DNA is the code of life!

The Basics: A general review of molecular biology: DNA Transcription RNA Translation Proteins

I deserved the nobel prize! Rosalind Franklin – She should be credited with discovering the structure of DNA

The answer is "yes" Polymers A polymer is a big molecule composed of smaller molecules linked together with similar bonds.

Synthetic polymers: nylon, kevlar, polyethylene Are these the secret of life?

Natural polymers: Cellulose, starch, chitin rubber Are these the secret of life?

No. The secret of life lies in a special kind of polymer. SUPER POLYMERS.

Super polymers are just like regular polymers, except 1.They are composed of more than one subunit but linked by the same type of bonds 2.The subunits are arranged in a specific order

Now, if all the elephants were the same, this would be a regular polymer. In DNA, one kind of SUPER POLYMER, there are four kind of elephants with the names: A, C, G, and T A C GT Note the backbone is the same for each one 5’ 3’ 5’

3’ 5’ 3’

5’ 3’

5’ 3’

All SUPER POLYMERS are made by adding one unit at a time on to the tail end of the chain (the 3` end). In the chain above, synthesis is said to proceed 5` to 3` 5’ 3’

Here's another question: Assume a large field with thousands of A, C, G, and T elephants. At the sound of bell, all the elephants form chains (remember they always grab on to the tail of another elephant). How could you make sure that all the chains stopped with an "A" elephant? 5’ 3’

SUPER POLYMERS fall into two categories 1.Some act primarily to carry instructions. They are said to be "informational" or "instructional" 2.Some are best at performing operations. They are said to be "operational". They are molecular machines.

DNA (deoxyribonucleic acid) is the genetic material It is an informational super polymer DNA structure-- a polymer of nucleotides -think of it as the blueprint

Nucleotides have : 1) a 5 carbon sugar 2) a ring-shaped nitrogen base 3) a phosphate group

Things to notice about the sugar: --sugars can circularize by eliminating an H 2 0 molecule and forming a bond between hydroxyl groups --the carbons in the sugar are given numbers in standard Nomenclature, designated as “prime” to distinguish from carbons on the nitrogen base these numbers are used to distinguish critical sites in The nucleotide and in the DNA strand. ribose is a 5-carbon sugar RNADNA

2’-deoxy-ribose is different from ribose in that it lacks a hydroxyl group (-OH) on the 2’ carbon DNA-2’-deoxy-ribose RNA-ribose The chemical difference associated contributes significantly to the differences between DNA and RNA biochemistry

The OH groups on the 5’ and 3’ carbons are the reactive groups through which nucleotides become joined a single, free nucleotide includes 3 phosphate groups joined at the 5’ position….. PO 4

What to know about the phosphate: 1) linked at 5’ carbon 2) can have 1, 2, or 3 phosphate residues (nucleotide mono-phosphate, nucleotide di-phosphate, nucleotide tri-phosphate) 3) ***the oxygens of the phosphate group are negatively charged at physiological pH. Therefore DNA carries a large net negative charge!

The polynucleotide chain To form the polynucleotide chain, the oxygen of the 3' hydroxyl group on the chain “attacks” the phosphate of a nucleotide triphosphate eliminating H 2 O and releasing the two outermost phosphate residues. The phospho- diester bond **Notice that the DNA chain is synthesized in a 5’ to 3’ direction.

***There is an asymmetry to the DNA chain! 5’ end--phosphate group 3’ end--free hydroxyl group 5’ end 3’ end Read as: 5’ ATGC 3’

Nucleotides have : 1) a 5 carbon sugar 2) a ring-shaped nitrogen base 3) a phosphate group

There are 4 bases (units) in DNA: A G C T Adenine and Guanine have 2 rings--purines Cytosine and Thymine have 1 ring--pyrimidines

DNA is double-stranded--two polynucleotide chains Hydrogen bonds between bases hold these together G and C have 3 H-bondsA and T make 2 H-bonds 15  GuanineCytosineAdenineThymine

DNA strands are arranged in an anti-parallel manner 5’ 3’ 5’ 3’ Complementary (Not “complimentary”)

Critical Properties of DNA 1)Negative charge (towards which pole will DNA migrate towards?) 2) DNA can be denatured and renatured (nucleic acid hybridization). 3) DNA is soluble in water. 4) DNA absorbs UV light. 5) DNA can be stained and amounts of DNA can be measured using ethidium bromide.

Ethidium bromide intercalates into the DNA double helix EthBR fluoresces under UV light, enabling us to “see” DNA no fluorescent color… fluorescent

Genes, chromosomes and genomes Gene: DNA devoted to making one specific polypeptide Genes are housed on chromosomes All DNA of an organism makes up its genome Ch. 1-6

Central dogma

Transcription -DNA is first transcribed into mRNA before protein is made -Product is messenger RNA or transcript -Process is transcription

Transcripts are made of single-stranded RNA Remember, RNA is fundamentally different from DNA: Uracil rather than thymine is used (can pair with A) Ribose is the sugar mRNA is predominantly single-stranded

RNA polymerase is the enzyme that catalyses mRNA synthesis The chain is extended from the 3’ end The chain grows in the 5’ to 3’ direction

The promoter is the site where RNA polymerase binds to initiate transcription Promoters are part of the DNA of the gene (called the 5’ non-coding region) but are not included in the transcript itself

Protein synthesis: translation (mRNA to protein) Proteins have catalytic and structural functions Proteins with catalytic functions are enzymes

Amino acids are the building blocks of proteins: Common to all: Distinguishing feature: R group; side chain conveys specific chemical properties Carboxyl groupAmino group Hydrogen atom

Fig 1-13 Different amino acid chains have different chemical properties

Protein synthesis--chain elongation mechanism Fig 1-14

Free amino group At the first residue Proteins also have a polarity to them-- distinct beginning and end Free carboxy group at the last residue OH Fig 1-15

The Genetic Code 1) triplet--3 bases in a row code specific amino acids 2) code is degenerate 3) initiation codons start (AUG = Met) 4) stop codons terminate (UAA, UAG, UGA) Codon--mRNA triplet that signals single AA addition Fig 1-16

5) “frame” is critical AAUUCGAGUUUGUG ASN-TRP-SER-LEU ILE-ALA-VAL-CYS PHE-GLU-PHE-TRP Reading frame is set by the initiation of translation Fig 1-17

Central dogma