• DNA and RNA are large macromolecules with several levels of complexity

• Nucleotides form the repeating units

• Phosphodiester bonds link nucleotides to form a strand

• Two strands interact to form a double helix

• The double helix interacts withproteins resulting in 3-D structuresin the form of chromatin

NUCLEIC ACID STRUCTURE

3D structure

9-25Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayFigure 9.8

Nucleotide Components

9-27Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

• Base + sugar nucleoside – Example

• Adenine + ribose = Adenosine• Adenine + deoxyribose = Deoxyadenosine

• Base + sugar + phosphate(s) nucleotide– Example

• Adenosine monophosphate (AMP)• Adenosine diphosphate (ADP)• Adenosine triphosphate (ATP)

Combining all the parts

9-28Figure 9.10

Base always attached here

Phosphates are attached there

9-26

Figure 9.9 The structure of nucleotides found in (a) DNA and (b) RNA

A, G, C or T A, G, C or U

dNMP NMP

Nucleotide Polymerization Reaction: Phosphodiester Bond Formation

9-30Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayFigure 9.11

9-31Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

• 1953, James Watson and Francis Crick discovered the double helical structure of DNA

• The scientific framework for their breakthrough was provided by other scientists including– Linus Pauling– Rosalind Franklin– Erwin Chargaff

Events Leading to DNA Structure Determination

Linus Pauling

Rosalind Franklin• Helical• Double stranded• 10 base pairs per turn

X-ray Diffraction Pattern of DNA

9-35Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

• It was assumed the four bases: A, G, C and T were in a repeating, tetranucleotide configuration

• Therefore, there should be the same amount of A, G, C & T in any molecule of DNA form any source

• Chargaff carefully determined the exact percentages of nuceotides in DNA from several sources

Erwin Chargaff’s Experiment

Erwin Chargaff’s Data

9-39

• % A = % T & %G = %C• However %AT DID NOT = %GC• This observation became known as Chargaff’s rule

Watson & Crick Model DNA Structure

Base Pairing Key to DNA Structure

Features of the DNA Double Helix

NH2

T

2 nm

One nucleotide0.34 nm

One completeturn 3.4 nm

O

O

HH

NN

H

H

HHOOO

OPO–

NH2

HN

N

NH

N

HH

H

OH

HHOOO

O–

PO–

HH

H

HHOOO

OPO–

NH2

O

O

H H

NN

H2N

HN

N

NH

N

H H

H

HHO

OOO–

PO

H H

H

HHO OO

O–

PO

H N

NH

N

N

H H

H

HHO

OOO–

PO–

H2N

HO5end 3end

3hydroxyl3end 5 end

5phosphate

TA

T A

T AP

PP

P

P

S

S

S

S

SS

S

S

A

C G

G

C G

C G

G

G

C

C

G C

GC

G C

C

P

PS

P

PP

P

P

S

SS

S

S

PP

P

P

PP

P

P

S

S SS

S

S

S

S

SP

S

S

P

PP

S

SS

SP

CH2

CH2

CH2

H2N

CH2

CH2

CH2

A

P

S

P

P

H

CH3H

NNHO

O

Space-filling model of DNA

Ball-and-stick model of DNA

Minorgroove

Majorgroove

Minorgroove

Majorgroove

Features of the DNA Double Helix

Major Helical Conformations of DNA

A-DNA B-DNA

A26

0

Melting Point Curve: Tm is Proportional to %GC

Tm= 68.9 + (0.41)(%GC)

9-55

The Three-Dimensional Structure of DNA

Figure 9.21

9-57

• The primary structure of an RNA strand is much like that of a DNA strand

• RNA is made as a single strand only, however it may form a double stranded structures

• RNA strands can be a 10s to1000s of nt in length

• RNA is made from a DNA template - only one of the two strands of a DNA helix is used as the template

• RNA contains uracil rather than thymine

RNA Structure

9-58Figure 9.22

9-60

Figure 9.23

RNA Secondary Structures

9-61

Figure 9.24

RNA Tertiary Structure – a tRNA