplasm

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Three sites on r-RNA

• P site (peptidyl t-RNA site) Holds the t-RNA
  that is carrying the growing polypeptide chain
• A site (aminoacyl t-RNA site) hold the t-RNA
  that is to be added to the polypeptide chain
• E site (exit site) t-RNAs that loose their amino
  acid depart at this site

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Translation

• The Ribosome floats free in the cytoplasm
• The m-RNA binds to it
• The codon of a t-RNA, with an amino acid,
  attaches at the A site, where the matching codon
  sequence is
• It then moves to the P site and another t-RNA
  attaches at the A site
• Amino acids from the t-RNA a the P site move to
  the A site
• That first t-RNA moves to the E site and
  eventually leaves to find another amino acid
• The cycle continues

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Termination of Translation

• The ribosome allows a protein called a release
  factor to come along board
• It doesnt have an amino acid, so therefore no
  more can be added to the polypeptide chain and
  the process is terminated
• The amino acids then go on to build proteins

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Nitrogen base Replenishment

• Food Mechanical and chemical digestion
• Cell burst When a cell breaks the nucleotides
  are absorbed by other cells

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DNA RNA

• Deoxyribonucleic Acid
• Double stranded
• A, G, C, T
• Nucleus only

• Ribonucleic Acid
• Single stranded
• A, G, C, U
• Nucleus and cytoplasm

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Fin