Genetics Lecture Notes

7.03 2005

Lectures 11 and 12
 Lecture 11

Analysis of Gene Sequences

Anatomy of a bacterial gene:

Coding Sequence (no stop codons)
Promoter

mRNA:

Transcription Translation Start Translation Stop

Start (AUG) (UAG, UAA, or UGA)
Transcription
S-D Sequence
Terminator

Sequence Element Function

To target RNA polymerase to DNA and to start transcription
Promoter of a mRNA copy of the gene sequence.

Transcription terminator To instruct RNA polymerase to stop transcription.

Shine-Dalgarno sequence S-D sequence in mRNA will load ribosomes to begin

translation. Translation almost always begins at an AUG
codon in the mRNA (an ATG in the DNA becomes an AUG in
the mRNA copy). Synthesis of the protein thus begins with a
methionine.

Coding Sequence Once translation starts, the coding sequence is translated by

the ribosome along with tRNAs which read three bases at a
time in linear sequence. Amino acids will be incorporated into
the growing polypeptide chain according to the genetic code.

Translation Stop When one of the three stop codons [UAG (amber),
UAA (ochre), or UGA is encountered during translation, the
polypeptide will be released from the ribosome.

Example: A gene coding sequence that is 1,200 nucleotide base pairs in length (including
the ATG but not including the stop codon) will specify the sequence of a protein 1200/3 =
400 amino acids long. Since the average molecular weight of an amino acid is 110 da, this
gene encodes a protein of about 44 kd — the size of an average protein.
The Genetic Code
 Classically, genes are identified by their function. That is the existence of the gene is
recognized because of mutations in the gene that give an observable phenotypic change.
Historically, many genes have been discovered because of their effects on phenotype.
Now, in the era of genomic sequencing, many genes of no known function can be detected
by looking for patterns in DNA sequences. The simplest method which works for
bacterial and phage genes (but not for most eukaryotic genes as we will see later) is to
look for stretches of sequence that lack stop codons. These are known as “open reading
frames” or ORF
ORFs. This works because a random sequence should contain an average of
one stop codon in every 21 codons. Thus, the probability of a random occurrence of even
a short open reading frame of say 100 codons without a stop codon is very small (61/
64)100 = 8.2 x 10–3
Identifying genes in DNA sequences from higher organisms is usally more difficult than in
bacteria. This is because in humans, for example, gene coding sequences are separated
by long sequences that do not code for proteins. Moreover, genes of higher eukaryotes
are interrupted by introns
introns, which are sequences that are spliced out of the RNA before
translation. The presence of introns breaks up the open reading frames into short
segments making them much harder to distinguish from non-coding sequences. The maps
below show 50 kbp segments of DNA from yeast, Drosophila, and humans. The dark grey
boxes represent coding sequences and the light grey boxes represent introns. The boxes
above the line are transcribed to the right ant the boxes below are transcribed to the
left. Names have been assigned to each of the identified genes. Although the yeast
genes are much like those of bacteria (few introns and packed closely together), the
Drosophila and human genes are spread apart and interrupted by many introns. Sophisti-
cated computer algorithms were used to identify these dispersed gene sequences.

Saccharomyces cerevisiae
YFL046W YFL040W YFL030W
RGD2 FET5 TUB2 RP041 YFL034W HAC1 STE2
0 50

SEC53 ACT1 MOB2 RIM15 CAK1 BST1 EPL1

YFL044C YPT1 RPL22B CAF16
YFL042C GYP8

Drosophila melanogaster CG3131

syt CG15400
0 50

CG16987 CG2964 CG3123

Human
GATA1 HDAC6 LOC139168
0 50

PCSK1N
To see how gene sequences are actually obtained, we will first need to consider some
fundamentals of the chemical structure of DNA. Each strand of DNA is directional. The
different ends are usually called the 5’ and 3’ ends; referring to different positions on
the ribose sugar ring where the linking phosphate residues attach.

In a double stranded DNA molecule the two strands run anti-parallel to one another and
the general structure can be diagramed like this:
5’ 3’
3’ 5’
• Note about representation of DNA sequences.

1) Single strands are always represented in direction of synthesis – 5’ to 3’

2) For double stranded DNA, usually one strand is represented in the 5’ to 3’ direction.
For a gene, the strand represented would correspond to the sequence of the mRNA.

DNA polymersaes are the key players in the methods that we will be considering. The
general reaction carried out by DNA polymerase is to synthesize a copy of a DNA
template starting with the chemical precursors (nucleotides) dATP, dGTP, dCTP, and
dTTP (dNTPs). All DNA polymerases have two fundamental properties in common.
(1) New DNA is synthesized only by elongation of an existing strand at its 3’ end.
(2) Synthesis requires nucleotide precursors, a free 3’ OH end, and a template strand.

