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DNA structure CC


Nucleic acids An overview of structure
These slides provides an introduction to the structure and function of nucleic acids (DNA and RNA) in relation to organisms, genes, gene expression and protein synthesis. Dr. Momna Hejmadi, University of Bath

DNA basics resources created by Dr. Momna Hejmadi, University of Bath, 2010, is licensed under the Creative Commons Attribution-Non-Commercial-Share Alike 2.0 UK: England & Wales License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/2.0/uk/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California 94105, USA. N.B. Some images used in these slides are from the textbooks listed and are not covered under the Creative Commons license as yet

Books:

Biochemistry (3e) by D Voet & J Voet Molecular biology of the cell (4th ed) by Alberts et al Essential Cell Biology by Alberts et al Life: The Science of Biology by Sadava et al (8th ed )
Key websites

http://www.dnaftb.org/dnaftb/ http://www.dnai.org/lesson/go/2166/1994
http://www.thelifewire.com History, structure and forms of DNA http://www.dnai.org/lesson/go/2166 See document: ‘References: DNA Structure and Function

Learning objectives
Understand the timeline of discoveries leading to elucidation of DNA structure
Describe / draw the structure of nucleotides Understand the alternative DNA conformations Understand RNA structure and diversity

Timeline
1869 1928

F Miescher - nucleic acids F. Griffith - Transforming principle

http://www.dnai.org/lesson/go/2166/1994

Discovery of transforming principle
1928 – Frederick Griffith – experiments with Streptococcus pneumoniae
Smooth (S) virulent strain (polysaccharide coat protects it from immune system)

Rough (R) nonvirulent strain (lacks the polysaccharide coat)

Griffith experiment showing that strains can be transformed by ‘transforming principle’

Bacterial transformation demonstrates transfer of genetic material

What is this transforming principle?

Timeline
1800’s 1928 1944

F Miescher - nucleic acids F. Griffith - Transforming principle

Avery, McCleod & McCarty- Transforming principle is DNA

http://www.dnai.org/lesson/go/2166/1994

Avery, MacLeod, McCarty Experiment

Avery, MacLeod, McCarty Experiment

Transforming principle is DNA

Timeline
1800’s 1928 1944 1949

F Miescher - nucleic acids F. Griffith - Transforming principle

Avery, McCleod & McCarty- Transforming principle is DNA
Erwin Chargaff – base ratios

http://www.dnai.org/lesson/go/2166/1994

E. Chargaff’s ratios
% GC constant for given species regardless of age, nutrition or tissue type

A=T C=G

A+G=C+T

Timeline
1800’s 1928 1944 1949 1952

F Miescher - nucleic acids F. Griffith - Transforming principle

Avery, McCleod & McCarty- Transforming principle is DNA
Erwin Chargaff – base ratios Hershey-Chase ‘blender’ experiment

http://www.dnai.org/lesson/go/2166/1994

Timeline
1800’s 1928 1944 1949 1952 1952

F Miescher - nucleic acids F. Griffith - Transforming principle

Avery, McCleod & McCarty- Transforming principle is DNA
Erwin Chargaff – base ratios Hershey-Chase ‘blender’ experiment R Franklin & M Wilkins–DNA diffraction pattern
http://www.dnai.org/lesson/go/2166/1994

X-ray diffraction patterns produced by DNA fibers Rosalind Franklin and Maurice Wilkins

Timeline
1800’s 1928 1944 1952 1952 1952

F Miescher - nucleic acids F. Griffith - Transforming principle

Avery, McCleod & McCarty- Transforming principle is DNA
Hershey-Chase ‘blender’ experiment Erwin Chargaff – base ratios R Franklin & M Wilkins–DNA diffraction pattern J Watson and F Crick – DNA structure solved
http://www.dnai.org/lesson/go/2166/1994

1953

The Watson-Crick Model: DNA is a double helix
Watson and Crick, 1953, Nature, 171

?

?

?

?

In 1951 Watson learns about x-ray diffraction pattern projected by DNA Erwin Chargaff’s experiments demonstrate that ratio of A and T are 1:1, and G and C are 1:1 Chemical structure of nucleotides were known (deoxyribose sugar, phosphate, and nitrogenous base) Putting this together…… ….in 1953 James Watson and Francis Crick propose their double helix model of DNA structure

1962 Nobel Prize in Physiology or Medicine
?

for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material"

James Watson Francis Crick

Maurice Wilkins

Nucleotides
Originally elucidated by Phoebus Levine and Alexander Todd in early 1950’s Made of 3 components 1) 5 carbon sugar (pentose) 2) nitrogenous base 3) phosphate group

