bb10006: cell & molecular biology

BB10006: Cell & Molecular biology

Dr. MV Hejmadi

Dr. JR Beeching (convenor)

Prof. RJ Scott

Prof. JMW Slack

Dr. Momna Hejmadi ([email protected])

Structure and function of nucleic acids

Books (any of these):Any bioscience textbook will do but my

favourites are Biochemistry (3e) by D Voet & J VoetMolecular biology of the cell (4th ed) by Alberts et alEssential Cell Biology by Alberts et al

Key websites http://www.dnaftb.org/dnaftb/ http://www.dnai.org/lesson/go/2166/1994 http://molvis.sdsc.edu/dna/index.htm

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

Outline of my lectures

Lecture 1. Nucleic acids – an introduction

Lecture 2. Properties and functions of nucleic

acids

Lecture 3. DNA replication

Lectures 4-6. Transcription and translation

Access to web lectures athttp://www.bath.ac.uk/bio-sci/hejmadi/teaching%202005-06.htm

Lecture 1 - Outline How investigators pinpointed DNA as the genetic materialThe elegant Watson-Crick model of DNA structureForms of DNA (A, B, Z)

References: History, structure and forms of DNA

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

Timeline1869 F Miescher - nucleic acids

1928 F. Griffith - Transforming principle



Discovery of transforming principle

1928 – Frederick Griffith – experiments with smooth (S) virulent

strain Streptococcus pneumoniae and rough (R) nonvirulent strain

Griffith experiment

What is this transforming principle?

Bacterial transformation demonstrates transfer of genetic material

Timeline1800’s F Miescher - nucleic acids


Avery, McCleod & McCarty- Transforming principle is DNA

1944



Avery, MacLeod, McCarty Experiment



1949


1944

Erwin Chargaff – base ratios



E. Chargaff’s ratios

A = TC = G

A + G = C + T% GC constant for given species



1952


1944

Hershey-Chase ‘blender’ experiment


1949 Erwin Chargaff – base ratios


Hershey and Chase experiments

1952 – Alfred Hershey and Martha Chase provide convincing evidence that DNA is genetic material

Waring blender experiment using T2 bacteriophage and bacteria

Radioactive labels 32P for DNA and 35S for protein



1952


1944



1952 R Franklin & M Wilkins–DNA diffraction pattern



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



1952


1944



1952 R Franklin & M Wilkins–DNA diffraction pattern

1953 J Watson and F Crick – DNA structure solved



The Watson-Crick Model: DNA is a double helix

1951 – James Watson learns about x-ray diffraction pattern projected by DNA

Knowledge of the chemical structure of nucleotides (deoxyribose sugar, phosphate, and nitrogenous base)

Erwin Chargaff’s experiments demonstrate that ratio of A and T are 1:1, and G and C are 1:1

1953 – James Watson and Francis Crick propose their double helix model of DNA structure

Human genome project

Public consortiumHeaded by F CollinsStarted in mid 80’sWorking draft completed

in 2001Final sequence 2003Nature: Feb 2001

Celera GenomicsHeaded by C VenterStarted in mid 90’sWorking draft completed

in 2001

Science: Feb 2001

Human genome = 3.3 X 10 9 base pairsNumber of genes = 26 – 32,000 genes

Goal: to sequence the entire human nuclear genome

The human genomeThe human genome

Nuclear genome (3.2 Gbp) 24 types of chromosomes Y- 51Mb and chr1 -279Mbp

Mitochondrial genome

DNA in forensicswhat can a single human hair tell

you?

nuclear DNAnuclear DNAHair rootHair root

mitochondrial DNAmitochondrial DNAHair shaftHair shaft

Types of RNATypes of RNA

Nucleotides

DNA RNA

Originally elucidated by Phoebus Levine and Alexander Todd in early 1950’s

2’-deoxy-D-ribose 2’-D-ribose

Made of 3 components1) 5 carbon sugar (pentose)2) nitrogenous base3) phosphate group

1) SUGARS

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

adenine

uracil

thymine

cytosine

guanine

pyrimidines

purines

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

Nucleotide monomernucleotide = phosphate ester monomer of pentosedinucleotide - Dimer

Oligonucleotide – short polymer (<10)

Polynucleotide – long polymer (>10)

Nucleoside = monomer of sugar + base

1) Phosphodiester bonds

5’ and 3’ links to pentose sugar

2) N-glycosidic bonds

Links nitrogenous base to C1’ pentose in beta configuration

5’ – 3’ polynucleotide linkages

3’ end

5’ end 5’ – 3’ polarity

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

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

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

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-DNAB-DNAA- DNAA- DNA Z-DNAZ-DNA

BB AA ZZ

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

Problem

http://www.dnaftb.org/dnaftb/19/concept/index.html

Maybe because RNA, not DNA, is prone to base-catalysed hydrolysis

Why has DNA evolved as the genetic material but not RNA?

linear

human chromosomes

Double stranded DNA

Genetic material may be DNA

Single stranded DNA

circular

linear

circularProkaryotesMitochondriaChloroplastsSome viruses(pox viruses)

Parvovirus

adeno-associated viruses

reoviruses

Double stranded RNA

Genetic material may be RNA

Single stranded RNA

Retroviruses like HIV

http://www.uchsc.edu/sm/neuro/tylerlab/images/home_r2_c2.jpg

RNA / DNA hybridse.g. during retroviral replication

What is the base found in RNA but not DNA? ?

A) CytosineB) Uracil

C) Thymine D) Adenine E) Guanine

What covalent bonds link nucleic acid monomers?

A) Carbon-Carbon double bondsB) Oxygen-Nitrogen Bonds

C) Carbon-Nitrogen bonds D) Hydrogen bonds

E) Phosphodiester bonds

What sugar is used in in a DNA monomer?

A) 3'-deoxyribose

B) 5'-deoxyribose

C) 2'-deoxyribose

D) Glucose

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'-hydroxylE) 2'-deoxyribose sugar, Nitrogenous base, 5'- phosphate

bb10006: cell & molecular biology

Documents

mccleod mccarty

dna replicationlectures

forms of dna http

mccarty experimentavery

dna fibers rosalind

function of nucleic

chargaff base ratioshershey

martha chase