Week #1 CHEM 3511 - Summer 2008 1

SURVEY OF BIOCHEMISTRY

Nucleic Acids

Week #1 CHEM 3511 - Summer 2008 2

What are nucleic acids?

• Building blocks of genetic material that a cell uses to direct cellular functions and heredity

• 3 Components: Sugar Moiety

O

OHHO

OHHOH2C O

HO

OHHOH2C

Ribose (in RNA) Deoxyribose (in DNA)

Week #1 CHEM 3511 - Summer 2008 3

Ring Numbering in Ribose

O

OHHO

OHHOH2C O

HO

OHHOH2C

1’

2’3’

4’

5’

DNA lacks the2’-OH group

Week #1 CHEM 3511 - Summer 2008 4

What are nucleic acids?

• Building blocks of genetic material that a cell uses to direct cellular functions and heredity

• 3 Components: Phosphate Moiety

Phosphoric Acid Phosphate Group

P

O

OHHO

OH

P

O

O

O-

O

Week #1 CHEM 3511 - Summer 2008 5

What are nucleic acids?

• Building blocks of genetic material that a cell uses to direct cellular functions and heredity

• 3 Components: 5 Nitrogenous Bases

N

N

NH2

N

N

R

AdenineA

HN

N

O

N

N

R

H2N

GuanineGPURINES

Week #1 CHEM 3511 - Summer 2008 6

What are nucleic acids?

• Building blocks of genetic material that a cell uses to direct cellular functions and heredity

• 3 Components: 5 Nitrogenous Bases

CytosineC Thymine

T

PYRIMIDINES

N

NO

NH2

HN

NO

O

CH3HN

NO

O

UracilU

Week #1 CHEM 3511 - Summer 2008 7

Ring Numbering in Bases

N

N

NH2

N

N

R

AdenineA

1

2

3

4

56

7

8

9

Week #1 CHEM 3511 - Summer 2008 8

Ring Numbering in Bases

CytosineC

1

2

3

4

5

6

N

NO

NH2

Week #1 CHEM 3511 - Summer 2008 9

Nomenclature

Base Nucleoside Nucleotide

Adenine Adenosine Adenosine A Monophosphate

Guanine Guanosine Guanosine G Monophosphate

Etc.

Study Table 3-1 for more details…

Week #1 CHEM 3511 - Summer 2008 10

How do nucleotides link?

Week #1 CHEM 3511 - Summer 2008 11

Base Pairing

Carbon

Nitrogen

Oxygen

Hydrogen

Week #1 CHEM 3511 - Summer 2008 12

Base Pairing

Carbon

Nitrogen

Oxygen

Hydrogen

Week #1 CHEM 3511 - Summer 2008 13

How Does RNA Differ from DNA?

• Ribose vs. Deoxyribose

• Bases and Base Pairing– T in DNA vs. U in RNA– A-T in DNA vs. A-U in RNA

• 3D Structure

• Role

Week #1 CHEM 3511 - Summer 2008 14

Protein Data Bank

http://www.rcsb.org/pdb/home/home.do

Week #1 CHEM 3511 - Summer 2008 15

Protein Data Bank

Download PDB file to Desktop

Use Freeware to View Contents RasMol PyMol Swiss PDB Viewer Protein Explorer

Week #1 CHEM 3511 - Summer 2008 16

Software for Viewing Structures

• Rasmol– http://www.rasmol.org

• Pymol– http://pymol.sourceforge.net

• SwissPDB Viewer– http://www.expasy.ch/spdbv/

• Protein Explorer– http://www.umass.edu/microbio/chime/

pe_beta/pe/protexpl/frntdoo2.htm

Week #1 CHEM 3511 - Summer 2008 17

DNA Double Helix

Week #1 CHEM 3511 - Summer 2008 18

DNA Structural Features

• Handedness

• Anti-parallel strands

• Major and minor grooves

Week #1 CHEM 3511 - Summer 2008 19

Different Conformations of DNA

Week #1 CHEM 3511 - Summer 2008 20

DNA has incredible flexibility!

Catabolite-Activator

Protein (CAP)+ DNA

Yale (1991)

Week #1 CHEM 3511 - Summer 2008 21

DNA has incredible flexibility!

DNA Octahedron

Ned SeemanNYU

International Society for Nanoscale Science, Computation, and Engineering

Week #1 CHEM 3511 - Summer 2008 22

More on Friday…

• Limitations to DNA Flexibility• Supercoiling and Topoisomerases• RNA Structure• Nucleic Acid Function• Recombinant DNA Technology• Potentially PRS questions…