A general substrate for DNA polymerase looks like this:

5’ 3’
3’ 5’
Note that the template strand can be as short as 1 base or as long as several thousand
bases.

After addition of DNA polymerase and nucleotide precursors this product will be readily
synthesized:
5’ 3’
3’ 5’
DNA Sequencing

Consider a segment of DNA that is about 1000 base pairs long that we wish to sequence.
(1) The two DNA strands are separated. Heating to 100˚C to melt the base pairing
hydrogen bonds that hold the strands together does this.

(2) A short oligonucleotide (ca. 18 bases) designed to be complimentary to the end of one
of the strands is allowed to anneal to the single stranded DNA. The resulting DNA
hybrid looks much like the general polymerase substrate shown previously.

(3) DNA polymerase is added along with the four nucleotide precursors (dATP, dGTP,
dCTP, and dTTP). The mixture is then divided into four separate reactions and to each
reaction a small quantity different dideoxy nucleotide precursor is added. Dideoxy
nucleotide precursors are abbreviated ddATP, ddGTP, ddCTP, and ddTTP.

(4) The polymerase reactions are allowed to proceed and, using one of a variety of
methods, radiolabel is incorporated into the newly synthesized DNA.

(5) After the DNA polymerase reactions are complete, the samples are melted and run on
a gel system that allows DNA strands of different lengths to be resolved. The DNA
sequence can be read from the gel by noting the positions of the radiolabeled fragments.

The crucial element of the sequencing reactions is the added dideoxynuclotides. These
molecules are identical to the normal nucleotide precursors in all respects except that
they lack a hydroxyl group at their 3’ position (3’ OH).

Thus dideoxynuclotides can be incorporated into DNA, but once a dideoxynuclotide has
been incorporated further elongation stops because the resulting DNA will no longer have
a free 3’ OH end. Each of the four reactions contains one of the dideoxynuclotides
added at about 1% the concentration of the normal nucleotide precursors. Thus, for
example, in the reaction with added ddATP about 1% of the elongated chains will
terminate at the position of each A in the sequence. Once all of the elongating chains
have been terminated there will be a population of labeled chains that have terminated at
the position of each A in the sequence.
A part of the final gel will look like this:

+ddGTP +ddATP +ddTTP +ddCTP

Top (—)

Bottom (+)

(Note that larger molecules migrate more slowly to the cathode on these gels)

The deduced DNA sequence obtained from this gel is: 5’ GGATCCTATC 3’
Polymerase Chain Reaction

Now let’s consider how to obtain DNA segments that are suitable for sequencing. At
first, DNA sequences were obtained from cloned DNA segments (we will discuss some
methods to clone new genes in a subsequent lecture). Presently the entire DNA sequence
for E. coli, as well as a variety of other bacterial species, has been determined. If we
want to find the sequence of a new mutant allele of a known gene we need an easy way to
obtain a quantity of this DNA from a culture of bacterial cells. The best way to do this
is to use a method known as PCR or polymerase chain reaction that was developed by Kary
Mullis in the mid-1980’s. The steps in a PCR reaction are as follows.

(1) A crude preparation of chromosomal DNA is extracted from the bacterial strain of
interest.

(2) Two short oligo nucleotide primers (each about 18 bases long) are added to the DNA.
The primers are designed from the known genomic sequence to be complimentary to
opposite strands of DNA and to flank the chromosomal segment of interest.

(3) The double stranded DNA is melted by heating to 100˚C and then the mixture is
cooled to allow the primers to anneal to the template DNA.

(4) DNA polymerase and the four nucleotide precursors are added and the reaction is
incubated at 37˚C for a period of time to allow a copy of the segment to be synthesized.

(5) Steps 3 and 4 are repeated multiple times. To avoid the inconvenience of having to
add new DNA polymerase in each cycle a special DNA polymerase that can withstand
heating to 100˚C is used.

The idea is that in each cycle of melting, annealing and DNA synthesis the amount of the
DNA segment is doubled. This gives an exponential increase in the amount of the specific
DNA as the cycles proceed. After 10 cycles the DNA is amplified 103 fold and after 20
cycles the DNA will be amplified 106 fold. Usually amplification is continued until all of
the nucleotide precursors are incorporated into synthesized DNA.
 Lecture 12

Gene Mutations

Let’s say that we are investigating the LacZ gene, which encodes the lactose hydrolyzing
enzyme ß-galactosidase. There is a useful compound known as X-gal that can be
hydrolyzed by ß-galactosidase to release a dark blue pigment. When X-gal is added to the
growth medium in petri plates, Lac+ E. coli colonies turn blue whereas Lac– colonies with
mutations in the LacZ gene are white. By screening many colonies on such plates it is
possible to isolate a collection of E. coli mutants with alterations in the LacZ gene. PCR
amplification of the LacZ gene from each mutant followed by DNA sequencing allows the
base changes that cause the LacZ– phenotype to be determined. A very large number of
different LacZ mutations can be found but they can be categorized into three general
types.

