DNA is the code of life!

Rosalind Franklin –
1920-1958
She should be credited with discovering the structure of DNA
I deserved the nobel prize!

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?

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

5’ 3’
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
5’ A C G
Note the backbone is the same for each one
T 3’

3’
3’
5’
5’

5’ 3’

5’ 3’

5’
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`
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?

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
-think of it as the blueprint
QuickTime™ and a
decompressor are needed to see this picture.
DNA structure-- a polymer of nucleotides

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

Things to notice about the sugar:
--sugars can circularize by eliminating an H
2 and forming a bond between hydroxyl groups
0 molecule
--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
RNA DNA

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:
PO
4
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 releasing the two outermost phosphate residues.
2
O and
Bond formation:
OOO-
O P O P O P O
O O O
5'
CH
2
O sugar
3' ..
X base
OOO-
O P O P
O O
O P O
O
5'
CH
2
O sugar
O
3'
X base
The phosphodiester bond
P base base
O
OOO-
O P O P O P O
O O O
5'
CH
2
O sugar
5'
CH
2
O sugar
OH
3'
X
X
3'
OH
** Notice that the DNA chain is synthesized in a 5’ to 3’
direction.

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

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

H
N
1
C
2
N H
2
C
6
5
C
3
N
4
C
N
7
8
C H
9
N
H
A d e n i n e
H
N
C
H
2
N
O
C
N
C
C
N
N
H
C H
G u a n i n e
H
H
H
C
4
C
5
6
C
N
3
2
C
1 N
O
N H
2
C y t o s i n e
H
C
C H
3
C
C
O
H
N N
C
O
T h y m i n e
H
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
1 5
Guanine Cytosine
G and C have 3 H-bonds
Adenine Thymine
A and T make 2 H-bonds

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

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:
Hydrogen atom
Amino group Carboxyl group
Distinguishing feature: R group; side chain conveys specific chemical properties

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

Protein synthesis--chain elongation mechanism
Fig 1-14

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

The Genetic Code
Codon--mRNA triplet that signals single AA addition
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)
Fig 1-16

1
2
3
Reading frame is set by the initiation of translation
Fig 1-17

Central dogma