DNA is the code of life!

DNA is the code of life!

The Basics: A general review of molecular biology:

DNA Transcription

RNATranslation

Proteins

I deserved the nobel prize!

Rosalind Franklin – 1920-1958She should be credited with discovering the structure of DNA

The answer is "yes"

PolymersA 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 G T

Note the backbone is the same for each one

5’

3’

3’

5’

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 blueprintQuickTime™ and a

decompressorare needed to see this picture.

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 H20 moleculeand forming a bond between hydroxyl groups

--the carbons in the sugar are given numbers in standardNomenclature, designated as “prime” to distinguish from carbons on the nitrogen base

these numbers are used to distinguish critical sites inThe nucleotide and in the DNA strand.

O OHHOH2C

H H

OH OH

H H

1'

2'3'

4'

5'

Ribose

O OHHOH2C

H H

OH

H H

1'

2'3'

4'

5'

H

Deoxyribose

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 differenceassociated contributessignificantly to the differences between DNA and RNA biochemistry

O OHHOH2C

H H

OH OH

H H

1'

2'3'

4'

5'

Ribose

O OHHOH2C

H H

OH

H H

1'

2'3'

4'

5'

H

Deoxyribose

O OHHOH2C

H H

OH OH

H H

1'

2'3'

4'

5'

Ribose

O OHHOH2C

H H

OH

H H

1'

2'3'

4'

5'

H

Deoxyribose

The OH groups on the 5’ and 3’ carbons are thereactive groups through which nucleotides become joined

a single, free nucleotide includes 3 phosphate groups joined at the 5’ position…..

PO4

O OHHOH2C

H H

OH OH

H H

1'

2'3'

4'

5'

Ribose

O OHHOH2C

H H

OH

H H

1'

2'3'

4'

5'

H

Deoxyribose

PO4

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 H2O and releasing the two outermost phosphate residues.

O P

O

O-

O P

O

O-

O P

O

O-

OO

O

CH2

X

5'

3'

O

OH

CH2

O

P

X

5'

3'

base

base

sugar

sugar

OH

base..

OCH25'

O P

O

O-

O P

O

O-

O P

O

O-

O

X3'

base

O

OH X3'

sugar

sugar

CH25'

O P

O

O-

O P

O

O-

O P

O

O-

O

Bond formation:

The phospho-diesterbond

**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:

C

NC

N C

C

N

N

C H

HH

N H2

C

NC

N C

C

N

N

C H

HH

2N

H

O

C

N

C

CN

C

H

H

H

O

N H2

C

N

C

CN

C

H

H

O

H

C H3

O

A d e n i n e Gu a n i n e Cy t o s i n e Th y m i n e

1

2

34

56

7

8

93

56

12

4

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-bonds A and T make 2 H-bonds

1 5

Guanine

Cytosine

Adenine

Thymine

DNA strands are arranged in an anti-parallel manner

OH

Free hydroxyl at 3' end

Free phosphate at 5' end

PO4OHThe base pairing of two DNA chains.

5’

3’ 5’

3’

Complementary

(Not “complimentary”)

Critical Properties of DNA1) Negative charge (towards which pole will DNA migrate towards?)

2) DNA can be denatured and renatured (nucleic acidhybridization).

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

Uracil Thymine Ribose Deoxyribose

RNA DNA RNA DNA

Bases Sugars

RNA polymerase is the enzyme that catalyses mRNA synthesis

The chain is extendedfrom the 3’ end

The chain grows in the5’ 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

H2N C

H

R1

C

O

N

H

C

H

R2

C

O

N

H

C

H

R3

C

O

N

H

C

H

R4

C

O

1 2 3 4

Free amino groupAt the first residue

Proteins also have a polarity to them--distinct beginning and end

Free carboxy groupat the last residue

OH

Fig 1-15

The Genetic Code

1) triplet--3 bases in a rowcode 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

AAUUCGAGUUUGUGASN-TRP-SER-LEU ILE-ALA-VAL-CYS PHE-GLU-PHE-TRP

1

2

3

Reading frame is set by the initiation of translation

Fig 1-17

Central dogma