bb10006: cell & molecular biology

BB10006: Cell & Molecular biologyDay Time Date Place Lecturer Topic

Monday 9:15 14.2.05 UniHall MVH Nucleic acidsMonday 14:15 14.2.05 ArtsLT MVH Nucleic acids

Wednesday 11:15 16.2.05 ArtsLT MVH Nucleic acidsMonday 9:15 21.2.05 UniHall MVH Nucleic acidsMonday 14:15 21.2.05 ArtsLT MVH Nucleic acids

Wednesday 11:15 23.2.05 ArtsLT MVH Nucleic acidsMonday 9:15 28.2.05 UniHall J RB RadiochemistryMonday 14:15 28.2.05 ArtsLT J RB Genetic modification

Wednesday 11:15 2.3.05 ArtsLT J RB Genetic modificationMonday 9:15 7.3.05 UniHall J RB Genetic modificationMonday 14:15 7.3.05 ArtsLT J RB Genetic modification




Wednesday 11:15 20.4.05 ArtsLT J RB Genetic modificationMonday 9:15 25.4.05 UniHall J RB Genetic modificationMonday 14:15 25.4.05 ArtsLT J MWS Animal development

Wednesday 11:15 27.4.05 ArtsLT J MWS Animal developmentWednesday 11:15 4.5.05 ArtsLT J MWS Animal development

Monday 9:15 9.5.05 UniHall J MWS Animal developmentMonday 14:15 9.5.05 ArtsLT RJ S Plant development

Wednesday 11:15 11.5.05 ArtsLT RJ S Plant developmentMonday 9:15 16.5.05 UniHall RJ S Plant development

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):1) Biochemistry (2/3e) by D Voet & J Voet2) Molecular biology of the cell (4th ed) by

Alberts et al3) Any biochemistry textbookKey websites 1) http://www.dnai.org/lesson/go/2166/19942) 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%202004-05.htm

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

References: History, structure and forms of DNA

http://www.dnai.org/lesson/go/2166Voet and Voet – Chapter 28

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

Timeline1800’s 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



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

Hershey and Chase experiments



1952


1944

Hershey-Chase ‘blender’ experiment

1952 Erwin Chargaff – base ratios

1952 R Franklin & M Wilkins–DNA diffraction pattern

1953 J Watson and F Crick – DNA structure solved



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

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 109 base pairsNumber of genes = 26 – 32,000 genes

Goal: to sequence the entire human nuclear genome

DNA, gene, genome?DNA = nucleic acidGene = segments of DNA that encode proteinGenome = entire nucleic acid component of

any organism

Nucleic acids: made up of individual nucleotides linked together

Protein - polypeptides made up of individual amino acids linked together -

http://www.ncc.gmu.edu/dna/amino.htm

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, hetercyclic 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

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

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

Why DNA evolved as the genetic material but not RNA?

B-DNA

Biologically dominant

Right-handed double helix

planes of base pairs are nearly perpendicular to the helix axis.

helix axis passes through the base pairs and hence B-DNA has no internal spaces B-DNA has a wide and deep major groove and a narrow and deep minor groove

DNA conformationsB-DNA:

right-handed double helix with a wide and narrow groove.

A-DNA major groove is very deep and the minor groove is

quite shallow

Z-DNA consists of dinucleotides, each with different

conformations

4 stranded DNA Telomeric DNA

DNA conformations

both form right-handed double helices

B-DNA helix has a larger pitch and hence a smaller width than

that of A

In B-DNA, the helix axis passes through the base pairs and hence

B-DNA has no internal spaces, whereas that of A-DNA has a 6

Angstrom diameter hole along its helical axis.

The planes of the base pairs in B-DNA are nearly perpendicular to the helix axis, whereas in A-DNA,

they are inclined from this. Therefore, B-DNA has a wide and deep major groove and a narrow and deep minor groove, whereas

A-DNA has a narrow and deep major groove, but a wide and

shallow minor groove.

A DNA B DNA

DNA conformations

B-DNA forms a right-handed double helix in

which the repeating unit is a nucleotide,

whereas Z-DNA forms a left-handed double helix in which the repeating unit is

adinucleotide.

The Z-DNA helix has a larger pitch and is

therefore narrower than that of B-DNA.

B-DNA has a wide and deep major groove and a narrow and deep minor groove, whereas Z-DNA has a narrow and deep

minor groove but a nonexistent major groove.

B DNAZ DNA

Types of RNAMessenger RNA (mRNA): Codes for proteinsTransfer RNA (tRNA): Adaptor between

mRNA & amino acidsRibosomal RNA (rRNA): Forms ribosome

core for translationHeterogenous nuclear RNA (hn RNA)Small nuclear RNA (sn RNA): involved in

post-transcriptional processing

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

dna replicationlectures

forms of dna http

mccleod mccarty

dna fibers rosalind

function of nucleic

martha chase

chase experimentshershey

mccarty experimentavery