The Dogma • Nucleic acid (DNA/RNA) is important…Why? • The central dogma of Molecular Biology – DNA (genes, chromosomes) begets itself (replication), as well as RNA (transcription)) – RNA begets protein (translation) – Which proteins a cell expresses (and how much), dictates what a cell does
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The Dogma Nucleic acid (DNA/RNA) is important…Why? The central dogma of Molecular Biology –DNA (genes, chromosomes) begets itself (replication), as well.
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The Dogma
• Nucleic acid (DNA/RNA) is important…Why?
• The central dogma of Molecular Biology– DNA (genes, chromosomes) begets itself
(replication), as well as RNA (transcription))– RNA begets protein (translation)– Which proteins a cell expresses (and how
much), dictates what a cell does
DNA structure
• DNA: an ideal molecule for storage of information.– Made of simple, stable(?) “bits” of information
(the nucleotide) (metaphor: letters)– Easily assembled/disassembled (metabolism)
(metaphor: words, sentences, books)– The information is easily “read” (replication,
transcription)
The nucleotide: Pentose sugar
Pentose Sugar (2’ OH=ribose, 2’H=deoxyribose)
1’4’
The nucleotide: Nitrogenous bases
Purines (BIG)
Pyrimidines (small)
From Kimball’s biology pages: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.html
The nucleotide
Nucleotide =sugar+phosphate+base
Phosphate
Base
Sugar (2’ OH=ribose, 2’H=deoxyribose)
The chain has polarity
DNA chains are connected by a phosphate between sugar carbons
The chain has polarity: the phosphate bridges between 5’ and 3’ carbons (almost never 5’ and 5’, or 3’ and 3’)
DNA metabolism
• Making phosphodiester bonds…– Synthesis (Nucleotide addition, nucleotide by
nucleotide)– Ligation (joining two polynucleotide chains
together)
• Breaking phosphodiester bonds….– Cleavage, or hydrolysis
Synthesis
Chemistry dictates addition is always to 3’ end of chain. In other words: synthesis is always 5’ to 3’
DNA synthesis• Synthesis: requires...• Substrates
– 3’ OH of existing chain (primer strand)– template strand (see replication lecture)– deoxynucleotide triphosphate (dNTP)
• Cofactors – Mg2+ (metal cofactor)
• Enzyme (DNA polymerase)• Products are…
• Chain that is longer by one nucleotide• Pyrophosphate (PPi)
Cleavage: Exonuclease
Cleavage (hydrolysis)• Chain is broken between phosphate and sugar (5’ carbon
usually retains phosphate)• Requires….• Substrate:
– DNA chain, usually double stranded– Water
• Enzyme (nuclease)• Co-factors; usually Mg2+• Product: broken chain
• If chain broken from end, enzyme is exonuclease– Exonucleases can chew from 3’ end (3’ to 5’ exo) or 5’ end (5’ to 3’ exo)
• If chain broken in middle, enzyme is endonuclease
Cleavage: Endonuclease
Restriction enzymes are endonucleases (see Lee lecture)
Ligation
Ligation• Requires…• Substrates
– two DNA chains– ATP
• Cofactors– Mg2+ (metal cofactor)
• Enzyme: ligase• Products are…
• Two chains joined together into one chain• AMP• Pyrophosphate (PPi)
DNA chains form helices• Single DNA chains will form a helix
(spiraling line; like threads on screw) because of….– Hydrophobic interactions between bases
• Bases are carbon rich rings that hide from water, and therefore stack on top of each other
– Ionic interactions• Phosphates are highly negatively charged, thus repel
each other
The double helix
• A single stranded DNA chain will form a helix but…
• Each base has a number of hydrogen donors and acceptors
• Donors like to form hydrogen bonds with acceptors
• Like this…..
Watson-Crick base pairs• A with T
• G pairs with C
• Why?
• Complementary pattern of hydrogen donors and acceptors