Nucleotides and Nucleic AcidsPart 1

Chapter 8

Nucleotides and Nucleic Acids

– Biological function of nucleotides and nucleic acids

– Structures of common nucleotides– Structure of double-stranded DNA– Structures of ribonucleic acids– How Proteins bind to DNA

Learning Goals

Functions ofNucleotides and Nucleic Acids

• Nucleotide Functions:– Energy for metabolism (ATP, GTP, CTP,

UTP)– Enzyme cofactors (NAD+, NADP+, FAD)– Signal transduction (cAMP, cGMP)

• Nucleic Acid Functions: – Storage of genetic info (DNA)– Transmission of genetic info (mRNA)– Processing of genetic information

(ribozymes)– Protein synthesis (tRNA and rRNA)

Nucleotides and Nucleosides

• Nucleotide = – Nitrogeneous base– Pentose– Phosphate

• Nucleoside = – Nitrogeneous base– Pentose

• Nucleobase = – Nitrogeneous base

b-N-Glycosidic Bond

• In nucleotides the pentose ring is attached to the nucleobase via N-glycosidic bond

• The bond is formed to the anomeric carbon of the sugar in -b configuration

• The bond is formed:

– to position N1 in pyrimidines

– to position N9 in purines

• This bond is quite stable toward hydrolysis, especially in pyrimidines

• Bond cleavage is catalyzed by acid

Modified Nucleotides

Modified Nucleotides - More

Chemical Instability of RNA at Alkaline pH’s

UV Spectrum

ds DNA

ds DNA on the English 2 Pound Coin

Watson and Crick Had Three Sets of Data

1. Rosalind Franklin’s X-ray crystallography

2. Chargaff’s Rules

3. Chemical Structures of Nucleotides

Rosalind Franklin’s X-ray Crystallography

Some of Chargaff’s Rules

1. DNA base composition varies between species.

2. DNA from different tissues of same species has the same base composition.

3. Base composition of a species does not vary with age, nutritional state, or change in environment.

4. No matter what species A = T and G = C and [purines] = [pyrimidines] which is A+G = T+C

Erwin Chargaff in the 1940’s worked out methods to measure each nucleotide in DNA. The rules made sense when applied to the Watson-Crick DNA structure.

DNA Bases – Pairing

Suppose you isolated DNA from two unidentified species of bacteria: species X and species Y.

You know that adenine makes up 32% of species X DNA and 13% of species Y DNA.

How much of each nucleotide are present in these two DNAs?

One species was isolated from a hot thermal spring, which is the most likely one?

The Watson-Crick Structures

The Beauty of the Watson-Crick

Structure was that it gave a way to do

Hi-fidelity Replication

DNA is not necessarily straight, and it can bend.

Most DNA is in the anti-conformation

DNA can From Three Types of Helices

Forces that hold two ssDNA dsDNA1. H-bonds and 2. hydrophobic stackingAbout equal in strength..look at the diagrams,

where’s the water?

DNA Helix Forms

A B Z

Looking Down the DNA Helix

How Long is Your Book Laid Page by Page?

Lehninger 5th Edition is 1,263 printed pages + a few blanks

pages are 21.5 cm wide x 27.5 cm high.

Placing the pages next to each other then the book is How Long?

Answers = 271.5 meters side by side .. or

347.3 meters tops to bottoms

or in Sports terms:

About 2.7 to 3.5 and football fields long.

NOW

EOC Problem 3: How long is your DNA? The average human has about 0.5 g DNA. The B-helix weighs about 10-18 g/1000 nucleotide pairs. What

more information do you need…to get the answer? Do it !!

B-Z JunctionsHow to Go from Right Handed to Left

Handed

Ha, et al. 2005. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature. 437:1183-1186.

Samsung Biomedical Research Institute, Seol, Korea

and Massachusetts Institute of Technology, Cambridge, MA.

B-Z Junctions – an AT pair flipped inside out.

B-Z Junction – Side View

Z DNA is a higher energy form of the double helix…stabilized by negative supercoiling (generated by transcription or unwrapping from nucleosomes).

Z DNA near the promoter stimulates transcription.

Stabilized by proteins…Kd in nM range.

But…can relax back to the B helix.

Extruded bases may be site for DNA modification.

DNA Binding Proteins – It’s all in the Grooves

EOC Problem 1 looks at H-bonding from the sides of the DNA strand..through the grooves.

Proteins that Bind DNA – Showing Major Groove

Helix Turn Helix Motif – Bacterial Lac Repressor

Lac Repressor (grey) Bound to DNA (blue)

Minor Groove is Also

Important

Rhos et al. Nature 461:1248 2009

Minor Groove narrowing with AT tracts variation in shape.

Enhances Arg Binding

Things to Know and Do Before Class

1. Structure and chemistry of the nucleotides.

2. Essence of Chargaff’s Rules.

3. Structure and properties of the dsDNA and dsRNA helices.

4. BZ junctions.

5. How proteins bind to DNA.

6. EOC Problems: 1-3