Nucleic acids

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Nucleic acids

• Nucleic acids
• Maintain genetic information
• Determine Protein Synthesis
• DNA deoxyribonucleic acid
• Master Copy for most cell information.
• Template for RNA
• RNA ribonucleic acid
• Transfers information from DNA
• Template for Proteins

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Nucleic Acids

• Chromosomes
• (in nucleus)

Have genes
1 gene
1 enzyme or protein
Enzymes determine external internal
characteristics
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NUCLEIC ACIDS

• Long chains (polymers) of repeating nucleotides.
• Each nucleotide has 3 parts

A heterocyclic Amine Base
A sugar
A phosphate unit
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Nucleotide phosphate sugar base
Base
Phosphate
Sugar
?-N-glycosidic linkage
Nucleoside sugar base
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Nucleic Acids

• Nucleic Acids polymers of Nucleotides.

base
B
B
B
B
B
B
S
S
S
S
S
S
P
P
P
P
P
P
phosphate
sugar
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THE SUGAR PART

• The major difference between RNA and DNA is the
  different form of sugar used.

Ribose C5H10O5 in RNA
DeoxyRibose C5H10O4 in DNA
The difference is at carbon 2.
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The Nitrogenous Bases

• 5 bases used fall in two classes
• Purines Pyrimidines

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The Nitrogenous Bases
Purines
Adenine (A)
Guanine (G)

• Pyrimidines

Thiamine (T) In DNA only
Uracil (U) In RNA only
Cytosine (C)
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Nucleotides Di- Tri- Phosphates
Adenine
ribose
Adenosine 5-monophosphate (AMP)
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Nucleotides Di- Tri- Phosphates
Adenine
ribose
Adenosine 5-monophosphate (AMP)
Adenosine 5-diphosphate (ADP)
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Nucleotides Di- Tri- Phosphates
Adenine
Adenosine 5-triphosphate (ATP)
ribose
Adenosine 5-monophosphate (AMP)
Adenosine 5-diphosphate (ADP)
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Primary structure
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Primary structure
Adenine (A)
Similar to proteins with their peptide bonds and
side groups.
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Guanine (G)
Thymine (T)
Phosphate bonds link DNA or RNA nucleotides
together in a linear sequence.
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Structure of DNA
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• In 1938 William Thomas Astbury took the first
  fiber diffraction pictures of DNA, correctly
  predicting, in an article in the journal Nature,
  the overall dimensions of the molecule and that
  the nucleotide bases were stacked at intervals of
  3.3Å perpendicular to its long axis. It was left,
  however, to Watson and Crick after the Second
  World War to elucidate the detailed double
  helical structure of DNA.

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Maurice Wilkins with one of the cameras he
developed specially for X-ray diffraction studies
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Work on x-ray diffraction patterns by Maurice
Wilkins and Rosalind Franklin in 1953, revealed
that the molecule had a "helical shape.
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• Rosalind Franklin is most associated
  with the discovery of the structure of DNA. At
  26, after she had her PhD, Franklin began working
  in x-ray diffraction - using x-rays to create
  images of crystallized solids. She pioneered the
  use of this method in analyzing complex,
  unorganized matter such as large biological
  molecules, and not just single crystals.Franklin
  made marked advances in x-ray diffraction
  techniques with DNA. She adjusted her equipment
  to produce an extremely fine beam of x-rays. She
  extracted finer DNA fibers than ever before and
  arranged them in parallel bundles. And she
  studied the fibers' reactions to humid
  conditions. All of these allowed her to discover
  crucial keys to DNA's structure. Maurice Wilkins,
  her laboratory's second-in-command, shared her
  data, without her knowledge, with James Watson
  and Francis Crick, at Cambridge University, and
  they pulled ahead in the race, ultimately
  publishing the proposed structure of DNA in
  March, 1953.It is clear that without an
  unauthorized peek at Franklin's unpublished data,
  Watson and Crick probably would neither have
  published their famous paper on the structure of
  DNA in 1953, nor won their Nobel Prizes in 1962.
  Franklin did not share the Nobel Prize she died
  in 1958 at the age of 37.

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1953, James Watson Francis Crick and their
scale model for DNA
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DNA secondary and tertiary structure

• Sugar-phosphate backbone
• Causes each DNA chain to coil around the outside
  of the attached bases like a spiral stair case.
• Base Pairing
• Hydrogen bonding occurs between purines and
  pyrimidines. This causes two DNA strands to bond
  together.
• adenine - thymine guanine - cytosine
• Always pair together!
• Results in a double helix structure.

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Base pairing and hydrogen bonding
guanine
cytosine
thymine
adenine
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DNA - Secondary Structure
Complementary Base Pairing Position of H bonds
and distance match with
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Hydrogen bonding
Each base wants to form either two or three
hydrogen bonds. Thats why only certain bases
will form pairs.
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Sugar-phosphate backbone DNA coils around
outside of attached bases like a spiral stair
case.
Results in a double helix structure.
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The double helix
One complete twist is 3.4 nm
The combination of the stairstep sugar-phosphate
backbone and the bonding between pairs
results in a double helix.
2 nm between strands
Distance between bases 0.34 nm
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DNA - Secondary Structure

• Complementary Base Pairing

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• The actual chain is like a coiled spring.
• It is something similar to what happens when
  protein chains form an alpha helix.
• It is the sequence (order) of the amines coming
  off of the backbone that give us all our genetic
  information
• Just like the sequence of words in a sentence
  give it meaning.
• Of the like in words meaning just sentence a give
  sequence it. (Get my meaning ? ?)

