Molecular Biology

Principles and Practice

INTRODUCTION

Copyright 2012 by W. H. Freeman and Company

What is Molecular Biology?

A. Understand cellular process in molecular terms: 1) Which molecules?

2) What complexes?
3) Structure/Function paradigm 4) How do these interactions regulate biological processes B. Most modern biology addressed at this level genetics immunology & pathogenesis virology & microbiology structural biology & computational biology cell & developmental biology neurobiology & evolution

Central Issues
A. Genetic information: 1) How encoded and stored 2) How passed to succeeding generations

3) How expressed and regulated

B. Central dogma (organizing principle): DNA (m)RNA C. Course outline: 1) Genes encoded as DNA: structure & chemistry (nucleic acids) proteins

2) Inheritance: replication (DNA DNA)

3) How expressed and regulated: transcription (DNA RNA),
3

gene regulation, translation (RNA proteins)

Nucleic Acid Chemistry

Nucleic acids differ in their pentose sugar

The two sugars present in nucleic acids.

Pyrimidine and purine bases

Pyrimidine, Pyrimidine bases

Purine, Purine bases

Uracil (U) 8

Deoxyribonucleosides

Ribonucleosides

10

Nucleotides have a phosphate group attached to the sugar

11

Bases, nucleosides, and nucleotides

Nucleosides: names are required; nucleotides: only symbols are required to write Other names are required to recognize only.
12

Bases, nucleosides, and nucleotides

Nucleosides: names are required; nucleotides: only symbols are required to write Other names are required to recognize only.

13

Bases, nucleosides, and nucleotides

14

Bases can form tautomers

15

Unusual bases

16

Other forms of nucleotides

17

Nucleotides are joined 5 3 in both DNA and RNA

18

DNA sequences

also: pA-C-G-T-AOH pApCpGpTpA ACGTA (most common)

19

Nucleic Acid Structure

An Introduction

20

Chargaff Rules (1940s) 1. base composition varies with species 2. base composition within species same for every tissue 3. base composition does not change with age, diet, environment 4. often, number of A = T, number of G = C

21

Franklin and Wilkins: X-ray diffraction of DNA

X-ray diffraction patterns of the A and B-form of the sodium salt of DNA.

22

The Watson-Crick model of DNA

23

Features of DNA

Base pairing
Base stacking

24

Base pairing in DNA

25

Nucleic Acid Function

An Introduction

26

Griffiths bacterial transformation

Mouse injections Virulent S strain = death Nonvirulent R strain = healthy Heat-killed S strain = healthy Nonvirulent R strain + heat-killed S strain = death

27

Avery, MacLeod, and McCarty showed the transforming principle is DNA

28

The Hershey-Chase experiment

29

Replication of DNA

30

The central dogma: DNARNA Protein

31

The translation machinery: ribosomes, mRNA, and tRNA

32

Summary of what I learned in this lecture

An introduction to molecular biology Nucleic Acid Chemistry: Nucleosides vs Nucleotides The purines: A, G The pyrimidines: T,C and U in RNA (T is only in DNA) Difference between the nucleoside and nucleotides is that nucleotides have a phosphate group attached to the sugar. Uracil tautomer: Lactam, Lactim, Double Lactim Chargaffs 4 rules in the 1940s: 1. base composition varies within species 2. base composition within species is the same for every tissue 3. base composition does not change with age, diet, enviroment, 4. often the number of As=Ts the number of Gs=Cs Franklin and Wilkins X-ray diffraction of DNA Watson and Crick= double helix of DNA 3 main experiments that we learned: Griffiths bacterial transforamtion, Avery MacLeod, and McCarthy showed transforming princple is DNA, The hersey chase experiment comparing Dna (labeled with radioactive P) and Proteins (labeled with radioactive S) Replication of DNA is semiconservative: When parent strands separate each parent serves as a template for the formation of a new daughter strand by means of A-T and C-G base pairing. The central dogma: DNA RNA protein 33

Practice Problems
1. 2. 3. 4. 5. 6. 7. 8. 9. 10. The compound that consists of ribose linked to N-9 of adenine is E) Adenosine A major component of RNA but not of DNA is: E)Uracil The difference between a ribonucleotide and a deoxyribonucleotide is:A)a deoxyribonucleotide has an H instead of an OH at C-2. The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA: E)JOIN THE 3 Oh of one nucleotide and a 5Phosphate (hydroxyl) of the next. The DNA oligonucleotide abbreviated pATCGAC: B) Has a hydroxy at its 3end. Draw the tautomeric forms of uracil: look at paint In ds nucleic acid, cytosine typically base pairs with B)guanine. Chargaffs rules state that is typical DNA: E)A+G=T+C The experiment of Avery, MacLeod, and McCarthy in which nonvirulent bacteria (r STRAIN) were made virulent by transformation was significant because it showed that: B) genetic materials are composed of DNA only. Which of the following is NOT true of all naturally occurring DNA? C) The ratio of A+T/G+C is constant for all natural DNAs.

34