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Primer on Molecular Genetics

DOE Human Genome Program

Primer on Molecular Genetics

Date Published: June 1992

U.S. Department of Energy

Office of Energy Research

Office of Health and Environmental Research

Washington, DC 20585

The "Primer on Molecular Genetics" is taken from the June 1992 DOE

Human

Genome 1991-92 Program Report.

The primer is intended to be an introduction to

basic principles of molecular genetics pertaining to the genome project.

Human Genome Management Information System

Oak Ridge National Laboratory

1060 Commerce Park

Oak Ridge, TN 37830

Voice: 865/576-6669

Fax: 865/574-9888

E-mail: bkq@ornl.gov

Contents

Primer on

Molecular

Genetics

Revised and expanded

by Denise Casey

(HGMIS) from the

primer contributed by

Charles Cantor and

Sylvia Spengler

(Lawrence Berkeley

Laboratory) and

published in the

Human Genome 1989–

90 Program Report.

Introduction

............................................................................................................. 5

DNA............................................................................................................................... 6

Genes ............................................................................................................................ 7

Chromosomes ............................................................................................................... 8

Mapping and Sequencing the Human Genome

...................................... 10

Mapping Strategies .....................................................................................................

Genetic Linkage Maps ............................................................................................

Physical Maps .........................................................................................................

Low-Resolution Physical Mapping......................................................................

Chromosomal map .........................................................................................

cDNA map ......................................................................................................

High-Resolution Physical Mapping .....................................................................

Macrorestriction maps: Top-down mapping ...................................................

Contig maps: Bottom-up mapping ..................................................................

Sequencing Technologies ...........................................................................................

Current Sequencing Technologies .........................................................................

Sequencing Technologies Under Development .....................................................

Partial Sequencing to Facilitate Mapping, Gene Identification ...............................

End Games: Completing Maps and Sequences; Finding Specific Genes .................. 25

Model Organism Research

.............................................................................. 27

Informatics: Data Collection and Interpretation

..................................... 27

Collecting and Storing Data ........................................................................................ 27

Interpreting Data ......................................................................................................... 28

Mapping Databases .................................................................................................... 29

Sequence Databases .................................................................................................. 29

Nucleic Acids (DNA and RNA) ................................................................................ 29

Proteins .................................................................................................................. 30

Impact of the Human Genome Project

....................................................... 30

Glossary...

.............................................................................................................. 32

Introduction

he complete set of instructions for making an organism is called its genome. It

contains the master blueprint for all cellular structures and activities for the lifetime of

the cell or organism. Found in every nucleus of a person’s many trillions of cells, the

human genome consists of tightly coiled threads of deoxyribonucleic acid (DNA) and

associated protein molecules, organized into structures called chromosomes (Fig. 1).

Fig. 1. The Human Genome at Four Levels of Detail.

Apart from reproductive cells (gametes) and

mature red blood cells, every cell in the human body contains 23 pairs of chromosomes, each a

packet of compressed and entwined DNA (1, 2). Each strand of DNA consists of repeating

nucleotide units composed of a phosphate group, a sugar (deoxyribose), and a base (guanine,

cytosine, thymine, or adenine) (3). Ordinarily, DNA takes the form of a highly regular double-

stranded helix, the strands of which are linked by hydrogen bonds between guanine and cytosine

and between thymine and adenine. Each such linkage is a base pair (bp); some 3 billion bp

constitute the human genome. The specificity of these base-pair linkages underlies the mechanism

of DNA replication illustrated here. Each strand of the double helix serves as a template for the

synthesis of a new strand; the nucleotide sequence (i.e., linear order of bases) of each strand is

strictly determined. Each new double helix is a twin, an exact replica, of its parent. (Figure and

caption text provided by the LBL Human Genome Center.)

Primer on

Molecular

Genetics

If unwound and tied together, the strands of DNA would stretch more than 5 feet but

would be only 50 trillionths of an inch wide. For each organism, the components of these

slender threads encode all the information necessary for building and maintaining life,

from simple bacteria to remarkably complex human beings. Understanding how DNA

performs this function requires some knowledge of its structure and organization.

DNA

In humans, as in other higher organisms, a DNA molecule consists of two strands that

wrap around each other to resemble a twisted ladder whose sides, made of sugar and

phosphate molecules, are connected by “rungs” of nitrogen-containing chemicals called

bases. Each strand is a linear arrangement of repeating similar units called nucleotides,

which are each composed of one sugar, one phosphate, and a nitrogenous base (Fig.

2). Four different bases are present in DNA—adenine (A), thymine (T), cytosine (C), and

guanine (G). The particular order of the bases arranged along the sugar-phosphate

backbone is called the DNA sequence; the sequence specifies the exact genetic instruc-

tions required to create a particular organism with its own unique traits.

The two DNA strands are held together

by weak bonds between the bases on

each strand, forming base pairs (bp).

Genome size is usually stated as the total

number of base pairs; the human genome

contains roughly 3 billion bp (Fig. 3).

Each time a cell divides into two daughter

cells, its full genome is duplicated; for

humans and other complex organisms,

this duplication occurs in the nucleus.

During cell division the DNA molecule

unwinds and the weak bonds between

the base pairs break, allowing the strands

to separate. Each strand directs the

synthesis of a complementary new

strand, with free nucleotides matching up

with their complementary bases on each

of the separated strands. Strict base-

pairing rules are adhered to—adenine will

pair only with thymine (an A-T pair) and

cytosine with guanine (a C-G pair). Each

daughter cell receives one old and one

new DNA strand (Figs. 1 and 4). The

cell’s adherence to these base-pairing

rules ensures that the new strand is an

exact copy of the old one. This minimizes

the incidence of errors (mutations) that

may greatly affect the resulting organism

or its offspring.

Fig. 2. DNA Structure.

The four nitrogenous

bases of DNA are

arranged along the sugar-

phosphate backbone in a

particular order (the DNA

sequence), encoding all

genetic instructions for an

organism. Adenine (A)

pairs with thymine (T),

while cytosine (C) pairs

with guanine (G). The two

DNA strands are held

together by weak bonds

between the bases.

A gene is a segment of

a DNA molecule (rang-

ing from fewer than

1 thousand bases to

several million), located

in a particular position on

a specific chromosome,

whose base sequence

contains the information

necessary for protein

synthesis.

Phosphate Molecule

Deoxyribose

Sugar Molecule

Nitrogenous

Bases

Weak Bonds

Between

Bases

Sugar-Phosphate

Backbone

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