NUCLEIC ACIDS

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NUCLEIC ACIDS
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Course outline

• 1 DNA and RNA
• 2 Structure
• 3 Elucidation of DNA as genetic material

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1 DNA and RNA ---a comparison
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Where is DNA found
Chromosome
Cells

• For human beings there are 22 pair of chromosomes
  which determines traits with 23rd pair
  determining sex. XX - female and XY - males.

Genes
DNA
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Components of Nucleic Acid

• Two type of nucleic acids in the cell
• DNA - deoxyribose nucleic acid
• RNA - ribose nucleic acid
• DNA is found in the chromosomes whereas RNA is
  found elsewhere in the nucleus.
• Building Blocks of DNA and RNA are Nucleotides
  Nucleotide are made of base, sugar (ribose or
  deoxyribose) and a phosphate.

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• Nucleoside - Base sugar

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Nucleotides

• Nucleotides can form DNA or RNA
• Nucleoside triphosphates can store energy such as
  ATP
• Nucleoside triphosphates are involved in cell
  signaling such as GTP

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Deoxyribonucleic Acid (DNA)

• Structural Components
• Sugar (deoxyribose) and phosphate
• Genetic material
• Bases
• Purines (Adenine and Guanine)
• Pyrimidines (Thymine and Cytosine)

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Deoxyribonucleotides
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Ribonucleosides
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What is the chemical difference between RNA and
DNA?
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Nucleotide Bases

• DNA is a polynucleotide containing A, T, G, and C
• RNA is a polynucleotide containing A, U, G, and C

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What are the different types of RNA and what is
their function?

• mRNAs
• codes for proteins
• rRNAs
• part of the ribosome, site of protein synthesis
• tRNAs
• carries amino acids to the ribosome

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Differences between procaryotic mRNA and
eucaryotic mRNA

• Polycistronic versus moncistronic
• 5 cap
• 3 tail
• Introns and Exons
• Compartmentalization

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Eucaryotic mRNAs have a 5 cap
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Eucaryotic mRNAs have a 3 poly(A) tail
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Eucaryotic mRNAs have introns
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2 DNA Structure

• Sugar-Phosphate backbone is invariable
• Sugar bound to phosphate in a phosphodiester bond
  between 5C and 3C
• Base region of DNA variable
• DNA is directional
• Always write sequence 5 to 3

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Backbone

• Nucleotides joined into chain by covalent bonds
  between phosphate and sugar units
• Bases extend to side joined to sugar
• Chemical Direction to chain
• Phosphate at one end, Hydroxyl in sugar at other
• 5 to 3 (Carbons) by convention

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3 Elucidation of DNA as Genetic Material

• 1928 - Griffith Experiment- bacteria
• 1944- Avery, Macleod and McCarty- isolated DNA
• 1952 - Hershey and Chase
• 1953- Watson and Crick

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Avery, Macleod, McCarty

• Determine the identity of the transforming agent
• Chemical analysis, electrophoresis and
  ultracentrifugation- consistent with DNA
• No loss of transforming activity when lipid or
  protein removed
• No loss of activity with proteases, lipases or
  ribonucleases
• Loss of activity with deoxyribonucleases

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DNA Double Helix ----secondary
structure

• 1953
• Rosalind Franklin Maurice Wilkins (X-ray
  studies)
• Watson and Crick elucidated the structure
• Antiparallel chains
• 5 to 3
• 3 to 5
• Right handed helix coiled about central axis

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Structure of B DNA

• Purines and pyrimidines on inside of helix
• Sugar-phosphate backbone on outside
• Sugars are perpendicular to bases
• Chains held together by hydrogen bonding
• A hydrogen bonds to T
• G hydrogen bonds to C

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Base Pairing
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Base Pairing

• Watson-Crick Complements (Pyrimidine to Purine)
• T-A
• C-G
• W-C Complements pair by hydrogen bonds
• Nucleotide Bases Hydrophobic

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Major groove and minor groove
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Unusual DNA Structures

• Palindromes
• Inverted repeat
• Mirror repeats
• Triple helix pairing

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Hoogsteen Pairing

• Unusual pairing formation
• Triple helix pairing at low pH

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Remember DNA Structure

• What are the chemical components of DNA?
• What chemical bond links the sugar-phosphate
  backbone?
• What is the difference between a 3 end and a 5
  end?
• What chemical bond links the sugar to the base?
• Describe the structure of DNA

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RNA

• RNA are single strand nucleic acid with Uracil as
  a base instead of Thymine. Sugar is ribose
  instead of deoxyribose.
• m-RNA (messenger RNA) transcribe info. from DNA
  a-helices.
• r-RNA (ribosome RNA) this is where protein
  synthesis occurs also known as the protein
  factory.
• t-RNA (transfer RNA) smallest of RNA, this
  chemical is responsible for carrying amino acids
  to the protein factory (r-RNA) and coordinating
  the amino acid monomeric unit to make a protein..

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Example of folded structures assumed by tRNA
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Denaturation Renaturation
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Denaturation Renaturation
The double helix of DNA can be reversibly melted
by heating the DNA solution This process is
called melting because it occurs abruptly at a
certain temperature. Tm (melting temperature)
half of the helical structure is lost. It
isdepends markedly on base composition(GC 20 to
78----77ºCto 100ºC). The AT rich regions are the
first to melt
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Denaturation Renaturation
Annealing separated complementary strands of DNA
reassociate to form a double helix when
temperature is lowered below Tm Hybridization
annealing of DNA strands from different origins
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Some property of DNA

• MW 106-109
• E.coli chromsome four million base pairs,
  2.6109D, 1.4mm (2nm in diameter) the largest
  chromsome of Drosophila melanogaster is 2.1cm in
  length.
• Absorbance 260nm
• Hyperchromism the unstacking of the base pairs
  results in the increased absorbance.
• Electrophoresis PAGE, Agrose gel