1) SUGARS DNA

RNA

2’-deoxy-D-ribose

2’-D-ribose

2) NITROGENOUS BASES
planar, aromatic, heterocyclic derivatives of purines/pyrimidines

purines

pyrimidines

adenine guanine

cytosine thymine

Note: Base carbons denoted as 1 etc Sugar carbons denoted as 1’ etc

uracil

nucleotide = phosphate
ester monomer of pentose
dinucleotide - Dimer

Nucleotide monomer

Oligonucleotide – short
polymer (<10) Polynucleotide – long polymer (>10)

Nucleoside = monomer
of sugar + base

5’ – 3’ polynucleotide linkages

2) N-glycosidic bonds Links nitrogenous base to C1’ pentose in beta configuration

1) Phosphodiester bonds 5’ and 3’ links to pentose sugar

5’ – 3’ polarity
5’ end

3’ end

?

?

Structurally, purines (A and G) pair best with pyrimidines (T and C) Thus, A pairs with T and G pairs with C, also explaining Chargaff’s ratios

Essential features of B-DNA
? Right twisting ? Double stranded helix ? Anti-parallel ? Bases on the inside (Perpendicular to axis) ? Uniform diameter (~20A) ? Major and minor groove ? Complementary base pairing

DNA conformations
A- DNA Helix Right-handed Widest planes of the base pairs inclined to the helix axis B-DNA Right-handed Intermediate planes of the base pairs nearly perpendicular to the helix axis Z-DNA Left-handed Narrowest planes of the base pairs nearly perpendicular to the helix axis

Width
Planes of bases

Central axis
Major groove Minor groove

6A hole along helix axis

tiny central axis

no internal spaces
No major groove

Narrow and deep Wide and deep

Wide and shallow Narrow and deep Narrow and deep

B-DNA
?

Right-handed helix

?
?

intermediate
planes of the base pairs nearly perpendicular to the helix axis tiny central axis wide + deep major groove narrow + deep minor groove

? ? ?

DNA conformations
A- DNA
?

Right-handed helix

?
?

Widest
planes of the base pairs inclined to the helix axis 6A hole along helix axis narrow + deep major groove Wide + shallow minor groove

? ?

?

DNA conformations
Z-DNA
? ? ?

Left-handed helix Narrowest planes of the base pairs nearly perpendicular to the helix axis no internal spaces no major groove narrow + deep minor groove

? ? ?

B

A

Z

RNA Structure
The tertiary structure is similar to DNA, but with several important differences: ? Single stranded but usually forms intra-molecular base pairs ? major and minor grooves are less pronounced ? Uracil instead of thymine ? Structural, adaptor and transfer roles of RNA are all involved in decoding the information carried by DNA

Types of RNA in the human genome

Class of RNA

Example types

Function Ribosomal subunits mRNA binding

Ribosomal RNA 16,23,18,28S Transfer RNA 22 mitochondrial 49 cytoplasmic

Small nuclear U1,U2,U4,U5 etc RNA(snRNA)
Small nucleolar RNA U3,U8 etc (snoRNA)

RNA splicing
rRNA modification and processing

microRNA (miRNA) >200 types
XIST RNA Imprinting H19 RNA associated RNA Antisense RNA >1500 types Telomerase RNA

Regulatory RNA
Inactivation of X chromosome Genomic imprinting Suppression of gene expression Telomere formation

What you need to remember from this lecture
Classic experiments that lead to the elucidation of DNA structure
Watson-Crick B-DNA structure (linkages, 5’-3’ polarity) Other DNA conformations Types of RNA

Self-test
1. Try the problem from this link: http://www.dnaftb.org/dnaftb/19/concept/index.html 2. Use the questions on the following slides

What sugar is used in in a DNA monomer?
A) 3'-deoxyribose
B) 5'-deoxyribose C) 2'-deoxyribose D) Glucose

What is the base found in RNA but not DNA?
A) Cytosine B) Uracil C) Thymine D) Adenine E) Guanine

What covalent bonds link nucleic acid monomers?
A) Carbon-Carbon double bonds B) Oxygen-Nitrogen Bonds C) Carbon-Nitrogen bonds D) Hydrogen bonds E) Phosphodiester bonds

Each deoxyribonucleotide is composed of
A) 2'-deoxyribose sugar, Nitrogenous base, 5'hydroxyl B) 3'-deoxyribose sugar, Nitrogenous base, 5'hydroxyl C) 3'-deoxyribose sugar, Nitrogenous base, 5'Phosphate D) Ribose sugar, Nitrogenous base, 5'-hydroxyl E) 2'-deoxyribose sugar, Nitrogenous base, 5'phosphate


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