Mutation Type Description

Missense A base change that converts one codon into another. Many missense
mutations are silent because the encoded amino acid remains the
same or the amino acid substitution is sufficiently subtle so as not to
compromise activity of the enzyme. Missense mutations that have a
marked effect often lie in the active site or grossly disrupt protein
folding.

Nonsense A base change that converts a codon within the coding sequence into
a stop codon. Note that there is only a limited set of sense codons
that can be converted to a stop codon by a single base change.
Nonsense mutations lead to a truncated protein product. Nonsense
mutations that lie early in the gene sequence will completely inactivate
the gene. Sometimes nonsense mutations that lie late in the gene
sequence will not disrupt gene function.

Frameshift The addition or deletion of a base or bases such that the coding
sequence is shifted out of register. Note that addition or deletion of
a multiple of three bases does not cause a frameshift. After the
frameshift mutation is encountered, missense codons will be read up
to the first stop codon. Like nonsense mutations, frameshift
mutations usually lead to complete inactivation of the gene.
 Although many different kinds of mutations occur spontaneously, the frequency with
which mutations occur can be increased as much as 103 fold by treatment of cells with a
mutagen. Here are some general categories of mutagens

Type of Mutagen Mechanism Examples Type of Mutations

Base Analog Analog is incorporated into 5-bromouracil A•T G•C, G•C A•T
DNA and can pair with more 2-aminopurine A•T G•C
than one base

Base modifying Chemical or photo damage to Hydroxylamine G•C A•T

agent DNA can be repaired, but EMS G•C A•T, C•G, or T•A
repair itself is error prone UV All changes

Intercalating Polycyclic compounds can fit Acridine Frameshifts (+ or –)

agent between bases and cause mis- Proflavine “
copying by polymerase to add or ICR-191 “
delete bases

Suppressor mutations

A powerful mode of genetic analysis is to investigate the types of mutations that can
reverse the phenotypic effects of a starting mutation. Starting with a LacZ– mutant of
E. coli (white on X-gal), we could mutagenize and then plate out a large number of colonies
on X-gal plates to screen for rare colonies that were blue on X-gal. These revertants
could have either been mutated such that the starting mutation was reversed or they
could have acquired a new mutation that somehow compensates for the starting mutation.

The possibilities are:

1) back mutation - true wild type

2) intragenic suppressor - compensating mutation in same gene

3) extragenic suppressor - compensating mutation in different gene

Nonsense suppressors.

An important class of extragenic suppressor mutations can suppress nonsense mutations

by changing the ability of the cells to read a nonsense codon as a sense codon. Such
extragenic revertants were originally isolated by selecting for reversion of amber (UAG)
mutations in two different genes. Since simultaneous back mutations at two different
sites is highly improbable the most frequent mechanism for suppression is a single
mutation in the gene for a tRNA that changes the codon recognition portion of the tRNA.
For example, one of several possible nonsense suppressors occurs in the gene for a serine
tRNA (tRNAser). One of six tRNAser normally contains the anticodon sequence CGA
which recognizes the serine codon UCG (by convention sequences are given in the 5’ to 3’
direction). A mutation that changes the anticodon to CUA allows the mutant tRNAser to
recognize a UAG codon and insert tryptophan when a UAG codon appears in a coding
sequence.

Recognition of UCG (serine codon) Recognition of UAG(stop codon)

by wild type tRNAser by amber suppressor mutant tRNAser

mRNA: 5’——————UCG——————3’ 5’————UAG––——————3’

AGC AUC
tRNA: 3' 3'

5' Ser 5' Ser

tRNAser suppressor tRNAser

The presence of an amber suppressing mutation is usually designated Su+ whereas a wild-
type (nonsuppressing) strain would be designated Su–.

Example: LacZam designates an amber (nonsense) mutation in the LacZ gene. Whereas a
LacZam E. coli strain is Lac- and therefore is white on X-gal plates, a strain with both a
LacZam mutation and an amber suppressor (Su+) mutation in a tRNA gene might be
phenotypically Lac+ because of extragenic suppression of the LacZam mutation.

The combined use of amber mutations and an amber suppressor produces a conditional
mutation, ie a mutation that is expressed under some circumstances but not under others.
Conditional mutants are especially useful for studying mutations in essential genes.
Another kind of conditional mutation is a temperature sensitive mutation for which the
mutant trait is exhibited at high temperature but not at low temperature.