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
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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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 tounge fern

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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
40 S
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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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Amino acid codons
alanine GCA, GCC, GCG GCU, AGA,
AGG arginine AGA, AGG, CGA CGC, CGG,
CGU asparagine AAC, AAU aspartate GAC, GAU
cysteine UGC, UGU glutamate GAA,
GAG glutamine CAA, CAG glycine GAA, GCC,
GGG GGU histidine CAC, CAU isoleucine AUA, AUC,
AUU leucine CUA, CUC, CUG CUU, UUA, UUG
lysine AAA, AAG methionine
AUG phenylalanine UUC, UUU proline CCA,
CCC CCG, CCU serine UCA, UCC
UCG, UCU AGC, AGU threonine ACA, ACC
ACG, ACU tryptophan UGG tyrosine UCA,
UCU valine GUA, GUC GUG, GUU
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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
40S
ribosome unit
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Translation
60S
Psite
A site
40S
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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Learning Check

• What is the sequence of bases in mRNA produced
• from a section of the template strand of DNA that
  has
• the sequence of bases 3CTAAGG5?
• 1. 5GATTCC3
• 2. 5GAUUCC3
• 3. 5CTAAGG3

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Solution

• What is the sequence of bases in mRNA produced
• from a section of the template strand of DNA that
  has
• the sequence of bases 3CTAAGG5?
• 3CTAAGG5?
• 2. 5GAUUCC5

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Learning Check

• The following section of DNA is used to build a
  mRNA
• for a protein.
• 3GAACCCTTT5
• A. What is the corresponding mRNA sequence?
• B. What are the anticodons on the tRNAs?
• C. What is the amino acid order in the peptide?

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Solution

• 3GAACCCTTT5 DNA
• A. What is the corresponding mRNA sequence?
• 5CUUGGGAAA3 mRNA
• B. What are the anticodons for the tRNAs?
• mRNA codons CUU GGG AAA
• tRNA anticodons GAA CCC UUU
• C. What is the amino acid order in the peptide?
• mRNA 5CUUGGGAAA3
• Leu Gly Lys