Structure of DNA & RNA (2.6 & 7.1 HL)IB Diploma Biology

Essential Idea: The structure of DNA allows efficient storage of

genetic information.

The human genome project which has decoded the case sequence for the whole 6 feet of the human genome requires a data warehouse (pictured) to store the information electronically.

Scientists have programmed nearly 500,000 DVD’s worth of data into 1 gram of DNA!

2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.

2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.

A Nucleotide: A single unit of a Nucleic Acid polymer

There are two types of Nucleic Acids: DNA and RNA.

Nucleic acids are very large molecules that are constructed by linking together nucleotides to form a polymer.

2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.

Covalent bond

Covalent bond

A Nucleotide: A single unit of a Nucleic Acid polymer

• Five carbon atoms = a pentose sugar• If the sugar is Deoxyribose the polymer is

Deoxyribose Nucleic Acid (DNA)• If the sugar Ribose the polymer is Ribose

Nucleic Acid (RNA)

• Acidic• Negatively charged

• Contains nitrogen• Has one or two rings in it’s

structure

2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.

There are four nitrogen bases in DNA:

Adenine (A) Guanine (G) Thymine (T) Cytosine (C)

RNA shares the same bases except that Uracil (U) replaces Thymine

NOTE: When talking about bases always use the full name on the first instance

• Adenine & Guanine are two-ringed bases called Purines• Thymine & Cytosine are one-ringed based called Pyrimidines

2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.

• Nucleotides a linked into a single strand via a condensation reaction

• Bonds are formed between the phosphate of one nucleotide and the pentose sugar of the next

• The phosphate group (attached to the 5'-C of the sugar) joins with the hydroxyl (OH) group attached to the 3'-C of the sugar

• This results in a Phosphodiester bondbetween the two nucleotides and the formation of a water molecule

• Successive condensation reactions between nucleotides results in the formation of a long single strand

DNA RNA

Type of Pentose Sugar

Number of Strands

Two anti-parallel, complementary strands

form a double helix

Single stranded, and often, but not always,

linear in shape

Nitrogen Bases

Adenine (A)Guanine (G)Thymine (T)Cytosine (C)

Adenine (A)Guanine (G)

Uracil (U)Cytosine (C)

2.6.2 DNA differs from RNA in the number of strands present, the base

composition and the type of pentose.

2.6.2 DNA differs from RNA in the number of strands present, the base

composition and the type of pentose.

2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked

by hydrogen bonding between complementary base pairs.

2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked

by hydrogen bonding between complementary base pairs.

2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked

by hydrogen bonding between complementary base pairs.

2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked by

hydrogen bonding between complementary base pairs.

• Each polynucleotide chain (strand) consists of a chain of nucleotides bonded covalently.

• Two polynucleotide chains of DNA are held together by hydrogen bonds between complementary base pairs:

Adenine pairs with Thymine (A=T) via twohydrogen bondsGuanine pairs with Cytosine (G=C) via threehydrogen bonds

• In order for bases to be facing each other and thus able to pair, the two strands must run in opposite directions (i.e. they are anti-parallel)

• As the polynucleotide chain lengthens, the atoms that make up the molecule will arrange themselves in an optimal energy configuration. This position of least resistance results in the double-stranded DNA twisting to form a double helix with approximately 10 - 15 bases per twist.

In Summary:

2.6.5 Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using

circles, pentagons and rectangles to represent phosphates, pentoses and bases.

To make sure you have learn this skill you need to practice it repeatedly...

DNA: RNA:

2.6.4 Crick and Watson’s elucidation of the structure of DNA using model making.

“We have discovered the secret of life!”– Francis Crick (An English pub, 1953)

In early 1953, Linus Pauling, an American chemist proposed a model for DNA with phosphate groups in the core of the molecule and the nitrogen bases facing outward…

After this was disproved, three major groups, including Pauling’s Cal Tech group, James Watson and Francis Crick at Cambridge, and Maurice Wilkins and Rosalind Franklin at the University of London, were competing to elucidate the correct structure of the molecule…

Whilst others worked using an experimental basis Watson and Crick used stick-and-ball models to test their ideas on the possible structure of DNA. Building models allowed them to visualize the molecule and to quickly see how well it fitted the available evidence.