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• Crick and Watson
• (1962 Nobel Prize)
• Proposed the basic structure of DNA
• 2 strands wrap around each other
• Strands are connected by H-bonds between the
  amines.
• Like steps of a spiral staircase

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Chromosomes
Chromosomes consists of DNA strands coiled around
protein - histomes. The acidic DNAs
are attracted to the basic histones.
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It also was clear in the 1960s that the
chromosomes of cells
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Chromosomes

• The normal number of chromosome pairs varies
  among the species.
• Animal Pairs Plant Pairs
• Man 23 Onion 8
• Cat 30 Rice 14
• Mouse 20 Rye 7
• Rabbit 22 Tomato 12
• Honeybee, White pine 12
• male 8 Adders 1262
• female 16 tongue fern

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Role of RNA and DNA in Heredity
RNA and DNA are involved in three major processes
in a cell related to heredity as shown below
Replication is an important process during mitosis

1. Replication (DNA copies itself)
2. Transcription (The genetic code in DNA is
   rewritten into RNA and carried to the ribosomes
   by mRNA
3. Translation (tRNA carries amino acids to the
   ribosomes as part of protein synthesis

Transcription and translation are two steps in
the biosynthesis of a protein
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DNA Self - Replication

• When a cell nucleus divides, the bridging
  hydrogen bonds break (with the aid of enzymes)
  and the intertwined strands unwind from each
  other.
• The amines left sticking out from each strand are
  now free to pick up new partners from the
  plentiful supply present in the cell.

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(No Transcript)
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DNA Self - Replication
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DNA Self - Replication
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Replication of DNA
Replication occurs on both halves in opposite
directions.
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DNA Replication

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RNA synthesis
In the first step, RNA polymerase binds to a
promotor sequence on the DNA chain. This insures
that transcription occurs in the correct
direction. The initial reaction is
to separate the two DNA strands.
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RNA synthesis
initiation sequence
termination sequence
Special base sequences in the DNA
indicate where RNA synthesis starts and stops.
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RNA synthesis
Once the termination sequence is reached,
the new RNA molecule and the RNA synthase are
released. The DNA recoils.
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• The messenger RNA (mRNA) move outside the nucleus
  to the cytoplasm where Ribosomes are anxiously
  awaiting their arrival.

rRNA
Nucleus
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• The messenger RNA (mRNA) move outside the nucleus
  to the cytoplasm where Ribosomes are anxiously
  awaiting their arrival.

rRNA
Nucleus
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• The messenger RNA (mRNA) move outside the nucleus
  to the cytoplasm where Ribosomes are anxiously
  awaiting their arrival.

rRNA
Nucleus
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• The messenger RNA (mRNA) move outside the nucleus
  to the cytoplasm where Ribosomes are anxiously
  awaiting their arrival.

rRNA
Nucleus
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Ribosomal RNA rRNA Platform for protein
synthesis. Holds mRNA in place and helps
assemble proteins.
rRNA
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• The Ribosomes are like train stations
• The mRNA is the train slowly moving through the
  station.

rRNA
Codons
mRNA
rRNA
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• Transfer RNA - tRNA
• relatively small compared to other RNAs
  (70-90 bases.)
• transports amino acids to site of protein
  synthesis.

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Anticodons on t-RNA
Site of amino acid attachment
Point of attachment to mRNA
Three base anticodon site
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UUU or UUC is the codon for Phe. UUG is the
codon for Leu. AUG is the codon for Met.
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Codons
There are two additional types of
codons Initiation AUG (same as
methionine) Termination UAG, UAA, UGA
A total of 64 condons are used for all
amino acids and for starting and stopping. All
protein synthesis starts with methionine. After
the poly- peptide has been made, an enzyme
removes this amino acid.
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Protein Synthesis1 Activation

• Each AA is activated by reacting with an ATP
• The activated AA is then attached to particular
  tRNA... (with the correct anticodon)

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Translation
Initiation factors
ribosome unit
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Translation
Psite
A site
ribosome unit
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Translation
ribosome unit
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Translation
Met
ribosome unit
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Translation
Met
ribosome unit
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Termination

• After the last translocation (the last codon is a
  STOP), no more AA are added.
• Releasing factors cleave the last AA from the
  tRNA
• The polypeptide is complete

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Recombinant DNA

• Circular DNA found in bacteria
• E.Coli plasmid bodies
• Restriction endonucleases cleave DNA at specific
  genes
• Result is a sticky end
• Addition of a gene from a second organism
• Spliced DNA is replaced and organism synthesizes
  the new protein

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Recombinant DNA
Bacterium
Remove gene segment
sticky ends
DNA Plasmid
Cut gene for insulin
Replace in bacterium
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