Chapter 2

The Structure of Genes

 Overview
•  Each species has a unique and fundamental set
of genetic blueprints – its genome.
•  The genome is composed of one or more DNA
molecules, each organized as a chromosome.
•  The prokaryotic genomes are mostly single
circular chromosomes.
•  Eukaryotic genomes consist of one or two sets
of linear chromosomes confined to the nucleus.
•  A gene is a segment of DNA that is transcribed
into a functional RNA molecule.
•  Introns interrupt many eukaryote genes.

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 Some definitions
Genome One unique set of the DNA of an organism.

Chromosome A linear end to end arrangement of genes and

other DNA; often associated with RNA and
protein.

Plasmid Autonomously replicating extra-chromosomal

DNA molecule.

Transformation Directed modification of a genome by the

external application of DNA from a cell of a
different genotype.

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How do we know the hereditary
material is DNA?
Transformation (uptake of foreign
DNA) in prokaryotes and eukaryotes
has repeatedly shown that DNA is
hereditary material.

1928: Griffith succeeded in

permanently transforming a
nonvirulent strain of
Pneumococcus into a virulent
strain using an extract of dead
virulent cells

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 How do we know the
hereditary material is DNA?
1944: Avery succeeded in showing
that the transforming principle
was DNA

Approach: Destroy all the major

categories of chemicals in the
extract one at a time to reveal the
chemical responsible for
transformation
Today, purified DNA is used to
transform cells on a routine basis
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 What are the roles of DNA?
•  The three roles of DNA
– DNA is accurately replicated prior to
each cell division.
– DNA encodes proteins needed by the
cell.
– DNA is capable of mutation, providing
raw material for evolutionary change.

A 4th role – stable storage of genetic

information
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 The DNA molecule

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 The DNA Nucleotide
•  Building block of DNA (and RNA)
•  Deoxyribose (pentose sugar), with 3’ –OH
•  Phosphate (on 5’ carbon)
N
•  Nitrogenous bases
base
–  purines
•  adenine N
•  guanine 5
P C
’
–  pyrimidines O
•  thymine
sugar
•  cytosine

OH
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3 8
’
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 The Double Helix
•  DNA normally consists of two antiparallel
polynucleotide chains
–  sugar–phosphate backbone
•  phosphodiester bonds
•  5’ to 3’ connection
–  complementary base pairs
•  A – T 5 3
•  G – C ’
3 ’
5
•  hydrogen bonds ’ ’
–  2 per A – T 5’-AATTGGCCGATC-3’
–  3 per G – C
3’-TTAACCGGCTAG-5’
•  5’ → 3’ chain polarity
•  Major and minor grooves

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 Problems 6 & 7

List the forces that hold the DNA double helix

together.

Covalent bonds in the DNA backbone

Hydrogen bonds between bases
Stacking interactions (mostly hydrophobic)

If thymine makes up 15% of the bases in a DNA

molecule, what percentage of bases must be cytosine?

35% of the bases must be cytosine

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 Questions 14 & 19
If the G+C content of a DNA sample is 48%, what will
be the proportions of the four different nucleotides?
Assuming double-stranded DNA
24% C; 24% G, 26% A and 26% T
In normal duplex DNA is it true that
A + C will always equal G + T? YES
A + G will always equal C + T? YES
Purines always equal pyrimidines? YES
Phosphate always equals deoxyribose sugar? YES

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 Question 28
What do the symbols 5’ and 3’
actually refer to in labeling the ends
of a DNA molecule?

The polarity of the sugar-phosphate

backbone is defined by the orientation
of the deoxyribose sugar. By
convention, the carbons are numbered
as primes to differentiate the atoms of
the base from those of the sugar. It is
useful to use 5’ and 3’ to define the
orientation of the DNA strands.