Watson and Crick ultimately won the race, publishing their model of DNA in a 900 word paper later in 1953

http://www.hhmi.org/biointeractive/watson-constructing-base-pair-models

2.6.4 Crick and Watson’s elucidation of the structure of DNA using model making.

It was not all easy going however. Their first model, a triple helix, was rejected for several reasons:• The ratio of Adenine to Thymine was not 1:1 (as discovered

by Erwin Chargaff)• It required too much magnesium (identified by Franklin)

From their setbacks they realized:• DNA must be a double helix.• The relationship between the bases and base pairing• The strands must be anti-parallel to allow base pairing to

happen

Because of the visual nature of their work the second and the correct model quickly suggested:• Possible mechanisms for replication• Information was encoded in triplets of bases

Watson and Crick gained Nobel prizes for their discovery. It should be remembered that their success was based on the evidence they gained from the work of others. In particular the work of Rosalind Franklin and Maurice Wilkins, who were using X-ray diffraction was critical to their success.

2.6.4 Crick and Watson’s elucidation of the structure of DNA using model making.

Nucleosomes• DNA in eukaryotes is associated with

proteins called histones. • The octamer & DNA combination is attached

to an H1 histone, forming a nucleosome. • The nucleosome serves to protect the DNA

from damage and to allow long lengths of DNA to be supercoiled

Supercoiling• Supercoiling allows the chromosomes to be

mobile in mitosis & meiosis. • Supercoiled DNA cannot be transcribed for

protein synthesis. Allows genes to be switched ON and OFF.

7.1.11 Utilize molecular visualization software to analyze the association between protein and DNA within a nucleosome.

Visit:http://www.rcsb.org/pdb/101/motm.do?momID=7

andhttp://www.rcsb.org/pdb/explore/jmol.do?structureId=1AOI&bionumber=1

Explore:

• Find the two copies of each histone protein by locating their “tails” (H2A, H2B, H3, and H4)

• Visualize the positively charged amino acids on the nucleosome core. How do they play a role in the association of the protein core with the negatively charged DNA?

7.1.6 Some regions of DNA do not code for proteins but have other important functions.

7.1.6 Some regions of DNA do not code for proteins but have other important functions.

7.1.6 Some regions of DNA do not code for proteins but have other important functions.

Functions of Non-Coding, Highly-Repetitive DNA Sequences (Introns)

Productionof RNA

Some regions on DNA function to produce tRNA and rRNA

Gene Expression

Non-coding regions can have an role in regulating the expression of genes by promoting (enhancers) or inhibiting (silencers).

Telomeres

Telomeres are located on the ends of eukaryote chromosomes, they have a protective function because DNA cannot be replicated all the way to the ends, so telomeres prevent loss of important genes.

7.1.7 Discuss Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray diffraction.

• Rosalind Franklin worked at King’s College in London as a technician doing X-ray crystallography.

• She improved the resolution of the cameras used in order to obtain the most detailed images yet of X-ray diffraction of DNA. These detailed images allowed her to make very exact measurements related to the structure of DNA.

• Her work was shared with James Watson without her permission.

• Watson and Crick used her measurements to show that the phosphate groups were on the outside of the DNA double helix, and that the nitrogenous bases were more hydrophobic and thus on the inside.

• Watson & Crick published the structure of DNA first, without crediting Franklin. They were awarded the Nobel prize. Franklin died of ovarian cancer she developed as a result of her work.

7.1.7 Discuss Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray diffraction.

X-Ray Crystallography:

• When X-rays pass through a substance, they diffract. • Crystals have a regularly repeating pattern, causing X-

rays to diffract in a regular pattern. • These patterns allow for measurements & calculations

to be made about the structure of molecules.

Franklin’s X-Ray “Photo 51” Showed…

• X pattern: DNA is a helix• Angle of X: Calculate the steepness of the helix• Distance between horizontal bars: Distance between

bases is 3.4nm. • Distance between center of X and top of image:

0.34nm vertically between the repeating units (bases) in the molecule- so 10 bases per turn of the helix.

7.1.10 Analysis of results of the Hershey and Chase experiment providing evidence that DNA is the genetic material.

• Until the Hershey-Chase experiment, it was widely assumed that protein was the genetic material that made up chromosomes because it had great variety in structures (20 Amino Acids would allow for greater range of coding than just 4 nucleotides…)

• Hershey & Chase took advantage of the fact that DNA contains phosphorus, but not sulfur, & protein contains sulfur, but not phosphorus. Viruses have protein coats surrounding DNA.

• They grew two types of viruses: Type 1 with radioactive phosphorus and Type 2 with radioactive sulfur.

• They had these viruses infect cells (which involved the injection of viral genetic material into the cell) and then checked for the radioactive labels.

• Cells infected by the Phosphorus-labeled viruses contained the radioactive labels. Cells infected by the Sulfur labeled viruses did not…

7.1.10 Analysis of results of the Hershey and Chase experiment providing evidence that DNA is the genetic material.

http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120076/bio21.swf::Hershey%20and%20Chase%20Experiment

THE END…

Bibliography / Acknowledgments

Jason de Nys

Chris Paine