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 Roles of DNA
How does the structure of DNA fulfill the 3
requirements of the hereditary molecule?
Replication:
each strand serves as template for synthesis
of its complement, using rules of base pairing
Information:
specified by sequence of nucleotides; may
be copied into RNA
Mutation:
replacement, insertion, deletion of nucleotide
results in altered sequence
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 What is the structure of a gene?
•  Gene encodes functional RNA molecule, mostly
mRNA (also tRNA, rRNA, etc.)
regulatory
region DNA encoding functional RNA

RNA primary transcript

•  Gene is functional part of chromosome which is
transcribed into RNA at the correct time and
place in development or cell cycle
•  Gene includes its adjacent regulatory region(s)

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 A Prokaryotic Gene

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 A Eukaryotic Gene
How are eukaryotic genes different from
prokaryotic genes?

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 Eukaryote: Introns and Exons
•  Intron: noncoding region of gene, excised by
processing from primary transcript
– zero to many per eukaryote gene
– variable length, may be bulk of gene
– unknown function
•  Exon: coding region of gene (sequence is
included in mature transcript)
transcript E1 I1 E2 I2 E3 I3 E4

nuclear processing steps

mature transcript E1 E2 E3 E4

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 Questions 23 & 25
The gene for the human protein albumin spans a
chromosomal region 25 kb long from the beginning of the
protein coding sequence to the end of the protein coding
sequence, but the mRNA for this protein is only 2.1 kb
long. What accounts for this huge difference? Introns

With this information can you predict either the number

or the size of the introns? NO
Devise a formula that relates the size of mRNA to gene
size, number of introns, average size of introns and the
size of the regulatory sequence.
mRNA = gene size – (number of introns X average size of introns)
– size of regulatory region
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 Gene Neighborhoods
•  In prokaryotes, genes are often tandemly
arranged, with little or no spacer
sequences in between
•  In eukaryotes, there is considerable
spacer DNA between genes
–  some is repetitive DNA: identical or nearly
identical repeated units
•  dispersed
•  tandem
–  much is derived from mobile genetic elements

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 Question 17
How many DNA molecules are there in the
nucleus of a human body cell? 46, there is a single
DNA molecule in each
chromosome

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 The genetic material of an RNA virus, a DNA virus, and a wombat (an Australian mammal) were
analyzed by a very disorganized laboratory technician, who lost the identification tags to the samples.
Identify the source of the nucleic acid for each sample, giving a reason for each choice.

Sample Adenine Cytosine Guanine Thymine Uracil

(a) 28.0 22.0 22.0 0.0 28.0

(b) 21.0 29.0 29.0 21.0 0.0

(c) 27.0 24.0 26.0 23.0 0.0

Solution:
(a) double-stranded RNA virus.
(b) wombat DNA.
(c) single-stranded DNA virus.
Reasoning: The presence of Uracil instead of Thymine is an indicator of RNA rather than DNA. Double-
stranded RNA or DNA will have equal proportions of whichever bases are paired in the double-stranded
molecule. For double-stranded DNA, the percentage of Adenine will equal the percentage of Thymine. Using
these two relationships, we can see that sample (a) must be RNA and it is double-stranded because Adenine and
Uracil are equal and Guanine and Cytosine are equal. Sample (b) is double-stranded DNA, and sample (c) is
single-stranded DNA

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 Question 22
The genome of the bacterium Hemophilus influenzae
is 1830 kb in size, and sequencing has shown it has
1703 genes.
What is the average spacing between central points of the
genes? 1.074 kb
If the average size of a coding region is 1 kb, what is
the average distance between genes? 0.074 kb
What is in this region? Regulatory sequences
What proportion of the genome is expected to be introns? 0

What is the average space between coding regions?

0.074 kb
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 Discussion Questions
How are the two chains of DNA held together?

Where do you find phosphodiester bonds in DNA?

Why are the two chains of DNA antiparallel?

How does DNA fulfill the requirements of a hereditary

molecule?

Discuss the main regions of a gene.

Can you identify some of the regulatory elements associated

with a gene?
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